@preamble{"Entries in this file are sorted by year (descending), then by citation key (ascending). Please maintain this sort order when adding entries manually."} @misc{Dehne_2026, abstract = {Quality assessment of Research Software Engineering (RSE) plays an important role in all scientific fields. From the canonical three criteria (reliability, validity, and objectivity) previous research has focussed on reliability and the FAIR principles. The RIGHT framework is introduced to fill the gap of existing frameworks for the validity aspect. The framework is constructed using the methods of theory transfer and process modelling. It is based on existing models of simulation research, design-based research, software engineering and empirical social sciences. The paper concludes with two case studies drawn from the field of learning technologies to illustrate the practical relevance of the framework for human-facing RSE.}, archiveprefix = {arXiv}, author = {Julian Dehne}, eprint = {2603.15366}, primaryclass = {cs.SE}, title = {To be FAIR or RIGHT? Methodological [R]esearch [I]ntegrity [G]iven [H]uman-facing [T]echnologies using the example of Learning Technologies}, url = {https://arxiv.org/abs/2603.15366}, year = {2026} } @article{Dorner_2026, author = {Dorner, Michael and Bauer, Andreas and Angermeir, Florian}, doi = {10.5334/jors.548}, issn = {2049-9647}, journal = {Journal of Open Research Software}, publisher = {Ubiquity Press, Ltd.}, title = {When Research Software Goes to Class: Lessons From Embedding Research Software Into Teaching}, url = {http://dx.doi.org/10.5334/jors.548}, volume = {14}, year = {2026} } @misc{Ernst_2026, abstract = {Research software (also called scientific software) is essential for advancing scientific endeavours. Research software encapsulates complex algorithms and domain-specific knowledge and is a fundamental component of all science. A pervasive challenge in developing research software is technical debt, which can adversely affect reliability, maintainability, and scientific validity. Research software often relies on the initiative of the scientific community for maintenance, requiring diverse expertise in both scientific and software engineering domains. The extent and nature of technical debt in research software are little studied, in particular, what forms it takes, and what the science teams developing this software think about their technical debt. In this paper we describe our multi-method study examining technical debt in research software. We begin by examining instances of self-reported technical debt in research code, examining 28k code comments across nine research software projects. Then, building on our findings, we interview research software engineers and scientists about how this technical debt manifests itself in their experience, and what costs it has for research software and research outputs more generally. We identify nine types of self-admitted technical debt unique to research software, and four themes impacting this technical debt.}, archiveprefix = {arXiv}, author = {Neil A. Ernst and Ahmed Musa Awon and Swapnil Hingmire and Ze Shi Li}, eprint = {2603.20415}, primaryclass = {cs.SE}, title = {The Nature of Technical Debt in Research Software}, url = {https://arxiv.org/abs/2603.20415}, year = {2026} } @article{Kolukula_2026, author = {Kolukula, Nitalaksheswara~Rao and Bolla, Jhansi~Vazram and Yenuga, Padma and Shaik, Nagul and Meka, James~Stephen}, doi = {10.1002/smr.70097}, issn = {2047-7481}, journal = {Journal of Software: Evolution and Process}, month = {April}, number = {4}, publisher = {Wiley}, title = {Software Cost Estimation Using a Hybrid Deep Convolutional LSTM and Optimization Approach}, url = {http://dx.doi.org/10.1002/smr.70097}, volume = {38}, year = {2026} } @report{McCracken_2026, author = {McCracken, Chelsea and Ruediger, Dylan and McBride, Mark and Masson, Patrick and Baron, Josh}, doi = {10.18665/sr.325189}, institution = {Ithaka S+R}, month = {March}, title = {Sustaining Open Source Software in the Research Enterprise: Findings from a One-Day Workshop}, url = {http://dx.doi.org/10.18665/sr.325189}, year = {2026} } @article{ondiJurki_2026, author = {\v{C}ondi\'{c}-Jurki\'{c}, Karmen and Alibay, Irfan and Sherman, Woody and Tollefson, Mallory R. and Walters, W. Patrick and Baker, Zachary and Chong, Lillian T. and Wei, Jennifer N. and Gray, Jeffrey and Weitzner, Brian D. and Smith, Daniel G. A. and Koehler Leman, Julia and Bahl, Chris and Mobley, David L.}, doi = {10.1021/acs.jcim.5c03137}, issn = {1549-960X}, journal = {Journal of Chemical Information and Modeling}, month = {March}, publisher = {American Chemical Society (ACS)}, title = {The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling}, url = {http://dx.doi.org/10.1021/acs.jcim.5c03137}, year = {2026} } @misc{Vogelsang_2026, abstract = {Drawing on ideas from continuous integration, we present concepts of an automated benchmarking pipeline for high performance applications. Customization and collaboration have been key design goals owing to the requirements of research-software development as a continuous community effort. We have extended our previous conceptual work on systematic benchmarking workflows with the functionality of user-agnostic operations as well as continuous benchmarking. This fosters reproducibility and re-use of benchmarking results to ensure sustainable technological progress. We provide software-engineering solutions to keep pace with the rapid evolution of both large-scale models and high-performance computing systems with a view towards the scientific domains of neuroscience and artificial intelligence.}, archiveprefix = {arXiv}, author = {Jan Vogelsang and Melissa Lober and Catherine Mia Sch\"{o}fmann and Jos\'{e} Villamar and Dennis Terhorst and Johanna Senk and Hans Ekkehard Plesser and Markus Diesmann and Susanne Kunkel and Anno C. Kurth}, eprint = {2604.15919}, primaryclass = {cs.DC}, title = {Continuous benchmarking: Keeping pace with an evolving ecosystem of models and technologies}, url = {https://arxiv.org/abs/2604.15919}, year = {2026} } @article{chourdakis_teaching_2025, author = {Chourdakis, Gerasimos and Ashraf, Hasan and Narvaez Rivas, Santiago and Neckel, Tobias and Bungartz, Hans-Joachim}, doi = {10.14279/eceasst.v83.2615}, journal = {Electronic Communications of the EASST}, month = {February}, title = {Teaching research software engineering skills for developing simulation software}, volume = {83}, year = {2025} } @article{christ_code_2025, abstract = {Die hier ver\"{o}ffentlichen Handlungsempfehlungen zur Verbesserung von Forschungssoftwarekompetenzen in der Wissenschaft richten sich an verschiedene Akteure im wissenschaftlichen System in Deutschland. Wir freuen uns \"{u}ber die Verbreitung dieser Ressource in zahlreichen Netzwerken und laden zu Austausch, Weiterentwicklung, und allgemeinem Feedback ein. Jede Form von R\"{u}ckmeldung kann in folgendem Matrix Chatraum stattfinden: matrix.to/\#/\#deRSE-FSKomp-Feedback:matrix.org .}, author = {Christ, Simon and Fritzsch, Bernadette and Grossmann, Yves Vincent and Kempf, Dominic and Linxweiler, Jan and L\"{o}ffler, Frank and Riedl, Lydia and Thiele, Jan Philipp and Wagner, Adina S. and Zanon, Lorenzo and Assmann, Cora and Br\"{o}mmel, Dirk and Caspart, Ren\'{e} and Dogan, Mustafa and Fillinger, Sven and Frangenberg, Jasmin and Franke, Michael and Frey, Annalena and Hagenberg, Jonas and Haupt, Carina and Kushnarenko, Volodymyr and Neuwirth, Sarah and Ribizel, Tobias and Saak, Jens and Schieberle, Andreas and Schima-Voigt, Kristine and Schmidt, Peter and Seibold, Heidi and Speck, Robert and Vleugel, Mathijs and Wellmann, Alexander and Wieder, Philipp and Wittke, Samantha}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.14273366}, keywords = {Research Software, deRSE, Forschungssoftware}, language = {de}, month = {February}, shorttitle = {Code for {Science}}, title = {Code for {Science}: {Bessere} {Forschung} durch bessere {Forschungssoftwarekompetenzen}}, url = {https://zenodo.org/doi/10.5281/zenodo.14273366}, urldate = {2025-03-21}, year = {2025} } @article{chue_hong_future_2025, author = {Chue Hong, Neil P. and Aragon, Selina and Hettrick, Simon and Jay, Caroline}, doi = {10.1016/j.patter.2025.101322}, issn = {2666-3899}, journal = {Patterns}, number = {7}, pages = {101322}, title = {The future of research software is the future of research}, volume = {6}, year = {2025} } @inproceedings{cordeiro_reviewing_2025, author = {Cordeiro, Andr\'{e} F. R. and Oliveira, Jr., Edson}, booktitle = {Proceedings of the 27{\textbackslash}textsuperscriptth {International} {Conference} on {Enterprise} {Information} {Systems} – {Volume} 2: {ICEIS}}, doi = {10.5220/0013456000003929}, isbn = {978-989-758-749-8}, pages = {364--371}, publisher = {SciTePress}, title = {Reviewing reproducibility in software engineering research}, year = {2025} } @article{czerniak_gi-_2025, author = {Czerniak, Andreas and Ehrenhofer, Adrian and Fritzsch, Bernadette and Funk, Maximilian and Goth, Florian and H\"{a}hnle, Reiner and Haupt, Carina and Konersmann, Marco and Linxweiler, Jan and L\"{o}ffler, Frank and L\"{u}pges, Alexander and Rumpe, Bernhard and Schieferdecker, Ina and Schlauch, Tobias and Speck, Robert and Struck, Alexander and Thiele, Jan Philipp and Tichy, Matthias and Ulusoy, Inga}, doi = {10.18420/2025-GI_DE-RSE}, keywords = {policy, guidelines}, language = {de}, title = {{GI}- und {DE}-{RSE} {Muster}-{Leitlinie} zur effizienten {Entwicklung} von {Forschungssoftware}}, url = {https://dl.gi.de/handle/20.500.12116/45664}, urldate = {2025-02-05}, year = {2025} } @article{deekshitha_decoding_2025, author = {{Deekshitha} and Bakhshi, Rena and van Nieuwpoort, Rob and Jansen, Slinger}, issn = {1613-0073}, journal = {CEUR Workshop Proceedings}, month = {February}, title = {Decoding research software impact}, url = {https://ceur-ws.org/Vol-3921/}, volume = {3921}, year = {2025} } @article{deutsche_forschungsgemeinschaft_ausschuss_fur_wissenschaftliche_bibliotheken_und_informationssysteme_digitale_2025, abstract = {In ihrem Diskussionspapier ,,Digitale Forschungspraxis und kooperative Informationsinfrastrukturen`` analysiert die DFG \"{u}bergreifende Herausforderungen und identifiziert Handlungsfelder f\"{u}r den Aufbau, die Weiterentwicklung und den langfristigen Betrieb wissenschaftlicher Informationsinfrastrukturen. Die im Papier entwickelten Handlungsfelder betreffen dabei sowohl das F\"{o}rderhandeln der DFG als auch das Gesamtsystem wissenschaftlicher Informationsinfrastrukturen: Erstens sollte die Anschlussf\"{a}higkeit von Informationsinfrastrukturen und digitalen Objekten optimiert werden. In erster Linie sind hier technische Verbesserungen vonn\"{o}ten; aber auch die organisatorische und soziale Anschlussf\"{a}higkeit sind mit zu bedenken. Zweitens ist es unverzichtbar, den kooperativen Betrieb von Informationsinfrastrukturen \"{u}ber geeignete Anreize weiter zu stimulieren. Drittens m\"{u}ssen die Nachnutzbarkeit vorhandener Technologien gef\"{o}rdert und der Betrieb wissenschaftsrelevanter Informationsinfrastrukturen auch langfristig gesichert werden. Nach \"{U}berzeugung der DFG lassen sich diese Handlungsfelder nur in geteilten Rollen und Verantwortlichkeiten unterschiedlicher Akteure aus Forschung, Einrichtungen der Informationsinfrastruktur, Forschungsf\"{o}rderorganisationen und Wissenschaftspolitik erfolgreich bearbeiten. Die DFG wird daher einen systematischen Dialogprozess initiieren, um \"{u}bergreifende Herausforderungen zu er\"{o}rtern und gemeinsam nach L\"{o}sungsans\"{a}tzen zu suchen. Ziele dieses Prozesses sind die weitere Konturierung \"{u}bergeordneter Herausforderungen und Handlungsfelder, die grunds\"{a}tzliche Kl\"{a}rung von Rollen und Verantwortlichkeiten, aber auch die Weitung des Blickes f\"{u}r neue Fragen und L\"{o}sungsans\"{a}tze. Als Ausgangspunkt f\"{u}r den Dialog formuliert die DFG in ihrem Papier ,,F\"{u}nf Thesen zur Zukunft der Informationsinfrastruktur``, die sich aus den im Papier beschriebenen Herausforderungen und den daraus abgeleiteten Handlungsfeldern ergeben. In its discussion paper ``Digital Research Practice and Cooperative Information Infrastructures'', the DFG analyses overarching challenges and identifies fields of action in the establishment and expansion of scientific information infrastructures and their long-term operation. The fields of action outlined in the paper relate to both the DFG's funding activities and the overall system of scientific information infrastructures. Firstly, the interoperability of information infrastructures and digital objects is to be optimised. This primarily requires technical improvements, though organisational and social interoperability also need to be taken into account. Secondly, it is essential to continue to foster the cooperative operation of information infrastructures based on the appropriate incentives. Thirdly, the reusability of existing technologies must be promoted, and the operation of research-related information infrastructures must be secured in the long term. The DFG believes that these fields of action can only be effectively addressed based on the sharing of roles and responsibilities among various stakeholders – including researchers, information infrastructure institutions, research funding organisations and research policy actors. For this reason, the DFG will initiate a systematic dialogue process to engage in discussion on overarching challenges and seek solutions on a collaborative basis. The objectives of this process are to further refine challenges and fields of action, fundamentally clarify roles and responsibilities, and broaden perspectives so as to be able to address new questions and solutions. As a starting point for this dialogue, the DFG presents ``Five Theses on the Future of Information Infrastructure'' in its paper, which draw on the challenges and fields of action set out in the discussion paper.}, author = {{Deutsche Forschungsgemeinschaft. Ausschuss f\"{u}r Wissenschaftliche Bibliotheken und Informationssysteme}}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.14621979}, keywords = {DFG, Finanzierung, Folgenutzung, Forschungsf\"{o}rderung, German Research Foundation, Informationsinfrastruktur, Kooperation}, language = {de}, month = {January}, title = {Digitale {Forschungspraxis} und kooperative {Informationsinfrastrukturen}. {Ein} {Diskussionspapier} der {Deutschen} {Forschungsgemeinschaft} zu {F\"{o}rderung} und {Finanzierung} wissenschaftlicher {Informationsinfrastrukturen}}, url = {https://zenodo.org/doi/10.5281/zenodo.14621979}, urldate = {2025-01-29}, year = {2025} } @article{di_cosmo_stop_2025, author = {Di Cosmo, Roberto and Granger, Sabrina and Hinsen, Konrad and Jullien, Nicolas and Le Berre, Daniel and Louvet, Violaine and Maumet, Camille and Maurice, Cl\'{e}mentine and Monat, Rapha\"{e}l and Rougier, Nicolas P.}, copyright = {https://www.springernature.com/gp/researchers/text-and-data-mining}, doi = {10.1038/d41586-025-03196-0}, issn = {0028-0836, 1476-4687}, journal = {Nature}, language = {en}, month = {October}, number = {8084}, pages = {284--286}, shorttitle = {Stop treating code like an afterthought}, title = {Stop treating code like an afterthought: record, share and value it}, url = {https://www.nature.com/articles/d41586-025-03196-0}, urldate = {2025-11-20}, volume = {646}, year = {2025} } @article{druskat_better_2025, author = {Druskat, Stephan and Eisty, Nasir U. and Chisholm, Robert and Chue Hong, Neil P. and Cocking, Ryan C. and Cohen, Myra B. and Felderer, Michael and Grunske, Lars and Harris, Sarah A. and Hasselbring, Wilhelm and Krause, Thomas and Linxweiler, Jan and Venters, Colin C.}, doi = {10.1109/MCSE.2025.3573887}, journal = {Computing in Science \& Engineering}, number = {2}, pages = {45--57}, title = {Better architecture, better software, better research}, volume = {27}, year = {2025} } @incollection{druskat_challenges_2025, address = {Cham}, author = {Druskat, Stephan and Theis, Sabine}, booktitle = {Human-{Computer} {Interaction}}, doi = {10.1007/978-3-031-93838-2_21}, editor = {Kurosu, Masaaki and Hashizume, Ayako}, isbn = {978-3-031-93837-5 978-3-031-93838-2}, language = {en}, pages = {321--343}, publisher = {Springer Nature Switzerland}, title = {Challenges in {Designing} {Research} {Infrastructure} {Software} in {Multi}-{Stakeholder} {Contexts}}, url = {https://link.springer.com/10.1007/978-3-031-93838-2\%5F21}, urldate = {2025-12-10}, volume = {15767}, year = {2025} } @inproceedings{dworatzyk_sharing_2025, address = {Cham}, author = {Dworatzyk, Katharina and Schlauch, Tobias}, booktitle = {Human-{Computer} {Interaction}}, doi = {10.1007/978-3-031-93835-1_10}, editor = {Kurosu, Masaaki and Hashizume, Ayako}, isbn = {978-3-031-93835-1}, pages = {157--174}, publisher = {Springer Nature Switzerland}, title = {Sharing is caring: the effect of knowledge exchange workshops on community commitment among research software engineers}, year = {2025} } @article{eisty_ten_2025, author = {Eisty, Nasir U. and Carver, Jeffrey C. and Cohoon, Johanna and Cosden, Ian A. and Goble, Carole and Grayson, Samuel}, copyright = {https://ieeexplore.ieee.org/Xplorehelp/downloads/license-information/IEEE.html}, doi = {10.1109/MCSE.2025.3569786}, issn = {1521-9615, 1558-366X}, journal = {Computing in Science \& Engineering}, keywords = {RSE research}, pages = {1--7}, title = {Ten {Simple} {Rules} for {Catalyzing} {Collaborations} and {Building} {Bridges} between {Research} {Software} {Engineers} and {Software} {Engineering} {Researchers}}, url = {https://ieeexplore.ieee.org/document/11003859/}, urldate = {2025-05-19}, year = {2025} } @article{felderer_investigating_2025, abstract = {Research software engineering research aims at understanding and improving how software is developed for research.}, author = {Felderer, Michael and Goedicke, Michael and Grunske, Lars and Hasselbring, Wilhelm and Lamprecht, Anna-Lena and Rumpe, Bernhard}, doi = {10.1145/3685265}, issn = {0001-0782, 1557-7317}, journal = {Communications of the ACM}, language = {en}, month = {February}, number = {2}, pages = {20--23}, shorttitle = {Investigating {Research} {Software} {Engineering}}, title = {Investigating {Research} {Software} {Engineering}: {Toward} {RSE} {Research}}, url = {https://dl.acm.org/doi/10.1145/3685265}, urldate = {2025-01-23}, volume = {68}, year = {2025} } @inproceedings{filinger_enabling_2025, address = {New York, USA}, author = {Filinger, Weronika and Hong, Neil Chue and Crouch, Stephen and Robinson, Martin and Cohen, Jeremy and Henty, David}, booktitle = {Practice and {Experience} in {Advanced} {Research} {Computing} 2025 ({PEARC} '25)}, doi = {10.1145/3708035.3736008}, isbn = {979-8-4007-1398-9}, month = {July}, publisher = {Association for Computing Machinery}, title = {Enabling new pathways for {Research} {Software} {Engineers}: three years of the {UNIVERSE}-{HPC} project}, year = {2025} } @article{gey_findsoftware_2025, abstract = {Across essentially all fields of research, many aspects of the respective research processes – whether experimental, theoretical, empirical or outright computational – are closely related to software. Yet the process of finding software that is directly suitable or at least a good starting point for a given research task is cumbersome. This project aims to develop a community-driven system that provides potential users of research software with a diversity of pathways towards actually finding software that closely matches their research needs if such software exists. Conversely, it will provide software developers with mechanisms to make their software findable for research-related tasks and it will highlight mismatches between software supply and demand for specific tasks. To this end, we will document how various stakeholders of the research landscape have been searching for – or stumbling upon – research software so far, identify variables associated with successful search outcomes and build workflows that assist in describing software and associated concepts in a standardised fashion. These descriptions will then be aligned across various sources of relevant information and integrated into Wikidata, the knowledge graph that anyone can edit and that already contains considerable breadth and depth of information related to research, software and their interactions. While keeping an eye on similar approaches to software discovery that might work in parts of the research ecosystem, existing Wikidata content and workflows will be reviewed and built upon. Additional documentation, tooling and workflows will be developed to enrich, expand, curate, query and explore this content, both for specific use cases and with ongoing engagement of the communities involved in research software, open data or collaborative curation. Within its three years, the project seeks to establish a dedicated community overseeing a well-documented and smoothly running infrastructure for software discovery and to devise a plan for how this can be sustained for the longer term.}, author = {Gey, Ronny and Mietchen, Daniel and Karras, Oliver and Wittenborg, Tim and Schubotz, Moritz and Bumberger, Jan}, doi = {10.3897/rio.11.e179253}, issn = {2367-7163}, journal = {Research Ideas and Outcomes}, month = {December}, pages = {e179253}, shorttitle = {find.software}, title = {find.software: {Foundations} for {Interdisciplinary} {Discovery} of ({Research}) {Software}}, url = {https://riojournal.com/article/179253/}, urldate = {2025-12-03}, volume = {11}, year = {2025} } @article{gey_seek_2025, abstract = {Software discovery is a crucial aspect of research, yet it remains a challenging process due to various reasons: The lack of a centralized or domain-tailored search and publication infrastructure, insufficient software citations, the prevailing unavailability of software (versions) and many others. Researchers tend to utilize general search engines and their social network before considering code repositories, (text + data) repositories, and package management platforms, among other locations, to find the software they need. The resulting fragmented ecosystem is characterized by parallel developments from different, yet partially overlapping, redundant and non-interoperable infrastructure providers and research communities. Moreover, the discovery process is further complicated by missing or imperfect metadata, which can lead to limited search results. To address these challenges, it is essential to gain a deeper understanding of the different software publication and discovery systems. We describe available discovery options, including code and publication repositories, domain, geographic, or institution-specific catalogs, classical search engines, curated lists, knowledge graphs, social networks, and all of these in various combinations, with and without the use of artificial intelligence. Besides characterizing each option, we will present examples, challenges and recommendations for an improved software discovery process. In addition, we will discuss the role of different stakeholders (e.g. developers, users, funders, publishers) and what they could do for better findability.}, author = {Gey, Ronny and Wittenborg, Tim and Mietchen, Daniel and Struck, Alexander and Karras, Oliver}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.14878607}, keywords = {Research Software Engineering, deRSE25, Research Software Discovery}, language = {en}, month = {February}, title = {Seek and {You} {Shall} {Find} - {Or} {Not}! {Why} {Can}'t {We} {Find} the {Research} {Software} {We} {Really} {Need}?}, url = {https://zenodo.org/doi/10.5281/zenodo.14878607}, urldate = {2025-09-11}, year = {2025} } @article{hasselbring_multidimensional_2025, author = {Hasselbring, Wilhelm and Druskat, Stephan and Bernoth, Jan and Betker, Philine and Felderer, Michael and Ferenz, Stephan and Hermann, Ben and Lamprecht, Anna-Lena and Linxweiler, Jan and Prat, Arnau and Rumpe, Bernhard and Sch\"{o}ning-Stierand, Katrin and Yang, Shinhyung}, copyright = {https://creativecommons.org/licenses/by/4.0/legalcode}, doi = {10.1109/MCSE.2025.3555023}, issn = {1521-9615, 1558-366X}, journal = {Computing in Science \& Engineering}, keywords = {Categorization}, month = {April}, number = {2}, pages = {59--68}, title = {Multidimensional {Research} {Software} {Categorization}}, url = {https://ieeexplore.ieee.org/document/10944238/}, urldate = {2025-08-14}, volume = {27}, year = {2025} } @article{houillon_facile-rs_2025, author = {Houillon, Marie and Klar, Jochen and Boutanios, Ziad and Stary, Tomas and Cojean, Terry and Anzt, Hartwig and Loewe, Axel}, copyright = {http://creativecommons.org/licenses/by/4.0/}, doi = {10.21105/joss.07330}, issn = {2475-9066}, journal = {Journal of Open Source Software}, month = {October}, number = {114}, pages = {7330}, shorttitle = {{FACILE}-{RS}}, title = {{FACILE}-{RS}: archiving and long-term preservation of research software repositories made easy}, url = {https://joss.theoj.org/papers/10.21105/joss.07330}, urldate = {2025-12-10}, volume = {10}, year = {2025} } @inproceedings{hounsri_good_2025, address = {Ottawa, ON, Canada}, author = {Hounsri, Anas El and Garijo, Daniel}, booktitle = {2025 {IEEE}/{ACM} 22nd {International} {Conference} on {Mining} {Software} {Repositories} ({MSR})}, copyright = {https://doi.org/10.15223/policy-029}, doi = {10.1109/MSR66628.2025.00028}, isbn = {979-8-3315-0183-9}, month = {April}, pages = {116--128}, publisher = {IEEE}, shorttitle = {Good practice versus reality}, title = {Good practice versus reality: {A} landscape analysis of {Research} {Software} metadata adoption in {European} {Open} {Science} {Clusters}}, url = {https://ieeexplore.ieee.org/document/11025739/}, urldate = {2025-12-10}, year = {2025} } @article{jensen_strategic_2025, author = {Jensen, Eric A. and Katz, Daniel S.}, doi = {10.12688/f1000research.155879.2}, journal = {F1000Research}, number = {1447}, title = {Strategic priorities and challenges in research software funding: {Results} from an international survey [version 2; peer review: 2 approved, 2 approved with reservations, 1 not approved]}, volume = {13}, year = {2025} } @article{Kehrer_2025, author = {Kehrer, Timo and Haines, Robert and Juckeland, Guido and Zhou, Shurui and Bernholdt, David E.}, doi = {10.1109/mcse.2025.3557236}, issn = {1558-366X}, journal = {Computing in Science \& Engineering}, month = {April}, number = {2}, pages = {18–26}, publisher = {Institute of Electrical and Electronics Engineers (IEEE)}, title = {Do Research Software Engineers and Software Engineering Researchers Speak the Same Language?}, url = {http://dx.doi.org/10.1109/MCSE.2025.3557236}, volume = {27}, year = {2025} } @article{pezze_2030_2025, author = {Pezz\`{e}, Mauro and Abrah\~{a}o, Silvia and Penzenstadler, Birgit and Poshyvanyk, Denys and Roychoudhury, Abhik and Yue, Tao}, doi = {10.1145/3731559}, issn = {1049-331X}, journal = {ACM Transactions on Software Engineering and Methodology}, month = {May}, number = {5}, title = {A 2030 roadmap for software engineering}, volume = {34}, year = {2025} } @article{simkute_ironies_2025, author = {Simkute, Auste and Tankelevitch, Lev and Kewenig, Viktor and Scott, Ava Elizabeth and Sellen, Abigail and Rintel, Sean}, doi = {10.1080/10447318.2024.2405782}, issn = {1044-7318}, journal = {International Journal of Human–Computer Interaction}, month = {March}, number = {5}, pages = {2898--2919}, title = {Ironies of generative {AI}: understanding and mitigating productivity loss in human-{AI} interaction}, volume = {41}, year = {2025} } @article{streicher_open_2025, abstract = {Digital tools, software and related infrastructures are central to modern science and research. With regards to open science, open software tools are becoming increasingly important as they promote and support collaboration, reproducibility and access to resources. Researchers are actively contributing to the development of these ``Open Research Tools (ORT)'' and are thus helping to shape the digital transformation of the science system. This change is also noticeable in Germany, where the area of research software is gaining increasing importance. The aim of the study is to systematically review the state of research on ORT, analyse key topics and critically reflect on the situation in Germany. Current research findings, challenges and trends are highlighted, and the assessments of relevant actors and stakeholders are included in the analysis. An open conceptual understanding was chosen for the research and analyses in order to allow a flexible and explorative approach. In terms of methodology, the study is based on a scoping review of the relevant literature and expert interviews. The results were discussed, reflected upon and further developed in workshops. The aim was also to identify key challenges, opportunities and strategies for ORT in Germany and to derive recommendations.}, author = {Streicher, J\"{u}rgen and Sch\"{u}tz, Marlies and Bl\"{u}mel, Clemens and Schniedermann, Alexander}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.15771943}, keywords = {Policy, OpenResearchTools OpenResearch OpenScience Forschungssoftware ResearchSoftware}, language = {de}, month = {June}, shorttitle = {Open {Research} {Tools}}, title = {Open {Research} {Tools}: {Stand} und {Herausforderungen} im {Spannungsfeld} von {Forschungssoftware}, {Offenheit} und digitaler {Infrastruktur}}, url = {https://zenodo.org/doi/10.5281/zenodo.15771943}, urldate = {2025-07-04}, year = {2025} } @inproceedings{thorgeirsson_what_2025, address = {New York, USA}, author = {Thorgeirsson, Sverrir and Ewen, Tracy and Su, Zhendong}, booktitle = {Proceedings of the 56{\textbackslash}textsuperscriptth {ACM} technical symposium on computer science education ({SIGCSETS} 2025), volume 1}, doi = {10.1145/3641554.3701873}, isbn = {979-8-4007-0531-1}, month = {February}, pages = {1127--1133}, publisher = {Association for Computing Machinery}, title = {What can computer science educators learn from the failures of top-down pedagogy?}, year = {2025} } @misc{Wolter_2025, abstract = {While experimental reproduction remains a pillar of the scientific method, we observe that the software best practices supporting the reproduction of machine learning ( ML ) research are often undervalued or overlooked, leading both to poor reproducibility and damage to trust in the ML community. We quantify these concerns by surveying the usage of software best practices in software repositories associated with publications at major ML conferences and journals such as NeurIPS, ICML, ICLR, TMLR, and MLOSS within the last decade. We report the results of this survey that identify areas where software best practices are lacking and areas with potential for growth in the ML community. Finally, we discuss the implications and present concrete recommendations on how we, as a community, can improve reproducibility in ML research.}, archiveprefix = {arXiv}, author = {Moritz Wolter and Lokesh Veeramacheneni and Charles Tapley Hoyt}, eprint = {2502.00902}, primaryclass = {cs.SE}, title = {More Rigorous Software Engineering Would Improve Reproducibility in Machine Learning Research}, url = {https://arxiv.org/abs/2502.00902}, year = {2025} } @misc{Bajraktari_2024, abstract = {Modern science is relying on software more than ever. The behavior and outcomes of this software shape the scientific and public discourse on important topics like climate change, economic growth, or the spread of infections. Most researchers creating software for scientific purposes are not trained in Software Engineering. As a consequence, research software is often developed ad hoc without following stringent processes. With this paper, we want to characterize research software as a new application domain that needs attention from the Requirements Engineering community. We conducted an exploratory study based on 8 interviews with 12 researchers who develop software. We describe how researchers elicit, document, and analyze requirements for research software and what processes they follow. From this, we derive specific challenges and describe a vision of Requirements Engineering for research software.}, archiveprefix = {arXiv}, author = {Adrian Bajraktari and Michelle Binder and Andreas Vogelsang}, eprint = {2405.07781}, primaryclass = {cs.SE}, title = {Requirements Engineering for Research Software: A Vision}, url = {https://arxiv.org/abs/2405.07781}, year = {2024} } @article{bajraktari_requirements_2024, abstract = {Modern science is relying on software more than ever. The behavior and outcomes of this software shape the scientific and public discourse on important topics like climate change, economic growth, or the spread of infections. Most researchers creating software for scientific purposes are not trained in Software Engineering. As a consequence, research software is often developed ad hoc without following stringent processes. With this paper, we want to characterize research software as a new application domain that needs attention from the Requirements Engineering community. We conducted an exploratory study based on 8 interviews with 12 researchers who develop software. We describe how researchers elicit, document, and analyze requirements for research software and what processes they follow. From this, we derive specific challenges and describe a vision of Requirements Engineering for research software.}, author = {Bajraktari, Adrian and Binder, Michelle and Vogelsang, Andreas}, copyright = {arXiv.org perpetual, non-exclusive license}, doi = {10.48550/ARXIV.2405.07781}, keywords = {FOS: Computer and information sciences, Software Engineering (cs.SE), requirements engineering}, month = {May}, title = {Requirements {Engineering} for {Research} {Software}: {A} {Vision}}, year = {2024} } @book{bannert_research_2024, author = {Bannert, Matthias}, doi = {10.1201/9781003286899}, isbn = {978-1-003-28689-9}, keywords = {open source}, month = {March}, publisher = {Chapman and Hall/CRC}, title = {Research {Software} {Engineering}: {A} {Guide} to the {Open} {Source} {Ecosystem}}, year = {2024} } @misc{Barakhshan_2024, abstract = {High-quality computational and data-intensive (CDI) applications are critical for advancing research frontiers in almost all disciplines. Despite their importance, there is a significant gap due to the lack of comprehensive best practices for developing such applications. CDI projects, characterized by specialized computational needs, high data volumes, and the necessity for cross-disciplinary collaboration, often involve intricate scientific software engineering processes. The interdisciplinary nature necessitates collaboration between domain scientists and CDI professionals (Xperts), who may come from diverse backgrounds. This paper aims to close the above gap by describing practices specifically applicable to CDI applications. They include general software engineering practices to the extent that they exhibit substantial differences from those already described in the literature as well as practices that have been called pivotal by Xperts in the field. The practices were evaluated using three main metrics: (1) participants' experience with each practice, (2) their perceived impact, and (3) their ease of application during development. The evaluations involved participants with varying levels of experience in adopting these practices. Despite differing experience levels, the evaluation results consistently showed high impact and usability for all practices. By establishing a best-practices guide for CDI research, the ultimate aim of this paper is to enhance CDI software quality, improve approaches to computational and data-intensive challenges, foster interdisciplinary collaboration, and thus accelerate scientific innovation and discovery.}, archiveprefix = {arXiv}, author = {Parinaz Barakhshan and Rudolf Eigenmann}, eprint = {2406.01780}, primaryclass = {cs.CE}, title = {Best Practices for Developing Computational and Data-Intensive (CDI) Applications}, url = {https://arxiv.org/abs/2406.01780}, year = {2024} } @article{bobier_clarifying_2024, author = {Bobier, Christopher and Hurst, Daniel J.}, doi = {10.1007/s13347-024-00827-8}, issn = {2210-5433, 2210-5441}, journal = {Philosophy \& Technology}, month = {December}, number = {4}, pages = {139}, title = {Clarifying {Dual} {Use} {Research} of {Concern}}, urldate = {2025-08-15}, volume = {37}, year = {2024} } @article{brown_teaching_2024, author = {Brown, Noelle and Xie, Benjamin and Sarder, Ella and Fiesler, Casey and Wiese, Eliane S.}, doi = {10.1145/3634685}, journal = {ACM Transactions on Computing Education}, month = {January}, number = {1}, title = {Teaching ethics in computing: {A} systematic literature review of {ACM} computer science education publications}, volume = {24}, year = {2024} } @misc{Castell_2024, abstract = {Research data and software are widely accepted as an outcome of scientific work. However, in comparison to text-based publications, there is not yet an established process to assess and evaluate quality of research data and research software publications. This paper presents an attempt to fill this gap. Initiated by the Working Group Open Science of the Helmholtz Association the Task Group Helmholtz Quality Indicators for Data and Software Publications currently develops a quality indicator for research data and research software publications to be used within the Association. This report summarizes the vision of the group of what all contributes to such an indicator. The proposed approach relies on generic well-established concepts for quality criteria, such as the FAIR Principles and the COBIT Maturity Model. It does - on purpose - not limit itself to technical implementation possibilities to avoid using an existing metric for a new purpose. The intention of this paper is to share the current state for further discussion with all stakeholders, particularly with other groups also working on similar metrics but also with entities that use the metrics.}, archiveprefix = {arXiv}, author = {Wolfgang zu Castell and Doris Dransch and Guido Juckeland and Marcel Meistring and Bernadette Fritzsch and Ronny Gey and Britta H\"{o}pfner and Martin K\"{o}hler and Christian Mee\ss{}en and Hela Mehrtens and Felix M\"{u}hlbauer and Sirko Schindler and Thomas Schnicke and Roland Bertelmann}, eprint = {2401.08804}, primaryclass = {cs.DL}, title = {Towards a Quality Indicator for Research Data publications and Research Software publications -- A vision from the Helmholtz Association}, url = {https://arxiv.org/abs/2401.08804}, year = {2024} } @article{castell_towards_2024, abstract = {Research data and software are widely accepted as an outcome of scientific work. However, in comparison to text-based publications, there is not yet an established process to assess and evaluate quality of research data and research software publications. This paper presents an attempt to fill this gap. Initiated by the Working Group Open Science of the Helmholtz Association the Task Group Helmholtz Quality Indicators for Data and Software Publications currently develops a quality indicator for research data and research software publications to be used within the Association. This report summarizes the vision of the group of what all contributes to such an indicator. The proposed approach relies on generic well-established concepts for quality criteria, such as the FAIR Principles and the COBIT Maturity Model. It does - on purpose - not limit itself to technical implementation possibilities to avoid using an existing metric for a new purpose. The intention of this paper is to share the current state for further discussion with all stakeholders, particularly with other groups also working on similar metrics but also with entities that use the metrics.}, author = {Castell, Wolfgang zu and Dransch, Doris and Juckeland, Guido and Meistring, Marcel and Fritzsch, Bernadette and Gey, Ronny and H\"{o}pfner, Britta and K\"{o}hler, Martin and Mee\ss{}en, Christian and Mehrtens, Hela and M\"{u}hlbauer, Felix and Schindler, Sirko and Schnicke, Thomas and Bertelmann, Roland}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.48550/ARXIV.2401.08804}, keywords = {FOS: Computer and information sciences, research data, publication, assessment, Computers and Society (cs.CY), Digital Libraries (cs.DL)}, month = {January}, title = {Towards a {Quality} {Indicator} for {Research} {Data} publications and {Research} {Software} publications – {A} vision from the {Helmholtz} {Association}}, year = {2024} } @inproceedings{chourdakis_coherent_2024, abstract = {What if your graduate programme actually prepared you with all the software engineering skills you need to participate in the research software community? The M.Sc. Computational Science and Engineering (CSE) at the Technical University of Munich gathers STEM graduates from all over the world and teaches them elements of numerics, computer science, and applications. CSE graduates are the perfect candidates for developing the next PETSc, OpenFOAM, or Tensorflow. And yet, the programming-related part of the curriculum needed some aligning and dusting. Over the past six years, we had the opportunity to look at the big picture, redesigning several courses that "tell a story" together. Nowadays, a CSE student can follow a coherent track that prepares them for working as software engineers in an RSE team developing simulation software. We start by preparing the ground with fundamental Linux, Git, Matlab/Octave, C++, and teamwork concepts in the 1-week onboarding course "CSE Primer". In the afternoons of that week, students also work in teams, developing small projects analyzing climate data. For the rest of the semester, CSE students have to follow "Advanced Programming", a course with an ambitious name which we put a lot of effort in justifying. With the "advanced", we aim to raise the level of the inexperienced, while still offering enough opportunities for already experienced students to grow. The material covers a pragmatic mixture of modern C++ with just enough references of legacy features to be able to work with existing codebases. The slides include code snippets that the students can interact with using the Compiler Explorer. The tutorial exercises include common tools that support the development, including a debugger, sanitizer, formatter, build tools, testing frameworks, and more. An optional project lets students develop their own idea in pairs, or contribute to existing open-source projects, while participating in a code peer-review process. The lectures and tutorial are hybrid, and the in-person exam is supported by TUMExam, a system that offers digital correction and review features. The redesign of this course attracted several students from additional study programs, with the original audience of CSE students now representing less than 10\% of the exponentially-growing total audience. After the first semester, students follow a practical (lab) course. One highlight is the Computaional Fluid Dynamics Lab, in which students work in groups to implement worksheets and their own final project, in a bare-minimum C++ PDE framework, receiving code reviews on GitLab and maving their first steps towards parallel programming and performance optimization. Cross-references between Advanced Programming and CFD Lab make the two courses coherent, without discouraging external students to join. The (not offered anymore due to staff shortage) seminar Partitioned Fluid-Structure Interaction lets students expand their research skills specific to CFD, writing their own paper and participating in peer-reviews. This talk will give an overview of these courses, discussing several didactical and technical elements applied in each, concluding with not-so-obvious good practices.}, author = {Chourdakis, Gerasimos}, booktitle = {{deRSE24}}, keywords = {education}, language = {en}, month = {March}, publisher = {Julius-Maximilians-Universit\"{a}t W\"{u}rzburg}, title = {A coherent curriculum track of {RSE} skills for simulation software}, url = {https://events.hifis.net/event/994/contributions/7961/}, year = {2024} } @article{correa_reproducible_2024, abstract = {The pursuit of reproducibility in research has long been emphasized. It is even more critical in geohazards research and practice, where model-based decision-making needs to be transparent for trustworthy applications. However, enabling reproducibility in process-based or machine learning workflows requires time, energy, and sometimes manual operations or even unavailable resources. Moreover, the diversity in modern compute environments, both in hardware and software, significantly hinders the path to reproducibility. While many researchers focus on reproducibility, we advocate that reusability holds greater value and inherently requires the former. Reusable datasets and simulations can allow for transparent and reliable decision support, analysis as well as benchmarking studies. Reusable research software can foster composition and faster development of complex projects, while avoiding the reinvention of complicated data structures and algorithms. Establishing reproducible workflows and compute environments is vital to enable and ensure reusability. Prioritising reproducible workflows is crucial for individual use, while both reproducible compute environments and workflows are essential for broader accessibility and reuse by others. We present herein various challenges faced in coming up with reproducible workflows and compute environments along with solution strategies and recommendations through experiences from two projects in geohazards research. We discuss an object-oriented approach to simulation workflows, automated metadata extraction and data upload, unique identification of datasets (assets) and simulation workflows (processes) through cryptographic hashes. We investigate essential factors, such as software versioning and dependency management, reproducibility across diverse hardware used by researchers, and time to first reproduction/reuse (TTFR), to establish reproducible computational environments. Finally, we shall explore the landscape of reproducibility in compute environments, covering language-agnostic package managers, containers, and language-specific package managers supporting binary dependencies.}, author = {Correa, Alan and Yildiz, Anil and Kowalski, Julia}, doi = {10.5194/egusphere-egu24-18724}, keywords = {reproducibility}, month = {March}, title = {Reproducible {Workflows} and {Compute} {Environments} for {Reusable} {Datasets}, {Simulations} and {Research} {Software}}, year = {2024} } @article{Damerow_2024, author = {Damerow, Julia and Koeser, Rebecca Sutton and Carver, Jeffrey C and Vogl, Malte}, doi = {10.1093/llc/fqae052}, issn = {2055-768X}, journal = {Digital Scholarship in the Humanities}, month = {September}, number = {Supplement\_1}, pages = {i18–i26}, publisher = {Oxford University Press (OUP)}, title = {Code review in digital humanities}, url = {http://dx.doi.org/10.1093/llc/fqae052}, volume = {40}, year = {2024} } @misc{Deekshitha_2024, abstract = {The organizations and researchers producing research software face a common problem of making their software sustainable beyond funding provided by a single research project. This is addressed by research software engineers through building communities around their software, providing appropriate licensing, creating reliable and reproducible research software, making it sustainable and impactful, promoting, and ensuring that the research software is easy to adopt in research workflows, etc. As a result, numerous practices and guidelines exist to enhance research software quality, reusability, and sustainability. However, there is a lack of a unified framework to systematically integrate these practices and help organizations and research software developers refine their development and management processes. Our paper aims at bridging this gap by introducing a novel framework: RSMM. It is designed through systematic literature review and insights from interviews with research software project experts. In short, RSMM offers a structured pathway for evaluating and refining research software project management by categorizing 79 best practices into 17 capabilities across 4 focus areas. From assessing code quality and security to measuring impact, sustainability, and reproducibility, the model provides a complete evaluation of a research software project maturity. With RSMM, individuals as well as organizations involved in research software development gain a systematic approach to tackling various research software engineering challenges. By utilizing RSMM as a comprehensive checklist, organizations can systematically evaluate and refine their project management practices and organizational structure.}, archiveprefix = {arXiv}, author = {Deekshitha and Rena Bakhshi and Jason Maassen and Carlos Martinez Ortiz and Rob van Nieuwpoort and Slinger Jansen}, eprint = {2406.01788}, primaryclass = {cs.SE}, title = {RSMM: A Framework to Assess Maturity of Research Software Project}, url = {https://arxiv.org/abs/2406.01788}, year = {2024} } @article{deekshitha_rsmm_2024, abstract = {The organizations and researchers producing research software face a common problem of making their software sustainable beyond funding provided by a single research project. This is addressed by research software engineers through building communities around their software, providing appropriate licensing, creating reliable and reproducible research software, making it sustainable and impactful, promoting, and ensuring that the research software is easy to adopt in research workflows, etc. As a result, numerous practices and guidelines exist to enhance research software quality, reusability, and sustainability. However, there is a lack of a unified framework to systematically integrate these practices and help organizations and research software developers refine their development and management processes. Our paper aims at bridging this gap by introducing a novel framework: RSMM. It is designed through systematic literature review and insights from interviews with research software project experts. In short, RSMM offers a structured pathway for evaluating and refining research software project management by categorizing 79 best practices into 17 capabilities across 4 focus areas. From assessing code quality and security to measuring impact, sustainability, and reproducibility, the model provides a complete evaluation of a research software project maturity. With RSMM, individuals as well as organizations involved in research software development gain a systematic approach to tackling various research software engineering challenges. By utilizing RSMM as a comprehensive checklist, organizations can systematically evaluate and refine their project management practices and organizational structure.}, author = {{Deekshitha} and Bakhshi, Rena and Maassen, Jason and Ortiz, Carlos Martinez and Nieuwpoort, Rob van and Jansen, Slinger}, keywords = {assessment, maturity, software projects}, month = {June}, title = {{RSMM}: {A} {Framework} to {Assess} {Maturity} of {Research} {Software} {Project}}, year = {2024} } @inproceedings{DiPenta_2024, author = {Di Penta, Massimiliano}, booktitle = {Proceedings of the 28th International Conference on Evaluation and Assessment in Software Engineering}, collection = {EASE 2024}, doi = {10.1145/3661167.3661270}, month = {June}, pages = {5–5}, publisher = {ACM}, series = {EASE 2024}, title = {Why Large Language Models will (not) Kill Software Engineering Research}, url = {http://dx.doi.org/10.1145/3661167.3661270}, year = {2024} } @misc{Dorner_2024, abstract = {Software is at the core of most scientific discoveries today. Therefore, the quality of research results highly depends on the quality of the research software. Rigorous testing, as we know it from software engineering in the industry, could ensure the quality of the research software but it also requires a substantial effort that is often not rewarded in academia. Therefore, this research explores the effects of research software testing integrated into teaching on research software. In an in-vivo experiment, we integrated the engineering of a test suite for a large-scale network simulation as group projects into a course on software testing at the Blekinge Institute of Technology, Sweden, and qualitatively measured the effects of this integration on the research software. We found that the research software benefited from the integration through substantially improved documentation and fewer hardware and software dependencies. However, this integration was effortful and although the student teams developed elegant and thoughtful test suites, no code by students went directly into the research software since we were not able to make the integration back into the research software obligatory or even remunerative. Although we strongly believe that integrating research software engineering such as testing into teaching is not only valuable for the research software itself but also for students, the research of the next generation, as they get in touch with research software engineering and bleeding-edge research in their field as part of their education, the uncertainty about the intellectual properties of students' code substantially limits the potential of integrating research software testing into teaching.}, archiveprefix = {arXiv}, author = {Michael Dorner and Andreas Bauer and Florian Angermeir}, eprint = {2405.11965}, primaryclass = {cs.SE}, title = {No Free Lunch: Research Software Testing in Teaching}, url = {https://arxiv.org/abs/2405.11965}, year = {2024} } @article{dorner_no_2024, abstract = {Software is at the core of most scientific discoveries today. Therefore, the quality of research results highly depends on the quality of the research software. Rigorous testing, as we know it from software engineering in the industry, could ensure the quality of the research software but it also requires a substantial effort that is often not rewarded in academia. Therefore, this research explores the effects of research software testing integrated into teaching on research software. In an in-vivo experiment, we integrated the engineering of a test suite for a large-scale network simulation as group projects into a course on software testing at the Blekinge Institute of Technology, Sweden, and qualitatively measured the effects of this integration on the research software. We found that the research software benefited from the integration through substantially improved documentation and fewer hardware and software dependencies. However, this integration was effortful and although the student teams developed elegant and thoughtful test suites, no code by students went directly into the research software since we were not able to make the integration back into the research software obligatory or even remunerative. Although we strongly believe that integrating research software engineering such as testing into teaching is not only valuable for the research software itself but also for students, the research of the next generation, as they get in touch with research software engineering and bleeding-edge research in their field as part of their education, the uncertainty about the intellectual properties of students' code substantially limits the potential of integrating research software testing into teaching.}, author = {Dorner, Michael and Bauer, Andreas and Angermeir, Florian}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.48550/ARXIV.2405.11965}, keywords = {FOS: Computer and information sciences, Software Engineering (cs.SE), testing}, month = {May}, title = {No {Free} {Lunch}: {Research} {Software} {Testing} in {Teaching}}, year = {2024} } @article{druskat_byte-sized_2024, author = {Druskat, Stephan and Siqueira, Abel Soares and Cushing, Reggie and Lyashevska, Olga and Carlos, Martinez}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.10838021}, keywords = {citation}, title = {Byte-sized {RSE}: {Season} 2, {Session} 5 - {Citation} {File} {Format} ({CFF}) / cffinit}, year = {2024} } @article{druskat_dont_2024, abstract = {Datasets collecting software mentions from scholarly publications can potentially be used for research into the software that has been used in the published research, as well as into the practice of software citation. Recently, new software mention datasets with different characteristics have been published. We present an approach to assess the usability of such datasets for research on research software. Our approach includes sampling and data preparation, manual annotation for quality and mention characteristics, and annotation analysis. We applied it to two software mention datasets for evaluation based on qualitative observation. Doing this, we were able to find challenges to working with the selected datasets to do research. Main issues refer to the structure of the dataset, the quality of the extracted mentions (54\% and 23\% of mentions respectively are not to software), and software accessibility. While one dataset does not provide links to mentioned software at all, the other does so in a way that can impede quantitative research endeavors: (1) Links may come from different sources and each point to different software for the same mention. (2) The quality of the automatically retrieved links is generally poor (in our sample, 65.4\% link the wrong software). (3) Links exist only for a small subset (in our sample, 20.5\%) of mentions, which may lead to skewed or disproportionate samples. However, the greatest challenge and underlying issue in working with software mention datasets is the still suboptimal practice of software citation: Software should not be mentioned, it should be cited following the software citation principles.}, author = {Druskat, Stephan and Hong, Neil P. Chue and Buzzard, Sammie and Konovalov, Olexandr and Kornek, Patrick}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.48550/ARXIV.2402.14602}, keywords = {FOS: Computer and information sciences, Software Engineering (cs.SE), citation, discovery}, month = {February}, title = {Don't mention it: {An} approach to assess challenges to using software mentions for citation and discoverability research}, year = {2024} } @article{druskat_research_2024, author = {Druskat, Stephan}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.10696026}, keywords = {requirements engineering}, language = {en}, title = {Research {Software} {Requirements} {Engineering}?}, year = {2024} } @article{druskat_software_2024, author = {Druskat, Stephan and Felderer, Michael and Haupt, Carina}, issn = {0720-8928}, journal = {Softwaretechnik-Trends}, number = {1}, title = {Software engineering, research software and requirements engineering}, url = {https://dl.gi.de/items/1b96d440-bd4d-48c4-8eb6-1b368206addd}, volume = {44}, year = {2024} } @inproceedings{druskat_software_2024-1, author = {Druskat, Stephan and Felderer, Michael and Haupt, Carina}, booktitle = {Softwaretechnik-{Trends} {Band} 44, {Heft} 1}, keywords = {software engineering, requirements engineering}, publisher = {Gesellschaft f\"{u}r Informatik eV}, title = {Software engineering, research software and requirements engineering}, year = {2024} } @inproceedings{feldman_non-expert_2024, address = {New York, USA}, author = {Feldman, Molly Q and Anderson, Carolyn Jane}, booktitle = {Proceedings of the 3{\textbackslash}textsuperscriptrd {Annual} {Meeting} of the {Symposium} on {Human}-{Computer} {Interaction} for {Work} ({CHIWORK} '24)}, doi = {10.1145/3663384.3663393}, editor = {Cecchinato, Marta E. and Constantinides, Marios and Gould, Sandy and Lallemand, Carine and Jain, Mohit}, isbn = {979-8-4007-1017-9}, month = {June}, pages = {1--19}, publisher = {Association for Computing Machinery}, title = {Non-expert programmers in the generative {AI} future}, year = {2024} } @article{gallagher_ten_2024, abstract = {Computational methods and associated software implementations are central to every field of scientific investigation. Modern biological research, particularly within systems biology, has relied heavily on the development of software tools to process and organize increasingly large datasets, simulate complex mechanistic models, provide tools for the analysis and management of data, and visualize and organize outputs. However, developing high-quality research software requires scientists to develop a host of software development skills, and teaching these skills to students is challenging. There has been a growing importance placed on ensuring reproducibility and good development practices in computational research. However, less attention has been devoted to informing the specific teaching strategies which are effective at nurturing in researchers the complex skillset required to produce high-quality software that, increasingly, is required to underpin both academic and industrial biomedical research. Recent articles in the Ten Simple Rules collection have discussed the teaching of foundational computer science and coding techniques to biology students. We advance this discussion by describing the specific steps for effectively teaching the necessary skills scientists need to develop sustainable software packages which are fit for (re-)use in academic research or more widely. Although our advice is likely to be applicable to all students and researchers hoping to improve their software development skills, our guidelines are directed towards an audience of students that have some programming literacy but little formal training in software development or engineering, typical of early doctoral students. These practices are also applicable outside of doctoral training environments, and we believe they should form a key part of postgraduate training schemes more generally in the life sciences.}, author = {Gallagher, Kit and Creswell, Richard and Lambert, Ben and Robinson, Martin and Lei, Chon Lok and Mirams, Gary R. and Gavaghan, David J.}, copyright = {arXiv.org perpetual, non-exclusive license}, doi = {10.48550/ARXIV.2402.04722}, keywords = {sustainability, FOS: Computer and information sciences, Software Engineering (cs.SE), Computers and Society (cs.CY), teaching}, month = {February}, title = {Ten simple rules for teaching sustainable software engineering}, year = {2024} } @article{goth_foundational_2024, author = {Goth, Florian and Alves, Renato and Braun, Matthias and Castro, Leyla Jael and Chourdakis, Gerasimos and Christ, Simon and Cohen, Jeremy and Druskat, Stephan and Erxleben, Fredo and Grad, Jean-No\"{e}l and Hagdorn, Magnus and Hodges, Toby and Juckeland, Guido and Kempf, Dominic and Lamprecht, Anna-Lena and Linxweiler, Jan and L\"{o}ffler, Frank and Martone, Michele and Schwarzmeier, Moritz and Seibold, Heidi and Thiele, Jan Philipp and von Waldow, Harald and Wittke, Samantha}, doi = {10.12688/f1000research.157778.1}, journal = {F1000Research}, number = {1429}, title = {Foundational {Competencies} and {Responsibilities} of a {Research} {Software} {Engineer} [version 1; peer review: 2 approved]}, volume = {13}, year = {2024} } @article{grossmann_software_2024, author = {Grossmann, Yves Vincent and Lanza, Giacomo and Biernacka, Katarzyna and Hasler, Tim and Helbig, Kerstin}, doi = {10.5334/dsj-2024-043}, issn = {1683-1470}, journal = {Data Science Journal}, keywords = {software management plans}, language = {en}, month = {September}, pages = {43}, title = {Software {Management} {Plans} – {Current} {Concepts}, {Tools}, and {Application}}, url = {https://datascience.codata.org/articles/10.5334/dsj-2024-043/}, urldate = {2024-09-26}, volume = {23}, year = {2024} } @article{grunske_research_2024, author = {Grunske, Lars and Lamprecht, Anna-Lena and Hasselbring, Wilhelm and Rumpe, Bernhard}, journal = {Forschung \& Lehre}, keywords = {sustainability}, number = {3}, pages = {186--188}, title = {Research {Software} {Engineering}-{Forschungssoftware} effizient erstellen und dauerhaft erhalten}, volume = {24}, year = {2024} } @article{guerrero_automated_2024, author = {Guerrero, Carlos Utrilla and Corcho, Oscar and Garijo, Daniel}, keywords = {documentation}, title = {Automated {Extraction} of {Research} {Software} {Installation} {Instructions} from {README} files: {An} {Initial} {Analysis}}, year = {2024} } @article{hammitzsch_nfdisoftware_2024, abstract = {This is the proposal for the initialisation phase of nfdi.software as a community version.}, author = {Hammitzsch, Martin and Hetenyi, Beate and Gr\"{u}ning, Bj\"{o}rn and Marcic, Aleksander and L\"{o}be, Matthias and Castro, Layla-Jael and Engel, Felix and H\"{o}fner, Konrad and Zacharias, Michael and Werth, Oliver and Seibert, Vasiliy and Rausch, Andreas}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.14507302}, month = {December}, title = {nfdi.software - {Initialisation} {Phase}}, url = {https://zenodo.org/doi/10.5281/zenodo.14507302}, urldate = {2025-01-22}, year = {2024} } @misc{Hasselbring_2024, abstract = {Research software has been categorized in different contexts to serve different goals. We start with a look at what research software is, before we discuss the purpose of research software categories. We propose a multi-dimensional categorization of research software. We present a template for characterizing such categories. As selected dimensions, we present our proposed role-based, developer-based, and maturity-based categories. Since our work has been inspired by various previous efforts to categorize research software, we discuss them as related works. We characterize all these categories via the previously introduced template, to enable a systematic comparison.}, archiveprefix = {arXiv}, author = {Wilhelm Hasselbring and Stephan Druskat and Jan Bernoth and Philine Betker and Michael Felderer and Stephan Ferenz and Anna-Lena Lamprecht and Jan Linxweiler and Bernhard Rumpe}, eprint = {2404.14364}, primaryclass = {cs.SE}, title = {Toward Research Software Categories}, url = {https://arxiv.org/abs/2404.14364}, year = {2024} } @article{hasselbring_toward_2024, abstract = {Research software has been categorized in different contexts to serve different goals. We start with a look at what research software is, before we discuss the purpose of research software categories. We propose a multi-dimensional categorization of research software. We present a template for characterizing such categories. As selected dimensions, we present our proposed role-based, developer-based, and maturity-based categories. Since our work has been inspired by various previous efforts to categorize research software, we discuss them as related works. We characterize all these categories via the previously introduced template, to enable a systematic comparison.}, author = {Hasselbring, Wilhelm and Druskat, Stephan and Bernoth, Jan and Betker, Philine and Felderer, Michael and Ferenz, Stephan and Lamprecht, Anna-Lena and Linxweiler, Jan and Rumpe, Bernhard}, copyright = {arXiv.org perpetual, non-exclusive license}, doi = {10.48550/ARXIV.2404.14364}, keywords = {FOS: Computer and information sciences, Software Engineering (cs.SE), categorization}, month = {April}, title = {Toward {Research} {Software} {Categories}}, year = {2024} } @article{hocquet_software_2024, abstract = {Software is much more than just code. It is time to confront the complexity of licenses, uses, governance, infrastructure and other facets of software in science. Their influence is ubiquitous yet overlooked.}, author = {Hocquet, Alexandre and Wieber, Fr\'{e}d\'{e}ric and Gramelsberger, Gabriele and Hinsen, Konrad and Diesmann, Markus and Pasquini Santos, Fernando and Landstr\"{o}m, Catharina and Peters, Benjamin and Kasprowicz, Dawid and Borrelli, Arianna and Roth, Phillip and Lee, Clarissa Ai Ling and Olteanu, Alin and B\"{o}schen, Stefan}, doi = {https://doi.org/10.1038/s43588-024-00651-2}, issn = {2662-8457}, journal = {Nature Computational Science}, title = {Software in science is ubiquitous yet overlooked}, url = {https://doi.org/10.1038/s43588-024-00651-2}, year = {2024} } @article{kappas_choice_2024, author = {Kappas, I and Promponas, VJ and Ouzounis, CA}, doi = {10.1038/s44319-023-00039-9}, issn = {1469-3178}, journal = {EMBO Reports}, keywords = {open source, licensing}, month = {January}, number = {2}, pages = {464--466}, title = {A choice, not an obligation: {Releasing} scientific software as open source should be the responsibility of the authors}, volume = {25}, year = {2024} } @article{katz_special_2024, author = {Katz, Daniel S. and Chue Hong, Neil P.}, doi = {10.7717/peerj-cs.1951}, issn = {2376-5992}, journal = {PeerJ Computer Science}, keywords = {citation, discovery}, month = {March}, pages = {e1951}, title = {Special issue on software citation, indexing, and discoverability}, volume = {10}, year = {2024} } @inproceedings{kirova_software_2024, address = {New York, USA}, author = {Kirova, Vassilka D. and Ku, Cyril S. and Laracy, Joseph R. and Marlowe, Thomas J.}, booktitle = {Proceedings of the 55{\textbackslash}textsuperscriptth {ACM} technical symposium on computer science education ({SIGCSE} 2024), volume 1}, doi = {10.1145/3626252.3630927}, isbn = {979-8-4007-0423-9}, month = {March}, pages = {666--672}, publisher = {Association for Computing Machinery}, title = {Software engineering education must adapt and evolve for an {LLM} environment}, year = {2024} } @article{kuckertz_datadesc_2024, author = {Kuckertz, Patrick and G\"{o}pfert, Jan and Karras, Oliver and Neuroth, David and Sch\"{o}nau, Julian and Pueblas, Rodrigo and Ferenz, Stephan and Engel, Felix and Pflugradt, Noah and Weinand, Jann M. and Nie\ss{}e, Astrid and Auer, S\"{o}ren and Stolten, Detlef}, doi = {10.1016/j.patter.2024.101064}, issn = {26663899}, journal = {Patterns}, keywords = {metadata}, language = {en}, month = {October}, pages = {101064}, shorttitle = {{DataDesc}}, title = {{DataDesc}: {A} framework for creating and sharing technical metadata for research software interfaces}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2666389924002149}, urldate = {2024-10-09}, year = {2024} } @inproceedings{liang_large-scale_2024, address = {New York, USA}, author = {Liang, Jenny T. and Yang, Chenyang and Myers, Brad A.}, booktitle = {Proceedings of the {IEEE}/{ACM} 46{\textbackslash}textsuperscriptth {International} {Conference} on {Software} {Engineering}}, doi = {10.1145/3597503.3608128}, isbn = {979-8-4007-0217-4}, month = {February}, pages = {1--13}, publisher = {Association for Computing Machinery}, series = {{ICSE} '24}, shorttitle = {A large-scale survey on the usability of {AI} programming assistants}, title = {A large-scale survey on the usability of {AI} programming assistants: {Successes} and challenges}, urldate = {2025-05-18}, year = {2024} } @inproceedings{Lorente_2024, author = {Lorente, Nuria P. and O'Toole, Simon J. and Davies, Elizabeth J. A. and Farrell, Tony J. and Miszalski, Brent and Fernando, Nuwanthika}, booktitle = {Observatory Operations: Strategies, Processes, and Systems X}, doi = {10.1117/12.3020652}, editor = {Storrie-Lombardi, Lisa J. and Benn, Chris R. and Chrysostomou, Antonio}, month = {July}, pages = {18}, publisher = {SPIE}, title = {Research software engineering as a model for inclusive and sustainable careers in astronomy}, url = {http://dx.doi.org/10.1117/12.3020652}, year = {2024} } @article{lowe_open_2024, abstract = {To initiate, maintain and accelerate behavioral change towards Open and FAIR practices, tangible benefits for scientific communities and especially early career scientists are a critical key success factor. The realization of such benefits, by due credit, funding, or other means requires underlying workflows, enabled by underlying infrastructures and standards, which are operational, reliable and trusted. Many education efforts are under way to educate and motivate researchers how to embrace and particpate in Open and FAIR efforts, including the open geospatial community software projects of the OSGeo foundation. Still, from the perspective of a developer of research software, the current general service quality of offerings for PID-/citation-based credit remains limited, fickle, partially unpredictable and frustrating. This presentation demonstrates these challenges by real world examples from OSGeo open geospatial projects, such as QGIS, GRASS GIS and proj and resulting PID-references in publications. Further, a service centered approach is introduced to enable both end users and Open/FAIR communities to assess the overall service quality through Technological Readiness Levels (TRL), to improve the user experience by building trust and to focus further development ressources.}, author = {L\"{o}we, Peter}, doi = {10.5194/egusphere-egu24-6254}, keywords = {open science, FAIR, geospatial software}, month = {March}, title = {Open geospatial research software in 2024: {Assessing} service quality with technology readiness levels}, year = {2024} } @inproceedings{naumann_differenzierbare_2024, author = {Naumann, Uwe}, booktitle = {Softwaretechnik-{Trends} {Band} 44, {Heft} 1}, keywords = {models, simulation}, publisher = {Gesellschaft f\"{u}r Informatik eV}, title = {Differenzierbare {Forschungssoftware}}, year = {2024} } @article{nowogrodzki_six_2024, author = {Nowogrodzki, Julian}, copyright = {https://www.springernature.com/gp/researchers/text-and-data-mining}, doi = {10.1038/d41586-024-03344-y}, issn = {0028-0836, 1476-4687}, journal = {Nature}, keywords = {dissemination}, language = {en}, month = {October}, number = {8034}, pages = {742--743}, title = {Six tips for going public with your lab's software}, url = {https://www.nature.com/articles/d41586-024-03344-y}, urldate = {2024-10-22}, volume = {634}, year = {2024} } @misc{OliveiraJr_2024, abstract = {Open Science aims to foster openness and collaboration in research, leading to more significant scientific and social impact. However, practicing Open Science comes with several challenges and is currently not properly rewarded. In this paper, we share our vision for addressing those challenges through a conceptual framework that connects essential building blocks for a change in the Software Engineering community, both culturally and technically. The idea behind this framework is that Open Science is treated as a first-class requirement for better Software Engineering research, practice, recognition, and relevant social impact. There is a long road for us, as a community, to truly embrace and gain from the benefits of Open Science. Nevertheless, we shed light on the directions for promoting the necessary culture shift and empowering the Software Engineering community.}, archiveprefix = {arXiv}, author = {Edson OliveiraJr and Fernanda Madeiral and Alcemir Rodrigues Santos and Christina von Flach and Sergio Soares}, eprint = {2405.12132}, primaryclass = {cs.SE}, title = {A Vision on Open Science for the Evolution of Software Engineering Research and Practice}, url = {https://arxiv.org/abs/2405.12132}, year = {2024} } @article{oliveirajr_vision_2024, abstract = {Open Science aims to foster openness and collaboration in research, leading to more significant scientific and social impact. However, practicing Open Science comes with several challenges and is currently not properly rewarded. In this paper, we share our vision for addressing those challenges through a conceptual framework that connects essential building blocks for a change in the Software Engineering community, both culturally and technically. The idea behind this framework is that Open Science is treated as a first-class requirement for better Software Engineering research, practice, recognition, and relevant social impact. There is a long road for us, as a community, to truly embrace and gain from the benefits of Open Science. Nevertheless, we shed light on the directions for promoting the necessary culture shift and empowering the Software Engineering community.}, address = {New York, USA}, author = {OliveiraJr, Edson and Madeiral, Fernanda and Santos, Alcemir Rodrigues and von Flach, Christina and Soares, Sergio}, booktitle = {Companion proceedings of the 32{\textbackslash}textsuperscriptnd {ACM} international conference on the {Foundations} of {Software} {Engineering} ({FSE} 2024)}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.1145/3663529.3663788}, isbn = {979-8-4007-0658-5}, keywords = {open science, FOS: Computer and information sciences, Software Engineering (cs.SE)}, month = {May}, pages = {512--516}, publisher = {Association for Computing Machinery}, title = {A {Vision} on {Open} {Science} for the {Evolution} of {Software} {Engineering} {Research} and {Practice}}, year = {2024} } @article{russo_navigating_2024, author = {Russo, Daniel}, doi = {10.1145/3652154}, issn = {1049-331X}, journal = {ACM Transactions on Software Engineering and Methodology}, month = {June}, number = {5}, title = {Navigating the complexity of generative {AI} adoption in software engineering}, volume = {33}, year = {2024} } @article{seibert_bettys_2024, author = {Seibert, Vasiliy and Rausch, Andreas and Wittek, Stefan}, journal = {ing. grid}, keywords = {search engine, software retrieval}, number = {2}, title = {Betty's ({Re}) {Search} {Engine}: {A} client-based search engine for research software stored in repositories.}, volume = {1}, year = {2024} } @article{smith_state_2024, author = {Smith, Spencer and Michalski, Peter and Carette, Jacques and Keshavarz-Motamed, Zahra}, doi = {10.1007/s11831-023-09981-2}, issn = {1886-1784}, journal = {Archives of Computational Methods in Engineering}, month = {January}, number = {1}, pages = {313--350}, title = {State of the practice for lattice {Boltzmann} method software}, volume = {31}, year = {2024} } @misc{Sochat_2024, abstract = {Research has become increasingly reliant on software, serving as the driving force behind bioinformatics, high performance computing, physics, machine learning and artificial intelligence, to name a few. While substantial progress has been made in advocating for the research software engineer, a kind of software engineer that typically works directly on software and associated assets that go into research, little attention has been placed on the workforce behind research infrastructure and innovation, namely compilers and compatibility tool development, orchestration and scheduling infrastructure, developer environments, container technologies, and workflow managers. As economic incentives are moving toward different models of cloud computing and innovating is required to develop new paradigms that represent the best of both worlds, an effort called "converged computing," the need for such a role is not just ideal, but essential for the continued success of science. While scattered staff in non-traditional roles have found time to work on some facets of this space, the lack of a larger workforce and incentive to support it has led to the scientific community falling behind. In this article we will highlight the importance of this missing layer, providing examples of how a missing role of infrastructure engineer has led to inefficiencies in the interoperability, portability, and reproducibility of science. We suggest that an inability to allocate, provide resources for, and sustain individuals to work explicitly on these technologies could lead to possible futures that are sub-optimal for the continued success of our scientific communities.}, archiveprefix = {arXiv}, author = {Vanessa Sochat}, eprint = {2405.10473}, primaryclass = {cs.SE}, title = {Infrastructure Engineering: A Still Missing, Undervalued Role in the Research Ecosystem}, url = {https://arxiv.org/abs/2405.10473}, year = {2024} } @article{sonabend_fair-use4os_2024, author = {Sonabend, Raphael and Gruson, Hugo and Wolansky, Leo and Kiragga, Agnes and Katz, Daniel S.}, doi = {10.1371/journal.pcbi.1012045}, editor = {Papin, Jason A.}, issn = {1553-7358}, journal = {PLOS Computational Biology}, keywords = {open source, FAIR}, month = {May}, number = {5}, pages = {e1012045}, title = {{FAIR}-{USE4OS}: {Guidelines} for creating impactful open-source software}, volume = {20}, year = {2024} } @article{sonabend_fair-use4os_2024-1, abstract = {This paper extends the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines to provide criteria for assessing if software conforms to best practices in open source. By adding 'USE' (User-Centered, Sustainable, Equitable), software development can adhere to open source best practice by incorporating user-input early on, ensuring front-end designs are accessible to all possible stakeholders, and planning long-term sustainability alongside software design. The FAIR-USE4OS guidelines will allow funders and researchers to more effectively evaluate and plan open source software projects. There is good evidence of funders increasingly mandating that all funded research software is open source; however, even under the FAIR guidelines, this could simply mean software released on public repositories with a Zenodo DOI. By creating FAIR-USE software, best practice can be demonstrated from the very beginning of the design process and the software has the greatest chance of success by being impactful.}, author = {Sonabend, Raphael and Gruson, Hugo and Wolansky, Leo and Kiragga, Agnes and Katz, Daniel S.}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.48550/ARXIV.2402.02824}, keywords = {open source, FOS: Computer and information sciences, Software Engineering (cs.SE), FAIR}, month = {February}, title = {{FAIR}-{USE4OS}: {Guidelines} for {Creating} {Impactful} {Open}-{Source} {Software}}, year = {2024} } @misc{Sorathiya_2024, abstract = {Context: The growing focus on ethics within SE, primarily due to the significant reliance of individuals' lives on software and the consequential social and ethical considerations that impact both people and society has brought focus on ethical software requirements identification and elicitation. User safety, privacy, and security concerns are of prime importance while developing software due to the widespread use of software across healthcare, education, and business domains. Thus, identifying and elicitating ethical software requirements from app user reviews, focusing on various aspects such as privacy, security, accountability, accessibility, transparency, fairness, safety, and social solidarity, are essential for developing trustworthy software solutions. Objective: This SLR aims to identify and analyze existing ethical requirements identification and elicitation techniques in the context of the formulated research questions. Method: We conducted an SLR based on Kitchenham et al's methodology. We identified and selected 47 primary articles for this study based on a predefined search protocol. Result: Ethical requirements gathering has recently driven drastic interest in the research community due to the rise of ML and AI-based approaches in decision-making within software applications. This SLR provides an overview of ethical requirements identification techniques and the implications of extracting and addressing them. This study also reports the data sources used for analyzing user reviews. Conclusion: This SLR provides an understanding of the ethical software requirements and underscores the importance of user reviews in developing trustworthy software. The findings can also help inform future research and guide software engineers or researchers in addressing software ethical requirements.}, archiveprefix = {arXiv}, author = {Aakash Sorathiya and Gouri Ginde}, eprint = {2410.01833}, primaryclass = {cs.SE}, title = {Ethical software requirements from user reviews: A systematic literature review}, url = {https://arxiv.org/abs/2410.01833}, year = {2024} } @article{stankovski_repofrompaper_2024, author = {Stankovski, Aleksandar and Garijo, Daniel}, keywords = {publication, code extraction}, title = {{RepoFromPaper}: {An} {Approach} to {Extract} {Software} {Code} {Implementations} from {Scientific} {Publications}}, year = {2024} } @inbook{Struck_2024, author = {Struck, Alexander and Bertuch, Oliver and Druskat, Stephan}, booktitle = {Praxishandbuch Bibliotheksmanagement}, doi = {10.1515/9783111046341-027}, isbn = {9783111046341}, month = {November}, pages = {433–454}, publisher = {De Gruyter}, title = {5.8 Forschungssoftware}, url = {http://dx.doi.org/10.1515/9783111046341-027}, year = {2024} } @article{sun_how_2024, abstract = {Scientific open-source software (OSS) has greatly benefited research communities through its transparent and collaborative nature. Given its critical role in scientific research, ensuring the sustainability of such software has become vital. Earlier studies have proposed sustainability strategies for conventional scientific software and open-source communities. However, it remains unclear whether these solutions can be easily adapted to the integrated framework of scientific OSS and its larger ecosystem. This study examines the challenges and opportunities to enhance the sustainability of scientific OSS in the context of interdisciplinary collaboration, open-source community, and multi-project ecosystem. We conducted a case study on a widely-used software ecosystem in the astrophysics domain, the Astropy Project, using a mixed-methods design approach. This approach includes an interview with core contributors regarding their participation in an interdisciplinary team, a survey of disengaged contributors about their motivations for contribution, reasons for disengagement, and suggestions for sustaining the communities, and finally, an analysis of cross-referenced issues and pull requests to understand best practices for collaboration on the ecosystem level. Our study reveals the implications of major challenges for sustaining scientific OSS and proposes concrete suggestions for tackling these challenges.}, author = {Sun, Jiayi and Patil, Aarya and Li, Youhai and Guo, Jin L. C. and Zhou, Shurui}, copyright = {arXiv.org perpetual, non-exclusive license}, doi = {10.48550/ARXIV.2402.15081}, keywords = {sustainability, open source, FOS: Computer and information sciences, Software Engineering (cs.SE)}, month = {February}, title = {How to {Sustain} a {Scientific} {Open}-{Source} {Software} {Ecosystem}: {Learning} from the {Astropy} {Project}}, year = {2024} } @inproceedings{sun_sustaining_2024, author = {Sun, Jiayi}, booktitle = {Proceedings of the 2024 {IEEE}/{ACM} 46{\textbackslash}textbackslashtextsuperscriptth {International} {Conference} on {Software} {Engineering}: {Companion} {Proceedings}}, doi = {10.1145/3639478.3639805}, keywords = {sustainability, open source}, month = {April}, publisher = {ACM}, series = {{ICSE}-{Companion} '24}, title = {Sustaining {Scientific} {Open}-{Source} {Software} {Ecosystems}: {Challenges}, {Practices}, and {Opportunities}}, year = {2024} } @article{wilkinson_fair_2024, author = {Wilkinson, Sean R.}, doi = {10.5194/egusphere-egu24-19486}, keywords = {FAIR, earth system science, workflows}, month = {March}, title = {{FAIR} {Workflows} and {Methods} for {Scaling}}, year = {2024} } @incollection{wolski_open_2024, author = {Wolski, Marcin and Todek, Jan and \L{}ab\k{e}dzki, Maciej and Walter, Bartosz}, booktitle = {Good {Practices} and {New} {Perspectives} in {Information} {Systems} and {Technologies}}, doi = {10.1007/978-3-031-60227-6_14}, isbn = {978-3-031-60227-6}, keywords = {discovery}, pages = {165--171}, publisher = {Springer Nature Switzerland}, title = {Open {Software} {Catalogue} – {Supporting} the {Management} of {Research} {Software}}, year = {2024} } @inproceedings{wyatt_building_2024, abstract = {What does it take to build a thriving community for research software engineers? How do we find RSEs and then engage them in our community? What activities should we focus our precious time and energy on?All these questions and more are often asked by those trying to build a community in research software engineering, in many countries and institutions with varying degrees of success. In this talk, I will draw from my experience in the UK and take a look at the successes and challenges in the UK RSE Community followed by presenting my current work of building an RSE community at Forschungszentrum J\"{u}lich in Germany. I will talk about the various activities that can be useful in building a community at a national and institutional level.}, author = {Wyatt, Claire}, keywords = {Community}, month = {December}, publisher = {Belgian RSE Conference 2024, Brussels (Belgium), 13 Dec 2024 - 13 Dec 2024}, title = {Building {RSE} {Communities}}, url = {https://juser.fz-juelich.de/record/1034677}, year = {2024} } @article{ahsan_implementation_2023, author = {Ahsan, Kamrul and Akbar, Suraiyah and Kam, Booi and Abdulrahman, Muhammad Dan-Asabe}, doi = {10.1007/s10639-023-11739-z}, journal = {Education and Information Technologies}, month = {March}, title = {Implementation of micro-credentials in higher education: {A} systematic literature review}, year = {2023} } @article{bacall_making_2023, author = {Bacall, Finn and Apaolaza, Aitor and Andrabi, Munazah and Child, Chris and Goble, Carole and Sand, Olivier and Botzki, Alexander}, doi = {10.1002/cpz1.682}, issn = {2691-1299}, journal = {Current Protocols}, month = {February}, number = {2}, title = {Making {Bioinformatics} {Training} {Events} and {Material} {More} {Discoverable} {Using} {TeSS}, the {ELIXIR} {Training} {Portal}}, volume = {3}, year = {2023} } @article{barr_continuously_2023, author = {Barr, Earl and Bell, Jonathan and Hilton, Michael and Mechtaev, Sergey and Timperley, Christopher}, keywords = {science, future, workflow}, title = {Continuously {Accelerating} {Research}}, year = {2023} } @article{blanc_catala_establishing_2023, author = {Blanc Catala, Isabelle and Di Cosmo, Roberto and Giraud, Mathieu and Le Berre, Daniel and Louvet, Violaine and Renaudin, Sophie}, doi = {10.12688/openreseurope.16069.1}, issn = {2732-5121}, journal = {Open Research Europe}, keywords = {assessment, award}, month = {October}, pages = {185}, title = {Establishing a national research software award}, volume = {3}, year = {2023} } @article{bouquin_advancing_2023, abstract = {Software is foundationally important to scientific and social progress, however, traditional acknowledgment of the use of others' work has not adapted in step with the rapid development and use of software in research. This report outlines a series of collaborative discussions that brought together an international group of stakeholders and experts representing many communities, forms of labor, and expertise. Participants addressed specific challenges about software citation that have so far gone unresolved. The discussions took place in summer 2022 both online and in-person and involved a total of 51 participants. The activities described in this paper were intended to identify and prioritize specific software citation problems, develop (potential) interventions, and lay out a series of mutually supporting approaches to address them. The outcomes of this report will be useful for the GLAM (Galleries, Libraries, Archives, Museums) community, repository managers and curators, research software developers, and publishers.}, author = {Bouquin, Daina and Trisovic, Ana and Bertuch, Oliver and Col\'{o}n-Marrero, Elena}, doi = {10.48550/ARXIV.2302.07500}, keywords = {citation}, month = {February}, title = {Advancing {Software} {Citation} {Implementation} ({Software} {Citation} {Workshop} 2022)}, year = {2023} } @article{brown_soft-search_2023, abstract = {Software is an important tool for scholarly work, but software produced for research is in many cases not easily identifiable or discoverable. A potential first step in linking research and software is software identification. In this paper we present two datasets to study the identification and production of research software. The first dataset contains almost 1000 human labeled annotations of software production from National Science Foundation (NSF) awarded research projects. We use this dataset to train models that predict software production. Our second dataset is created by applying the trained predictive models across the abstracts and project outcomes reports for all NSF funded projects between the years of 2010 and 2023. The result is an inferred dataset of software production for over 150,000 NSF awards. We release the Soft-Search dataset to aid in identifying and understanding research software production: https://github.com/si2-urssi/eager}, author = {Brown, Eva Maxfield and Schwartz, Lindsey and Huang, Richard Lewei and Weber, Nicholas}, doi = {10.48550/ARXIV.2302.14177}, keywords = {identification, production}, month = {February}, title = {Soft-{Search}: {Two} {Datasets} to {Study} the {Identification} and {Production} of {Research} {Software}}, year = {2023} } @article{cain_emphin_2023, author = {Cain, Jason Y. and Yu, Jessica S. and Bagheri, Neda}, doi = {10.1016/j.cels.2022.11.006}, journal = {Cell Systems}, month = {January}, number = {1}, pages = {1--6}, title = {The \emph{in silico} lab: {Improving} academic code using lessons from biology}, volume = {14}, year = {2023} } @inproceedings{carlin_softwhere_2023, abstract = {REF, the UK's Research Excellence Framework, periodically assesses the quality and impact of higher education research in the UK. There has been a steep decline in submissions of research software to REF from 2008 to 2021, despite the rapid growth of the RSE discipline in the same time period. To date, there has been no investigation into how the official academic Institutional Repositories (IRs) have impacted these low return rates. In what we believe to be the first such census of its kind, we queried 180 online repositories of over 150 UK universities. We found that the prevalence of software records within UK IRs is worryingly low, while significantly few contain software as recognised academic output. Of greater concern, we found that a large majority of repositories simply cannot record software as a distinct type of research output, despite using controlled metadata formats and vocabularies that include software as an entity. Several Universities appeared to have even removed software as a defined type from the default settings of their repository, indicating institutional policy being an underlying issue. Indeed, for the most popular repository platform, a single word in a config file would permit a software type. We also explored potential correlational variables, such as having an RSE team listed at the institution, but failed to find correlations between these metadata and the prevalence of records of software. This then begs the question, where is all the research software in the UK? In the second part of this research, we sought to establish where research software from UK Academic Institutions is kept/recorded/registered. We compared records of software in institutional repositories to the recorded outputs in the UK's Gateway to Research, a publicly accessible database of all outputs claimed from government-funded research. We found the latter contained five times the amount of software outputs of the former. Of these 7232 software outputs, only 71\% had a URL linking to the software, while fewer than 4000 of these worked. Categorizing these URLs, we found the single largest source category was commercial code repositories. The overwhelming majority of software was found in GitHub, which stores the software of around 1/3 of working disclosed URLs from publicly funded research. Finally, we discuss the implications of these findings with regard to the lack of recognition of software as a discrete research output in institutions, despite the opposite being mandated by funders, and we make recommendations for changes in policies and operating procedures.}, author = {Carlin, Domhnall}, keywords = {UK, discovery}, language = {English}, month = {October}, title = {{SoftWhere}? {Searching} for research software in the {UK}}, url = {https://se4science.org/workshops/se4rse23/index.htm}, year = {2023} } @article{carlin_where_2023, author = {Carlin, Domhnall and Rainer, Austen and Wilson, David}, doi = {10.7717/peerj-cs.1546}, issn = {2376-5992}, journal = {PeerJ Computer Science}, keywords = {assessment}, month = {November}, pages = {e1546}, title = {Where is all the research software? {An} analysis of software in {UK} academic repositories}, volume = {9}, year = {2023} } @article{castro_bioschemas_2023, author = {Castro, Leyla Jael and Palagi, Patricia M. and Beard, Niall and Attwood, Teresa K. and Brazas, Michelle D.}, doi = {10.1371/journal.pcbi.1011120}, editor = {Ouellette, Francis}, journal = {PLOS Computational Biology}, month = {June}, number = {6}, pages = {e1011120}, title = {Bioschemas training profiles: {A} set of specifications for standardizing training information to facilitate the discovery of training programs and resources}, volume = {19}, year = {2023} } @article{chicco_ten_2023, author = {Chicco, Davide and Jurman, Giuseppe}, doi = {10.1186/s13040-023-00326-0}, journal = {BioData Mining}, month = {February}, number = {1}, title = {Ten simple rules for providing bioinformatics support within a hospital}, volume = {16}, year = {2023} } @inproceedings{chue_hong_can_2023, author = {Chue Hong, Neil}, doi = {10.6084/m9.figshare.22186417}, month = {March}, publisher = {figshare}, title = {Can software metrics improve (research) software quality?}, year = {2023} } @article{chue_hong_d52_2023, author = {Chue Hong, Neil and Breitmoser, Elena and Antonioletti, Mario and Davidson, Joy and Garijo, Daniel and Gonzalez-Beltran, Alejandra and Gruenpeter, Morane and Huber, Robert and Jonquet, Clement and priddy, Mike and Shepeherdson, John and Verburg, Maaike and Wood, Chris}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.10047400}, keywords = {FAIR, FAIR metrics, FAIR-IMPACT, Social Sciences}, language = {en}, title = {D5.2 - {Metrics} for automated {FAIR} software assessment in a disciplinary context}, year = {2023} } @article{combemale_research_2023, author = {Combemale, Benoit and Gray, Jeff and Rumpe, Bernhard}, doi = {10.1007/s10270-023-01119-z}, issn = {1619-1374}, journal = {Software and Systems Modeling}, keywords = {software engineering, modelling}, month = {July}, number = {4}, pages = {1081--1083}, title = {Research software engineering and the importance of scientific models}, volume = {22}, year = {2023} } @inproceedings{cutcher-gershenfeld_professionalization_2023, author = {Cutcher-Gershenfeld, Joel and Battelle, Torey and Brunson, Dana and Cheatham, Thomas and Fosso Tande, Jacob and Jennewein, Douglas and Ma, Julie and Michael, Lauren A. and Middelkoop, Timothy and Neeman, Henry and Schmitz, Patrick}, booktitle = {Practice and {Experience} in {Advanced} {Research} {Computing}}, doi = {10.1145/3569951.3593610}, keywords = {profession}, month = {July}, publisher = {ACM}, series = {{PEARC} '23}, title = {Professionalization of {Research} {Computing} and {Data}: {An} {Expanded} {Agenda}}, year = {2023} } @inproceedings{dam_towards_2023, address = {New York, New York, USA}, author = {Dam, Tobias and Klausner, Lukas Daniel and Neumaier, Sebastian}, booktitle = {Companion {Proceedings} of the {ACM} {Web} {Conference} 2023}, doi = {10.1145/3543873.3587336}, isbn = {978-1-4503-9419-2}, month = {April}, pages = {156--159}, publisher = {ACM}, title = {Towards a {Critical} {Open}-{Source} {Software} {Database}}, year = {2023} } @inproceedings{deekshitha_fairseco_2023, author = {{Deekshitha} and Farshidi, Siamak and Maassen, Jason and Bakhshi, Rena and Van Nieuwpoort, Rob and Jansen, Slinger}, booktitle = {2023 {IEEE} 19{\textbackslash}textbackslashtextsuperscriptth {International} {Conference} on e-{Science} (e-{Science})}, doi = {10.1109/e-science58273.2023.10254664}, keywords = {FAIR, assessment, software quality}, month = {October}, publisher = {IEEE}, title = {{FAIRSECO}: {An} {Extensible} {Framework} for {Impact} {Measurement} of {Research} {Software}}, year = {2023} } @misc{Deschamps_2023, abstract = {In the past decade, enormous progress has been made in advancing the state-of-the-art in bioimage analysis - a young computational field that works in close collaboration with the life sciences on the quantitative analysis of scientific image data. In many cases, tremendous effort has been spent to package these new advances into usable software tools and, as a result, users can nowadays routinely apply cutting-edge methods to their analysis problems using software tools such as ilastik [1], cellprofiler [2], Fiji/ImageJ2 [3,4] and its many modern plugins that build on the BigDataViewer ecosystem [5], and many others. Such software tools have now become part of a critical infrastructure for science [6]. Unfortunately, overshadowed by the few exceptions that have had long-lasting impact, many other potentially useful tools fail to find their way into the hands of users. While there are many reasons for this, we believe that at least some of the underlying problems, which we discuss in more detail below, can be mitigated. In this opinion piece, we specifically argue that embedding teams of research software engineers (RSEs) within imaging and image analysis core facilities would be a major step towards sustainable bioimage analysis software.}, archiveprefix = {arXiv}, author = {Joran Deschamps and Damian Dalle Nogare and Florian Jug}, eprint = {2307.03934}, primaryclass = {q-bio.OT}, title = {Better Research Software Tools to Elevate the Rate of Scientific Discovery -- or why we need to invest in research software engineering}, url = {https://arxiv.org/abs/2307.03934}, year = {2023} } @article{deschamps_better_2023, abstract = {In the past decade, enormous progress has been made in advancing the state-of-the-art in bioimage analysis - a young computational field that works in close collaboration with the life sciences on the quantitative analysis of scientific image data. In many cases, tremendous effort has been spent to package these new advances into usable software tools and, as a result, users can nowadays routinely apply cutting-edge methods to their analysis problems using software tools such as ilastik [1], cellprofiler [2], Fiji/ImageJ2 [3,4] and its many modern plugins that build on the BigDataViewer ecosystem [5], and many others. Such software tools have now become part of a critical infrastructure for science [6]. Unfortunately, overshadowed by the few exceptions that have had long-lasting impact, many other potentially useful tools fail to find their way into the hands of users. While there are many reasons for this, we believe that at least some of the underlying problems, which we discuss in more detail below, can be mitigated. In this opinion piece, we specifically argue that embedding teams of research software engineers (RSEs) within imaging and image analysis core facilities would be a major step towards sustainable bioimage analysis software.}, author = {Deschamps, Joran and Nogare, Damian Dalle and Jug, Florian}, copyright = {Creative Commons Attribution Non Commercial Share Alike 4.0 International}, doi = {10.48550/ARXIV.2307.03934}, month = {July}, title = {Better {Research} {Software} {Tools} to {Elevate} the {Rate} of {Scientific} {Discovery} – or why we need to invest in research software engineering}, year = {2023} } @article{druskat_and_2023, author = {Druskat, Stephan and Spaaks, Jurriaan H.}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.8304229}, keywords = {open source, governance}, language = {en}, title = {And then there were users: {Designing} and implementing governance for open research software projects}, year = {2023} } @article{druskat_citation_2023, author = {Druskat, Stephan}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.7655140}, keywords = {software citation, Citation File Format}, language = {en}, title = {The {Citation} {File} {Format}: {Providing} citation metadata for research software}, year = {2023} } @article{druskat_four_2023, author = {Druskat, Stephan and Krause, Thomas}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.7654778}, keywords = {linguistic annotation software, research software sustainability, software documentation, software maintenance, technical sustainability}, language = {en}, title = {The four elements of achieving research software sustainability for long tail projects}, year = {2023} } @article{druskat_hermes_2023, author = {Druskat, Stephan and Bertuch, Oliver and Knodel, Oliver and Meinel, Michael and Juckeland, Guido and Schlauch, Tobias and Kelling, Jeffrey and Pape, David}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.7654819}, keywords = {FAIR4RS, HERMES, software metadata, software publication}, language = {en}, title = {{HERMES}: {Easing} the path to {FAIR} software publications}, year = {2023} } @article{druskat_hermes_2023-1, author = {Druskat, Stephan}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.7963967}, keywords = {HERMES, Automation, DataCite, Software metadata, Software publication}, language = {en}, title = {{HERMES}: {Automating} software publication with rich metadata}, year = {2023} } @article{druskat_towards_2023, author = {Druskat, Stephan and Bertuch, Oliver and Struck, Alexander}, doi = {10.1515/abitech-2023-0031}, issn = {0720-6763}, journal = {ABI Technik}, keywords = {libraries}, month = {August}, number = {3}, pages = {168--178}, title = {Towards {Research} {Software}-ready {Libraries}: {Forschungssoftware} in {Bibliotheken}}, volume = {43}, year = {2023} } @inproceedings{dworatzyk_human_2023, abstract = {At the German Aerospace Center (DLR), research software is developed at over 50 institutes at 30 locations and ranges from small data analysis scripts developed by individual researchers to mission-critical software and production-ready software developed in cooperation with industry partners. Tools and training to support collaborative and sustainable software engineering of software at different maturity levels are offered by DLR's Software Engineering Initiative. In addition to assuring a high-quality standard, the Software Engineering Initiative provides a platform to create, share and discuss content related to software engineering. To better understand the diverse contexts in which software engineering support is needed and to evaluate the community-building activities, qualitative and quantitative studies are conducted. To facilitate participation in such studies and the recruitment of relevant target groups, we are currently building a human subject pool. Our future goal is to expand this human subject pool beyond DLR, including research software engineers from other research organizations in Germany and abroad, to provide a tool for longitudinal and cross-sectional studies across different scientific domains and contexts. In our talk, we will present the current status and discuss how a large-scale human subject pool can contribute to empirical research on research software engineering.}, author = {Dworatzyk, Katharina and Schlauch, Tobias}, booktitle = {The {PASC23} {Conference} - {Minisymposium} {Code} complete and more: {Emerging} efforts to improve software quality}, keywords = {human factor}, month = {June}, title = {Human factors in industrial research software engineering}, url = {https://elib.dlr.de/195820/}, year = {2023} } @incollection{escamilla_cited_2023, author = {Escamilla, Emily and Klein, Martin and Cooper, Talya and Rampin, Vicky and Weigle, Michele C. and Nelson, Michael L.}, booktitle = {Lecture {Notes} in {Computer} {Science}}, doi = {10.1007/978-981-99-8088-8_17}, isbn = {978-981-99-8088-8}, keywords = {citation}, pages = {194--207}, publisher = {Springer Nature Singapore}, title = {Cited {But} {Not} {Archived}: {Analyzing} the {Status} of {Code} {References} in {Scholarly} {Articles}}, year = {2023} } @inproceedings{feitosa_understanding_2023, author = {Feitosa, Daniela and von Flach, Christina and Costa, Joenio}, booktitle = {{WORKSHOP} {DE} {PR\'{A}TICAS} {DE} {CI\^{E}NCIA} {ABERTA} {PARA} {ENGENHARIA} {DE} {SOFTWARE} ({OPENSCIENSE})}, keywords = {sustainability, practice}, publisher = {Universidade Federal da Bahia}, title = {Understanding practices and challenges of developing sustainable research software: a pilot interview.}, year = {2023} } @inproceedings{felderer_toward_2023, author = {Felderer, Michael and Goedicke, Michael and Grunske, Lars and Hasselbring, Wilhelm and Rumpe, Bernhard}, title = {Toward {Research} {Software} {Engineering} {Research}}, url = {https://api.semanticscholar.org/CorpusID:259372928}, year = {2023} } @article{ferenz_towards_2023, author = {Ferenz, Stephan and Nie\ss{}e, Astrid}, keywords = {metadata}, title = {Towards {Improved} {Findability} of {Energy} {Research} {Software} by {Introducing} a {Metadata}-based {Registry}}, year = {2023} } @article{fritzsch_research_2023, author = {Fritzsch, Bernadette}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.8341375}, language = {en}, title = {Research {Software} - from ugly ducklings to beautiful swans}, year = {2023} } @article{ghiringhelli_shared_2023, author = {Ghiringhelli, Luca M. and Baldauf, Carsten and Bereau, Tristan and Brockhauser, Sandor and Carbogno, Christian and Chamanara, Javad and Cozzini, Stefano and Curtarolo, Stefano and Draxl, Claudia and Dwaraknath, Shyam and Fekete, \'{A}d\'{a}m and Kermode, James and Koch, Christoph T. and K\"{u}hbach, Markus and Ladines, Alvin Noe and Lambrix, Patrick and Himmer, Maja-Olivia and Levchenko, Sergey V. and Oliveira, Micael and Michalchuk, Adam and Miller, Ronald E. and Onat, Berk and Pavone, Pasquale and Pizzi, Giovanni and Regler, Benjamin and Rignanese, Gian-Marco and Schaarschmidt, J\"{o}rg and Scheidgen, Markus and Schneidewind, Astrid and Sheveleva, Tatyana and Su, Chuanxun and Usvyat, Denis and Valsson, Omar and W\"{o}ll, Christof and Scheffler, Matthias}, doi = {10.1038/s41597-023-02501-8}, issn = {2052–4463}, journal = {Scientific Data}, month = {September}, number = {1}, title = {Shared metadata for data-centric materials science}, volume = {10}, year = {2023} } @article{giraldo_machine-actionable_2023, author = {Giraldo, Olga and Dessi, Danilo and Dietze, Stefan and Rebholz-Schuhmann, Dietrich and Castro, Leyla Jael}, doi = {10.52825/cordi.v1i.279}, issn = {2941-296X}, journal = {Proceedings of the Conference on Research Data Infrastructure}, keywords = {metadata, software management plans}, month = {September}, title = {Machine-{Actionable} {Metadata} for {Software} and {Software} {Management} {Plans} for {NFDI}}, volume = {1}, year = {2023} } @inproceedings{giraldo_metadata_2023, author = {Giraldo, Olga L and Alves, Renato and Bampalikis, Dimitrios and Fern\'{a}ndez, Jos\'{e} M and Del Pico, Eva Martin and Psomopoulos, Fotis E and Qui\~{n}ones, Nelson and Solanki, Dhwani and Via, Allegra and Castro, Leyla Jael}, booktitle = {{SWAT4HCLS}}, keywords = {metadata, software management plan}, pages = {145--146}, title = {A metadata analysis for machine-actionable {Software} {Management} {Plans}.}, year = {2023} } @misc{Godoy_2023, abstract = {We provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions runners, and NVIDIA and AMD GPUs in pre-exascale systems, using self-hosted hardware; (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, sustainable maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the sustainability of community HPC codes and scientific discovery at scale.}, archiveprefix = {arXiv}, author = {William F. Godoy and Steven E. Hahn and Michael M. Walsh and Philip W. Fackler and Jaron T. Krogel and Peter W. Doak and Paul R. C. Kent and Alfredo A. Correa and Ye Luo and Mark Dewing}, eprint = {2307.11502}, primaryclass = {cs.SE}, title = {Software engineering to sustain a high-performance computing scientific application: QMCPACK}, url = {https://arxiv.org/abs/2307.11502}, year = {2023} } @article{gold_afterlife_2023, author = {Gold, Nicolas E and Lawson, Ian and Oxtoby, Neil P}, doi = {10.1177/17470161231178450}, issn = {2047-6094}, journal = {Research Ethics}, keywords = {ethics}, month = {June}, number = {4}, pages = {433--448}, title = {Afterlife: the post-research affect and effect of software}, volume = {19}, year = {2023} } @article{gonzalez-barahona_revisiting_2023, author = {Gonzalez-Barahona, Jesus M. and Robles, Gregorio}, doi = {10.1016/j.infsof.2023.107318}, issn = {0950-5849}, journal = {Information and Software Technology}, keywords = {reproducibility, empirical software engineering}, month = {December}, pages = {107318}, title = {Revisiting the reproducibility of empirical software engineering studies based on data retrieved from development repositories}, volume = {164}, year = {2023} } @inproceedings{gonzalez-guardia_softalias-kg_2023, author = {Gonz\'{a}lez-Guardia, Esteban and Lopez, Hector and Garijo, Daniel}, booktitle = {{ISWC} ({Posters}/{Demos}/{Industry})}, keywords = {citation, knowledge graph}, title = {Softalias-{KG}: {Reconciling} {Software} {Mentions} in {Scientific} {Literature}.}, year = {2023} } @misc{Goth_2023, abstract = {The term Research Software Engineer, or RSE, emerged a little over 10 years ago as a way to represent individuals working in the research community but focusing on software development. The term has been widely adopted and there are a number of high-level definitions of what an RSE is. However, the roles of RSEs vary depending on the institutional context they work in. At one end of the spectrum, RSE roles may look similar to a traditional research role. At the other extreme, they resemble that of a software engineer in industry. Most RSE roles inhabit the space between these two extremes. Therefore, providing a straightforward, comprehensive definition of what an RSE does and what experience, skills and competencies are required to become one is challenging. In this community paper we define the broad notion of what an RSE is, explore the different types of work they undertake, and define a list of fundamental competencies as well as values that define the general profile of an RSE. On this basis, we elaborate on the progression of these skills along different dimensions, looking at specific types of RSE roles, proposing recommendations for organisations, and giving examples of future specialisations. An appendix details how existing curricula fit into this framework.}, archiveprefix = {arXiv}, author = {Florian Goth and Renato Alves and Matthias Braun and Leyla Jael Castro and Gerasimos Chourdakis and Simon Christ and Jeremy Cohen and Stephan Druskat and Fredo Erxleben and Jean-No\"{e}l Grad and Magnus Hagdorn and Toby Hodges and Guido Juckeland and Dominic Kempf and Anna-Lena Lamprecht and Jan Linxweiler and Frank L\"{o}ffler and Michele Martone and Moritz Schwarzmeier and Heidi Seibold and Jan Philipp Thiele and Harald von Waldow and Samantha Wittke}, eprint = {2311.11457}, primaryclass = {cs.SE}, title = {Foundational Competencies and Responsibilities of a Research Software Engineer: Current State and Suggestions for Future Directions}, url = {https://arxiv.org/abs/2311.11457}, year = {2023} } @article{grossmann_software_2023, author = {Grossmann, Yves Vincent and Franke, Michael}, journal = {b.i.t.online}, month = {October}, number = {5}, pages = {457--463}, title = {Software ist kein {Beiprodukt}! {Nachhaltige} {Forschungssoftware} durch {Software}-{Management}-{Pl\"{a}ne}}, url = {https://www.b-i-t-online.de/heft/2023-05-fachbeitrag-grossmann.pdf}, volume = {26}, year = {2023} } @article{gruenpeter_software_2023, author = {Gruenpeter, Morane}, copyright = {Creative Commons Attribution Share Alike 4.0 International}, doi = {10.5281/ZENODO.7964043}, keywords = {PID, Software citation, DOI, SWHID}, language = {en}, title = {Software as a first class output in the scholarly ecosystem}, year = {2023} } @article{gupta_building_2023, author = {Gupta, Rinku and Bernholdt, David E and Bartlett, Roscoe A and Grubel, Patricia A and Heroux, Michael A and McInnes, LC and Miller, MC and Salim, K and Shuler, J and Stevens, D and {others}}, journal = {Preprint, submitted to IEEE CiSE, https://doi.org/10.6084/m9.figshare}, keywords = {community}, title = {Building and sustaining a community resource for best practices in scientific software: {The} story of {BSSw}. io}, volume = {25143671}, year = {2023} } @article{hiltemann_galaxy_2023, author = {Hiltemann, Saskia and Rasche, Helena and Gladman, Simon and Hotz, Hans-Rudolf and Larivi\`{e}re, Delphine and Blankenberg, Daniel and Jagtap, Pratik D. and Wollmann, Thomas and Bretaudeau, Anthony and Gou\'{e}, Nadia and Griffin, Timothy J. and Royaux, Coline and Le Bras, Yvan and Mehta, Subina and Syme, Anna and Coppens, Frederik and Droesbeke, Bert and Soranzo, Nicola and Bacon, Wendi and Psomopoulos, Fotis and Gallardo-Alba, Crist\'{o}bal and Davis, John and F\"{o}ll, Melanie Christine and Fahrner, Matthias and Doyle, Maria A. and Serrano-Solano, Beatriz and Fouilloux, Anne Claire and van Heusden, Peter and Maier, Wolfgang and Clements, Dave and Heyl, Florian and {Galaxy Training Network} and Gr\"{u}ning, Bj\"{o}rn and Batut, B\'{e}r\'{e}nice}, doi = {10.1371/journal.pcbi.1010752}, editor = {Ouellette, Francis}, journal = {PLOS Computational Biology}, month = {January}, number = {1}, pages = {e1010752}, title = {Galaxy {Training}: {A} powerful framework for teaching!}, volume = {19}, year = {2023} } @article{horsfall_research_2023, author = {Horsfall, David and Cool, Jonah and Hettrick, Simon and Pisco, Angela Oliveira and Hong, Neil Chue and Haniffa, Muzlifah}, doi = {10.1038/s41591-023-02353-0}, issn = {1546-170X}, journal = {Nature Medicine}, keywords = {biomedicine}, month = {June}, number = {6}, pages = {1313--1316}, title = {Research software engineering accelerates the translation of biomedical research for health}, volume = {29}, year = {2023} } @article{houillon_automated_2023, author = {Houillon, Marie ; Klar, Jochen ; Stary, Tomas ; Loewe, Axel}, doi = {10.11588/HEIDOK.00033137}, keywords = {codemeta, Open science}, title = {Automated {Software} {Metadata} {Conversion} and {Publication} {Based} on {CodeMeta}}, year = {2023} } @inproceedings{iglesias-molina_towards_2023, author = {Iglesias-Molina, Ana and Garijo, Daniel}, booktitle = {{SEMANTiCS} ({Posters} \& {Demos})}, keywords = {FAIR}, title = {Towards {Assessing} {FAIR} {Research} {Software} {Best} {Practices} in an {Organization} {Using} {RDF}-star.}, year = {2023} } @article{inamorato_dos_santos_digital_2023, author = {Inamorato dos Santos, Andreia and Chinkes, Ernesto and Carvalho, Marco A. G. and Sol\'{o}rzano, Claudia M. V. and Marroni, Lilian S.}, doi = {10.1186/s41239-022-00376-0}, issn = {2365-9440}, journal = {International Journal of Educational Technology in Higher Education}, month = {February}, number = {1}, title = {The digital competence of academics in higher education: is the glass half empty or half full?}, volume = {20}, year = {2023} } @article{isik_grand_2023, author = {I\c{s}\i{}k, Esra B\"{u}\c{s}ra and Brazas, Michelle D. and Schwartz, Russell and Gaeta, Bruno and Palagi, Patricia M. and Gelder, Celia W. G. van and Suravajhala, Prashanth and Singh, Harpreet and Morgan, Sarah L. and Zahroh, Hilyatuz and Ling, Maurice and Satagopam, Venkata P. and McGrath, Annette and Nakai, Kenta and Tan, Tin Wee and Gao, Ge and Mulder, Nicola and Sch\"{o}nbach, Christian and Zheng, Yun and De Las Rivas, Javier and Khan, Asif M.}, doi = {10.1038/s41587-023-01891-9}, journal = {Nature Biotechnology}, month = {August}, number = {8}, pages = {1171--1174}, title = {Grand challenges in bioinformatics education and training}, volume = {41}, year = {2023} } @article{jensen_code_2023, author = {Jensen, Eric A. and Katz, Daniel S.}, journal = {Commonplace}, keywords = {human resource, reputation}, month = {December}, title = {From {Code} to {Tenure}: {Valuing} {Research} {Software} in {Academia}}, year = {2023} } @article{kampf_research_2023, author = {K\"{a}mpf, Christoph and Scholz, Alexander and Kreuz, Markus and Reiche, Kristin}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.7751723}, keywords = {certification, regulation}, language = {en}, title = {From {Research} to {Regulated} {Software}}, year = {2023} } @misc{Katz_2023, abstract = {This position paper for an invited talk on the "Future of eScience" discusses the Research Software Engineering Movement and where it might be in 2030. Because of the authors' experiences, it is aimed globally but with examples that focus on the United States and United Kingdom.}, archiveprefix = {arXiv}, author = {Daniel S. Katz and Simon Hettrick}, eprint = {2308.07796}, primaryclass = {cs.SE}, title = {Research Software Engineering in 2030}, url = {https://arxiv.org/abs/2308.07796}, year = {2023} } @article{katz_changing_2023, abstract = {This position paper describes the Parsl open source research software project and its various phases over seven years. It defines four types of research software engineers (RSEs) who have been important to the project in those phases; we believe this is also applicable to other research software projects.}, author = {Katz, Daniel S. and Clifford, Ben and Babuji, Yadu and Kesling, Kevin Hunter and Woodard, Anna and Chard, Kyle}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.48550/ARXIV.2307.11060}, keywords = {research software engineers, roles}, month = {July}, title = {The {Changing} {Role} of {RSEs} over the {Lifetime} of {Parsl}}, year = {2023} } @inproceedings{katz_research_2023, abstract = {This position paper for an invited talk on the "Future of eScience" discusses the Research Software Engineering Movement and where it might be in 2030. Because of the authors' experiences, it is aimed globally but with examples that focus on the United States and United Kingdom.}, author = {Katz, Daniel S. and Hettrick, Simon}, booktitle = {2023 {IEEE} 19{\textbackslash}textbackslashtextsuperscriptth {International} {Conference} on e-{Science} (e-{Science})}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.1109/e-science58273.2023.10254813}, keywords = {software engineering}, month = {August}, publisher = {IEEE}, title = {Research {Software} {Engineering} in 2030}, year = {2023} } @article{koch_sustainable_2023, abstract = {Research software is an integral part of most research today and it is widely accepted that research software artifacts should be accessible and reproducible. However, the sustainable archival of research software artifacts is an ongoing effort. We identify research software artifacts as snapshots of the current state of research and an integral part of a sustainable cycle of software development, research, and publication. We develop requirements and recommendations to improve the archival, access, and reuse of research software artifacts based on installable, configurable, extensible research software, and sustainable public open-access infrastructure. The described goal is to enable the reuse and exploration of research software beyond published research results, in parallel with reproducibility efforts, and in line with the FAIR principles for data and software. Research software artifacts can be reused in varying scenarios. To this end, we design a multi-modal representation concept supporting multiple reuse scenarios. We identify types of research software artifacts that can be viewed as different modes of the same software-based research result, for example, installation-free configurable browser-based apps to containerized environments, descriptions in journal publications and software documentation, or source code with installation instructions. We discuss how the sustainability and reuse of research software are enhanced or enabled by a suitable archive infrastructure. Finally, at the example of a pilot project at the University of Stuttgart, Germany – a collaborative effort between research software developers and infrastructure providers – we outline practical challenges and experiences}, author = {Koch, Timo and Gl\"{a}ser, Dennis and Seeland, Anett and Roy, Sarbani and Schulze, Katharina and Weishaupt, Kilian and Boehringer, David and Hermann, Sibylle and Flemisch, Bernd}, doi = {10.48550/ARXIV.2301.12830}, keywords = {FAIR, infrastructure}, month = {January}, title = {A sustainable infrastructure concept for improved accessibility, reusability, and archival of research software}, year = {2023} } @article{lamprecht_neue_2023, author = {Lamprecht, Anna-Lena and Hasselbring, Wilhelm and Dietrich, Jan Philipp and Fritzsch, Bernadette and Goedicke, Michael and Grunske, Lars and Haupt, Carina and Janosch, Stephan and L\"{o}ffler, Frank and Rumpe, Bernhard and Speck, Robert}, issn = {0720-8928}, journal = {Softwaretechnik-Trends}, number = {3}, title = {Neue {Fachgruppe} ,,{Research} {Software} {Engineering}`` gegr\"{u}ndet}, url = {https://dl.gi.de/items/e91d1e43-6168-4686-a81d-b29f27090752}, volume = {43}, year = {2023} } @article{lannelongue_greener_2023, author = {Lannelongue, Lo\"{\i}c and Aronson, Hans-Erik G. and Bateman, Alex and Birney, Ewan and Caplan, Talia and Juckes, Martin and McEntyre, Johanna and Morris, Andrew D. and Reilly, Gerry and Inouye, Michael}, doi = {10.1038/s43588-023-00461-y}, issn = {2662-8457}, journal = {Nature Computational Science}, month = {June}, number = {6}, pages = {514--521}, title = {{GREENER} principles for environmentally sustainable computational science}, volume = {3}, year = {2023} } @inproceedings{lovbak_management_2023, author = {L\o{}vbak, Emil and Dikmen, Mustafa and Muhammad, Naeem and Samaey, Giovanni}, booktitle = {proceedings 2023}, doi = {10.21428/1192f2f8.e175b077}, keywords = {software engineering, mathematics}, publisher = {PubPub}, title = {Management of mathematical research software and data}, year = {2023} } @misc{Mari_2023, abstract = {University research groups in Computational Science and Engineering (CSE) generally lack dedicated funding and personnel for Research Software Engineering (RSE), which, combined with the pressure to maximize the number of scientific publications, shifts the focus away from sustainable research software development and reproducible results. The neglect of RSE in CSE at University research groups negatively impacts the scientific output: research data - including research software - related to a CSE publication cannot be found, reproduced, or re-used, different ideas are not combined easily into new ideas, and published methods must very often be re-implemented to be investigated further. This slows down CSE research significantly, resulting in considerable losses in time and, consequentially, public funding. We propose a RSE workflow for Computational Science and Engineering (CSE) that addresses these challenges, that improves the quality of research output in CSE. Our workflow applies established software engineering practices adapted for CSE: software testing, result visualization, and periodical cross-linking of software with reports/publications and data, timed by milestones in the scientific publication process. The workflow introduces minimal work overhead, crucial for university research groups, and delivers modular and tested software linked to publications whose results can easily be reproduced. We define research software quality from a perspective of a pragmatic researcher: the ability to quickly find the publication, data, and software related to a published research idea, quickly reproduce results, understand or re-use a CSE method, and finally extend the method with new research ideas.}, archiveprefix = {arXiv}, author = {Tomislav Mari\'{c} and Dennis Gl\"{a}ser and Jan-Patrick Lehr and Ioannis Papagiannidis and Benjamin Lambie and Christian Bischof and Dieter Bothe}, eprint = {2310.00960}, primaryclass = {cs.SE}, title = {A pragmatic workflow for research software engineering in computational science}, url = {https://arxiv.org/abs/2310.00960}, year = {2023} } @article{mcguire_sustainability_2023, abstract = {Background: Sustainable software engineering (SSE) means creating software in a way that meets present needs without undermining our collective capacity to meet our future needs. It is typically conceptualized as several intersecting dimensions or ``pillars'' – environmental, social, economic, technical and individual. However; these pillars are theoretically underdeveloped and require refinement. Objectives: The objective of this paper is to generate a better theory of SSE. Method: First, a scoping review was conducted to understand the state of research on SSE and identify existing models thereof. Next, a meta-synthesis of qualitative research on SSE was conducted to critique and improve the existing models identified. Results: 961 potentially relevant articles were extracted from five article databases. These articles were de-duplicated and then screened independently by two screeners, leaving 243 articles to examine. Of these, 109 were non-empirical, the most common empirical method was systematic review, and no randomized controlled experiments were found. Most papers focus on ecological sustainability (158) and the sustainability of software products (148) rather than processes. A meta-synthesis of 36 qualitative studies produced several key propositions, most notably, that sustainability is stratified (has different meanings at different levels of abstraction) and multisystemic (emerges from interactions among multiple social, technical, and sociotechnical systems). Conclusion: The academic literature on SSE is surprisingly non-empirical. More empirical evaluations of specific sustainability interventions are needed. The sustainability of software development products and processes should be conceptualized as multisystemic and stratified, and assessed accordingly.}, author = {McGuire, Sean and Shultz, Erin and Ayoola, Bimpe and Ralph, Paul}, doi = {10.48550/ARXIV.2301.11129}, keywords = {sustainability, software engineering}, month = {January}, title = {Sustainability is {Stratified}: {Toward} a {Better} {Theory} of {Sustainable} {Software} {Engineering}}, year = {2023} } @misc{McInnes_2023, abstract = {Computational and data-enabled science and engineering are revolutionizing advances throughout science and society, at all scales of computing. For example, teams in the U.S. DOE Exascale Computing Project have been tackling new frontiers in modeling, simulation, and analysis by exploiting unprecedented exascale computing capabilities-building an advanced software ecosystem that supports next-generation applications and addresses disruptive changes in computer architectures. However, concerns are growing about the productivity of the developers of scientific software, its sustainability, and the trustworthiness of the results that it produces. Members of the IDEAS project serve as catalysts to address these challenges through fostering software communities, incubating and curating methodologies and resources, and disseminating knowledge to advance developer productivity and software sustainability. This paper discusses how these synergistic activities are advancing scientific discovery-mitigating technical risks by building a firmer foundation for reproducible, sustainable science at all scales of computing, from laptops to clusters to exascale and beyond.}, archiveprefix = {arXiv}, author = {Lois Curfman McInnes and Michael Heroux and David E. Bernholdt and Anshu Dubey and Elsa Gonsiorowski and Rinku Gupta and Osni Marques and J. David Moulton and Hai Ah Nam and Boyana Norris and Elaine M. Raybourn and Jim Willenbring and Ann Almgren and Ross Bartlett and Kita Cranfill and Stephen Fickas and Don Frederick and William Godoy and Patricia Grubel and Rebecca Hartman-Baker and Axel Huebl and Rose Lynch and Addi Malviya Thakur and Reed Milewicz and Mark C. Miller and Miranda Mundt and Erik Palmer and Suzanne Parete-Koon and Megan Phinney and Katherine Riley and David M. Rogers and Ben Sims and Deborah Stevens and Gregory R. Watson}, eprint = {2311.02010}, primaryclass = {cs.CY}, title = {A cast of thousands: How the IDEAS Productivity project has advanced software productivity and sustainability}, url = {https://arxiv.org/abs/2311.02010}, year = {2023} } @article{mcinnes_cast_2023, abstract = {Computational and data-enabled science and engineering are revolutionizing advances throughout science and society, at all scales of computing. For example, teams in the U.S. DOE Exascale Computing Project have been tackling new frontiers in modeling, simulation, and analysis by exploiting unprecedented exascale computing capabilities-building an advanced software ecosystem that supports next-generation applications and addresses disruptive changes in computer architectures. However, concerns are growing about the productivity of the developers of scientific software, its sustainability, and the trustworthiness of the results that it produces. Members of the IDEAS project serve as catalysts to address these challenges through fostering software communities, incubating and curating methodologies and resources, and disseminating knowledge to advance developer productivity and software sustainability. This paper discusses how these synergistic activities are advancing scientific discovery-mitigating technical risks by building a firmer foundation for reproducible, sustainable science at all scales of computing, from laptops to clusters to exascale and beyond.}, author = {McInnes, Lois Curfman and Heroux, Michael and Bernholdt, David E. and Dubey, Anshu and Gonsiorowski, Elsa and Gupta, Rinku and Marques, Osni and Moulton, J. David and Nam, Hai Ah and Norris, Boyana and Raybourn, Elaine M. and Willenbring, Jim and Almgren, Ann and Bartlett, Ross and Cranfill, Kita and Fickas, Stephen and Frederick, Don and Godoy, William and Grubel, Patricia and Hartman-Baker, Rebecca and Huebl, Axel and Lynch, Rose and Thakur, Addi Malviya and Milewicz, Reed and Miller, Mark C. and Mundt, Miranda and Palmer, Erik and Parete-Koon, Suzanne and Phinney, Megan and Riley, Katherine and Rogers, David M. and Sims, Ben and Stevens, Deborah and Watson, Gregory R.}, copyright = {arXiv.org perpetual, non-exclusive license}, doi = {10.48550/ARXIV.2311.02010}, keywords = {sustainability, software productivity}, month = {November}, title = {A cast of thousands: {How} the {IDEAS} {Productivity} project has advanced software productivity and sustainability}, year = {2023} } @article{mckiernan_policy_2023, author = {McKiernan, Erin C. and Barba, Lorena and Bourne, Philip E. and Carter, Caitlin and Chandler, Zach and Choudhury, Sayeed and Jacobs, Stephen and Katz, Daniel S. and Lieggi, Stefanie and Plale, Beth and Tananbaum, Greg}, doi = {10.1371/journal.pbio.3002204}, issn = {1545-7885}, journal = {PLOS Biology}, keywords = {open science, policies}, month = {July}, number = {7}, pages = {e3002204}, title = {Policy recommendations to ensure that research software is openly accessible and reusable}, volume = {21}, year = {2023} } @incollection{menzel_developing_2023, author = {Menzel, Michael}, booktitle = {Distributed {Learning} {Ecosystems}}, doi = {10.1007/978-3-658-38703-7_14}, editor = {Otto, Daniel and Scharnberg, Gianna and Kerres, Michael and Zawacki-Richter, Olaf}, isbn = {978-3-658-38703-7}, pages = {263--278}, publisher = {Springer Fachmedien Wiesbaden}, title = {Developing a {Metadata} {Profile} for {Higher} {Education} {OER} {Repositories}}, year = {2023} } @article{merow_better_2023, author = {Merow, Cory and Boyle, Brad and Enquist, Brian J. and Feng, Xiao and Kass, Jamie M. and Maitner, Brian S. and McGill, Brian and Owens, Hannah and Park, Daniel S. and Paz, Andrea and Pinilla-Buitrago, Gonzalo E. and Urban, Mark C. and Varela, Sara and Wilson, Adam M.}, doi = {10.1038/s41559-023-02008-w}, journal = {Nature Ecology \& Evolution}, keywords = {incentives}, month = {February}, title = {Better incentives are needed to reward academic software development}, year = {2023} } @article{milewicz_seeking_2023, abstract = {Evidence-based practice (EBP) in software engineering aims to improve decision-making in software development by complementing practitioners' professional judgment with high-quality evidence from research. We believe the use of EBP techniques may be helpful for research software engineers (RSEs) in their work to bring software engineering best practices to scientific software development. In this study, we present an experience report on the use of a particular EBP technique, rapid reviews, within an RSE team at Sandia National Laboratories, and present practical recommendations for how to address barriers to EBP adoption within the RSE community.}, author = {Milewicz, Reed and Bisila, Jon and Mundt, Miranda and Teves, Joshua}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.5281/ZENODO.10420969}, month = {March}, title = {Seeking {Enlightenment}: {Incorporating} {Evidence}-{Based} {Practice} {Techniques} in a {Research} {Software} {Engineering} {Team}}, year = {2023} } @inproceedings{milewicz_towards_2023, author = {Milewicz, Reed and Mundt, Miranda}, booktitle = {Proceedings of the 2023 {ACM} {Conference} on {Reproducibility} and {Replicability}}, doi = {10.1145/3589806.3600040}, keywords = {reproducibility, software quality}, month = {June}, publisher = {ACM}, series = {{ACM} {REP} '23}, title = {Towards {Evidence}-{Based} {Software} {Quality} {Practices} for {Reproducibility}: {Preliminary} {Results} and {Research} {Directions}}, year = {2023} } @article{moreau_containers_2023, author = {Moreau, David and Wiebels, Kristina and Boettiger, Carl}, doi = {10.1038/s43586-023-00236-9}, issn = {2662-8449}, journal = {Nature Reviews Methods Primers}, keywords = {reproducibility, containers}, month = {July}, number = {1}, title = {Containers for computational reproducibility}, volume = {3}, year = {2023} } @incollection{mourao_investigating_2023, author = {Mour\~{a}o, Erica and Trevisan, Daniela and Viterbo, Jos\'{e} and Pantoja, Carlos Eduardo}, booktitle = {New {Sustainable} {Horizons} in {Artificial} {Intelligence} and {Digital} {Solutions}}, doi = {10.1007/978-3-031-50040-4_2}, isbn = {978-3-031-50040-4}, keywords = {perception, software engineering, success factors}, pages = {14--26}, publisher = {Springer Nature Switzerland}, title = {Investigating {Developers}' {Perception} on {Success} {Factors} for {Research} {Software} {Development}}, year = {2023} } @article{pampel_3_2023, author = {Pampel, Heinz and Ferguson, Lea Maria and Druskat, Stephan and Konrad, Uwe and Hammitzsch, Martin and Mee\ss{}en, Christian and Sch\"{a}fer, David and Speck, Robert and Diesmann, Markus and Streit, Achim and Caspart, Rene}, doi = {10.48440/OS.HELMHOLTZ.057}, title = {3. {Helmholtz} {Open} {Science} {Forum} {Forschungssoftware}. {Helmholtz} {Open} {Science} {Briefing}}, year = {2023} } @article{pilgrim_ten_2023, author = {Pilgrim, Charlie and Kent, Paul and Hosseini, Kasra and Chalstrey, Ed}, doi = {10.1371/journal.pcbi.1011031}, editor = {Schwartz, Russell}, issn = {1553-7358}, journal = {PLOS Computational Biology}, keywords = {reproducability, reusability}, month = {April}, number = {4}, pages = {e1011031}, title = {Ten simple rules for working with other people's code}, volume = {19}, year = {2023} } @article{politze_supporting_2023, author = {Politze, Marius and Christoph, Uta and Decker, Bernd and Hristov, Petar and Lang, Ilona and Nellesen, Marcel and Yazdi, M Amin}, journal = {Proceedings of European University}, keywords = {software engineering, gitlab}, pages = {229--238}, title = {Supporting {Software} {Development} {Processes} for {Academia} with {GitLab}}, volume = {95}, year = {2023} } @article{pownall_teaching_2023, author = {Pownall, Madeleine and Azevedo, Fl\'{a}vio and K\"{o}nig, Laura M. and Slack, Hannah R. and Evans, Thomas Rhys and Flack, Zoe and Grinschgl, Sandra and Elsherif, Mahmoud M. and Gilligan-Lee, Katie A. and Oliveira, Catia M. F. de and Gjoneska, Biljana and Kalandadze, Tamara and Button, Katherine and Ashcroft-Jones, Sarah and Terry, Jenny and Albayrak-Aydemir, Nihan and D\v{e}cht\v{e}renko, Filip and Alzahawi, Shilaan and Baker, Bradley J. and Pittelkow, Merle-Marie and Riedl, Lydia and Schmidt, Kathleen and Pennington, Charlotte R. and Shaw, John J. and L\"{u}ke, Timo and Makel, Matthew C. and Hartmann, Helena and Zaneva, Mirela and Walker, Daniel and Verheyen, Steven and Cox, Daniel and Mattschey, Jennifer and Gallagher-Mitchell, Tom and Branney, Peter and Weisberg, Yanna and Izydorczak, Kamil and Al-Hoorie, Ali H. and Creaven, Ann-Marie and Stewart, Suzanne L. K. and Krautter, Kai and Matvienko-Sikar, Karen and Westwood, Samuel J. and Arriaga, Patr\'{\i}cia and Liu, Meng and Baum, Myriam A. and Wingen, Tobias and Ross, Robert M. and O'Mahony, Aoife and Bochynska, Agata and Jamieson, Michelle and Vel Tromp, Myrthe and Yeung, Siu Kit and Vasilev, Martin R. and Gourdon-Kanhukamwe, Am\'{e}lie and Micheli, Leticia and Konkol, Markus and Moreau, David and Bartlett, James E. and Clark, Kait and Brekelmans, Gwen and Gkinopoulos, Theofilos and Tyler, Samantha L. and R\"{o}er, Jan Philipp and Ilchovska, Zlatomira G. and Madan, Christopher R. and Robertson, Olly and Iley, Bethan J. and Guay, Samuel and Sladekova, Martina and Sadhwani, Shanu and {FORTT}}, doi = {10.1098/rsos.221255}, issn = {2054-5703}, journal = {Royal Society Open Science}, month = {May}, number = {5}, pages = {221255}, title = {Teaching open and reproducible scholarship: a critical review of the evidence base for current pedagogical methods and their outcomes}, volume = {10}, year = {2023} } @article{richardson_earth_2023, author = {Richardson, Katherine and Steffen, Will and Lucht, Wolfgang and Bendtsen, J\o{}rgen and Cornell, Sarah E. and Donges, Jonathan F. and Dr\"{u}ke, Markus and Fetzer, Ingo and Bala, Govindasamy and Bloh, Werner von and Feulner, Georg and Fiedler, Stephanie and Gerten, Dieter and Gleeson, Tom and Hofmann, Matthias and Huiskamp, Willem and Kummu, Matti and Mohan, Chinchu and Nogu\'{e}s-Bravo, David and Petri, Stefan and Porkka, Miina and Rahmstorf, Stefan and Schaphoff, Sibyll and Thonicke, Kirsten and Tobian, Arne and Virkki, Vili and Wang-Erlandsson, Lan and Weber, Lisa and Rockstr\"{o}m, Johan}, doi = {10.1126/sciadv.adh2458}, journal = {Science Advances}, number = {37}, pages = {eadh2458}, title = {Earth beyond six of nine planetary boundaries}, volume = {9}, year = {2023} } @article{schindler_multi-level_2023, abstract = {Software is a central part of modern science, and knowledge of its use is crucial for the scientific community with respect to reproducibility and attribution of its developers. Several studies have investigated in-text mentions of software and its quality, while the quality of formal software citations has only been analyzed superficially. This study performs an in-depth evaluation of formal software citation based on a set of manually annotated software references. It examines which resources are cited for software usage, to what extend they allow proper identification of software and its specific version, how this information is made available by scientific publishers, and how well it is represented in large-scale bibliographic databases. The results show that software articles are the most cited resource for software, while direct software citations are better suited for identification of software versions. Moreover, we found current practices by both, publishers and bibliographic databases, to be unsuited to represent these direct software citations, hindering large-scale analyses such as assessing software impact. We argue that current practices for representing software citations – the recommended way to cite software by current citation standards – stand in the way of their adaption by the scientific community, and urge providers of bibliographic data to explicitly model scientific software.}, author = {Schindler, David and Hossain, Tazin and Spors, Sascha and Kr\"{u}ger, Frank}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.48550/ARXIV.2306.17535}, keywords = {citation}, month = {June}, title = {A multi-level analysis of data quality for formal software citation}, year = {2023} } @article{schoch_computational_2023, abstract = {Replication crises have shaken the scientific landscape during the last decade. As potential solutions, open science practices were heavily discussed and have been implemented with varying success in different disciplines. We argue that computational-x disciplines such as computational social science, are also susceptible for the symptoms of the crises, but in terms of reproducibility. We expand the binary definition of reproducibility into a tier system which allows increasing levels of reproducibility based on external verfiability to counteract the practice of open-washing. We provide solutions for barriers in Computational Social Science that hinder researchers from obtaining the highest level of reproducibility, including the use of alternate data sources and considering reproducibility proactively.}, author = {Schoch, David and Chan, Chung-hong and Wagner, Claudia and Bleier, Arnim}, copyright = {Creative Commons Attribution Share Alike 4.0 International}, doi = {10.48550/ARXIV.2307.01918}, keywords = {reproducibility, social sciences}, month = {July}, title = {Computational {Reproducibility} in {Computational} {Social} {Science}}, year = {2023} } @incollection{schon_development_2023, author = {Sch\"{o}n, Sandra and Ebner, Martin and Berger, Elfriede and Brandhofer, Gerhard and Edelsbrunner, Sarah and Gr\"{o}blinger, Ortrun and Hackl, Claudia and Jadin, Tanja and Kopp, Michael and Neub\"{o}ck, Kristina and Proinger, Judith and Schm\"{o}lz, Alexander and Steinbacher, Hans-Peter}, booktitle = {Distributed {Learning} {Ecosystems}}, doi = {10.1007/978-3-658-38703-7_9}, editor = {Otto, Daniel and Scharnberg, Gianna and Kerres, Michael and Zawacki-Richter, Olaf}, isbn = {978-3-658-38703-7}, pages = {161--182}, publisher = {Springer Fachmedien Wiesbaden}, title = {Development of an {Austrian} {OER} {Certification} for {Higher} {Education} {Institutions} and {Their} {Employees}}, year = {2023} } @article{stall_journal_2023, author = {Stall, Shelley and Bilder, Geoffrey and Cannon, Matthew and Hong, Neil Chue and Edmunds, Scott and Erdmann, Christopher C. and Evans, Michael and Farmer, Rosemary and Feeney, Patricia and Friedman, Michael and Giampoala, Matthew and Hanson, R. Brooks and Harrison, Melissa and Karaiskos, Dimitris and Katz, Daniel S. and Letizia, Viviana and Lizzi, Vincent and MacCallum, Catriona and Muench, August and Perry, Kate and Ratner, Howard and Schindler, Uwe and Sedora, Brian and Stockhause, Martina and Townsend, Randy and Yeston, Jake and Clark, Timothy}, doi = {10.1038/s41597-023-02491-7}, journal = {Scientific Data}, keywords = {research data, citation}, month = {September}, number = {1}, title = {Journal {Production} {Guidance} for {Software} and {Data} {Citations}}, volume = {10}, year = {2023} } @article{tucker_lessons_2023, author = {Tucker, Gregory and Kettner, Albert and Hutton, Eric and Piper, Mark and Gan, Tian and Campforts, Benjamin and Overeem, Irina and Rossi, Matthew}, doi = {10.5194/egusphere-egu23-3711}, keywords = {FAIR, modelling}, month = {February}, title = {Lessons in {FAIR} software from the {Community} {Surface} {Dynamics} {Modeling} {System}}, year = {2023} } @article{van_kampen_encore_2023, author = {van Kampen, Antoine and Mahamune, Utkarsh and Jongejan, Aldo and van Schaik, Barbera and Balashova, Daria and Lashgari, Danial and Pras-Raves, Mia and Wever, Eric and Valiente, Rodrigo Garcia and Dane, Adrie and {others}}, keywords = {reproducibility, computational research}, title = {{ENCORE}. {A} practical implementation to improve reproducibility and transparency of computational research.}, year = {2023} } @article{van_nieuwpoort_defining_2023, author = {van Nieuwpoort, Rob and Katz, Daniel S.}, doi = {10.54900/9akm9y5-5ject5y}, keywords = {sustainability, classification}, month = {March}, title = {Defining the roles of research software}, year = {2023} } @book{van_tuyl_hiring_2023, doi = {10.5281/zenodo.8264152}, editor = {Van Tuyl, Steve}, month = {August}, publisher = {Academic Data Science Alliance}, title = {Hiring, {Managing}, and {Retaining} {Data} {Scientists} and {Research} {Software} {Engineers} in {Academia}: {A} {Career} {Guidebook} from {ADSA} and {US}-{RSE}}, year = {2023} } @article{venters_sustainable_2023, author = {Venters, Colin C. and Capilla, Rafael and Nakagawa, Elisa Yumi and Betz, Stefanie and Penzenstadler, Birgit and Crick, Tom and Brooks, Ian}, doi = {10.1016/j.infsof.2023.107316}, issn = {0950-5849}, journal = {Information and Software Technology}, keywords = {sustainability}, month = {December}, pages = {107316}, title = {Sustainable software engineering: {Reflections} on advances in research and practice}, volume = {164}, year = {2023} } @article{von_suchdoletz_sicherstellung_2023, author = {von Suchdoletz, Dirk and Brettschneider, Peter and Axtmann, Alexandra and Heber, Maximilian and Oberl\"{a}nder, Lars and Leendertse, Jan and Schumm, Irene and Brandt, Olaf and Schmidt, Karsten and Gertis, Livia and Selzer, Michael and Ulrich, Robert and Iglezakis, Dorothea and Boda, Valerie}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.17192/BFDM.2023.5.8555}, keywords = {Forschungssoftware, FAIR-Prinzipien, gute wissenschaftliche Praxis, Reproduzierbarkeit}, language = {de}, title = {Sicherstellung der {Reproduzierbarkeit} von {Forschungsergebnissen} durch {Bewahrung} des {Zugriffs} auf {Forschungssoftware}}, year = {2023} } @article{vuillaume_escape_2023, author = {Vuillaume, Thomas and Al-Turany, Mohammad and F\"{u}\ss{}ling, Matthias and Gal, Tamas and Garcia, Enrique and Graf, Kay and Hughes, Gareth and Kettenis, Mark and Kresan, Dmytro and Schnabel, Jutta and Tacke, Christian and Verkouter, Marjolein}, doi = {10.12688/openreseurope.15692.2}, issn = {2732-5121}, journal = {Open Research Europe}, keywords = {open source, repository}, month = {November}, pages = {46}, title = {The {ESCAPE} {Open}-source {Software} and {Service} {Repository}}, volume = {3}, year = {2023} } @article{watson_open_2023, abstract = {Research software plays a crucial role in advancing scientific knowledge, but ensuring its sustainability, maintainability, and long-term viability is an ongoing challenge. To address these concerns, the Sustainable Research Software Institute (SRSI) Model presents a comprehensive framework designed to promote sustainable practices in the research software community. This white paper provides an in-depth overview of the SRSI Model, outlining its objectives, services, funding mechanisms, collaborations, and the significant potential impact it could have on the research software community. It explores the wide range of services offered, diverse funding sources, extensive collaboration opportunities, and the transformative influence of the SRSI Model on the research software landscape}, author = {Watson, Gregory R. and Malviya-Thakur, Addi and Katz, Daniel S. and Raybourn, Elaine M. and Hoffman, Bill and Robinson, Dana and Kellerman, John and Roundy, Clark}, copyright = {arXiv.org perpetual, non-exclusive license}, doi = {10.48550/ARXIV.2308.14953}, keywords = {sustainability, SSI}, month = {August}, title = {An {Open} {Community}-{Driven} {Model} {For} {Sustainable} {Research} {Software}: {Sustainable} {Research} {Software} {Institute}}, year = {2023} } @article{allen_its_2022, abstract = {Are others using software you've written in their research and citing it as you want it to be cited? Software can be cited in different ways, some good, and some not good at all for tracking and counting citations in indexers such as ADS and Clarivate's Web of Science. Generally, these resources need to match citations to resources, such as journal articles or software records, they ingest. This presentation covered common reasons as to why a code might not be cited well (in a trackable/countable way), which citation methods are trackable, how to specify this information for your software, and where this information should be placed. It also covered standard software metadata files, how to create them, and how to use them. Creating a metadata file, such as a CITATION.cff or codemeta.json, and adding it to the root of your code repo is easy to do with the ASCL's metadata file creation overlay, and will help out anyone wanting to give you credit for your computational method, whether it's a huge carefully-written and tested package, or a short quick-and-dirty-but-oh-so-useful code.}, author = {Allen, Alice}, doi = {10.48550/ARXIV.2212.12683}, keywords = {citation}, month = {December}, title = {It's your software! {Get} it cited the way you want!}, year = {2022} } @article{astigarraga_se_2022, author = {Astigarraga, Julen and Cruz-Alonso, Ver\'{o}nica}, doi = {10.7818/ecos.2332}, issn = {1697-2473}, journal = {Ecosistemas}, month = {April}, number = {1}, pages = {2332}, title = {\textexclamdown{}{Se} puede entender c\'{o}mo funcionan {Git} y {GitHub}!}, volume = {31}, year = {2022} } @article{bain_bringing_2022, author = {Bain, Stevie A. and Plaisier, Heleen and Anderson, Felicity and Cook, Nicola and Crouch, Kathryn and Meagher, Thomas R. and Ritchie, Michael G. and Wallace, Edward W. J. and Barker, Daniel}, doi = {10.1371/journal.pcbi.1009705}, editor = {Ouellette, Francis}, journal = {PLOS Computational Biology}, month = {January}, number = {1}, pages = {e1009705}, title = {Bringing bioinformatics to schools with the 4273pi project}, volume = {18}, year = {2022} } @inproceedings{barakhshan_exchanging_2022, author = {Barakhshan, Parinaz and Eigenmann, Rudolf}, doi = {10.1145/3491418.3530293}, keywords = {human resource, research data, community}, month = {July}, publisher = {ACM}, title = {Exchanging {Best} {Practices} for {Supporting} {Computational} and {Data}-{Intensive} {Research}, {The} {Xpert} {Network}}, year = {2022} } @article{barba_defining_2022, abstract = {Reproducibility is inseparable from transparency, as sharing data, code and computational environment is a pre-requisite for being able to retrace the steps of producing the research results. Others have made the case that this artifact sharing should adopt appropriate licensing schemes that permit reuse, modification and redistribution. I make a new proposal for the role of open source software, stemming from the lessons it teaches about distributed collaboration and a commitment-based culture. Reviewing the defining features of open source software (licensing, development, communities), I look for explanation of its success from the perspectives of connectivism – a learning theory for the digital age – and the language-action framework of Winograd and Flores. I contend that reproducibility is about trust, which we build in community via conversations, and open source software is a route to learn how to be more effective learning (discovering) together.}, author = {Barba, Lorena A.}, keywords = {open source, open science, reproducibility}, month = {April}, title = {Defining the role of open source software in research reproducibility}, year = {2022} } @article{barker_introducing_2022, abstract = {Research software is a fundamental and vital part of research, yet significant challenges to discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the practice of scholarship is a common goal of the open science, open source, and FAIR (Findable, Accessible, Interoperable and Reusable) communities and research software is now being understood as a type of digital object to which FAIR should be applied. This emergence reflects a maturation of the research community to better understand the crucial role of FAIR research software in maximising research value. The FAIR for Research Software (FAIR4RS) Working Group has adapted the FAIR Guiding Principles to create the FAIR Principles for Research Software (FAIR4RS Principles). The contents and context of the FAIR4RS Principles are summarised here to provide the basis for discussion of their adoption. Examples of implementation by organisations are provided to share information on how to maximise the value of research outputs, and to encourage others to amplify the importance and impact of this work.}, author = {Barker, Michelle and Chue Hong, Neil P. and Katz, Daniel S. and Lamprecht, Anna-Lena and Martinez-Ortiz, Carlos and Psomopoulos, Fotis and Harrow, Jennifer and Castro, Leyla Jael and Gruenpeter, Morane and Martinez, Paula Andrea and Honeyman, Tom}, doi = {10.1038/s41597-022-01710-x}, journal = {Scientific Data}, keywords = {FAIR}, number = {1}, pages = {622--622}, title = {Introducing the {FAIR} {Principles} for research software}, url = {https://doi.org/10.1038/s41597-022-01710-x}, volume = {9}, year = {2022} } @misc{blech_suresoft_2022, author = {Blech, Christopher and Dreyer, Nils and Friebel, Matthias and Jacob, Christoph and Shamil Jassim, Mostafa and Jehl, Leander and Kapitza, R\"{u}diger and Krafczyk, Manfred and K\"{u}rner, Thomas and Langer, Sabine Christine and Linxweiler, Jan and Mahhouk, Mohammad and Marcus, Sven and Messadi, Ines and Peters, S\"{o}ren and Pilawa, Jan-Marc and Sreekumar, Harikrishnan K. and Str\"{o}tgen, Robert and Stump, Katrin and Vogel, Arne and Wolter, Mario}, doi = {10.24355/dbbs.084-202210121528-0}, note = {Published: Technische Universit\"{a}t Braunschweig}, title = {{SURESOFT}: {Towards} {Sustainable} {Research} {Software}}, year = {2022} } @article{brouat_what_2022, author = {Brouat, Sophie and Tolley, Clare and Bates, David W. and Jenson, James and Slight, Sarah P.}, doi = {10.1016/j.imu.2022.101014}, issn = {2352-9148}, journal = {Informatics in Medicine Unlocked}, pages = {101014}, title = {What unique knowledge and experiences do healthcare professionals have working in clinical informatics?}, volume = {32}, year = {2022} } @article{bygstad_dual_2022, author = {Bygstad, Bendik and \O{}vrelid, Egil and Ludvigsen, Sten and D\ae{}hlen, Morten}, doi = {10.1016/j.compedu.2022.104463}, issn = {0360-1315}, journal = {Computers \& Education}, pages = {104463}, title = {From dual digitalization to digital learning space: {Exploring} the digital transformation of higher education}, volume = {182}, year = {2022} } @article{cadwallader_survey_2022, abstract = {This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code sharing. We surveyed 188 researchers in computational biology. Respondents were asked about how often and why they look at code, which methods of accessing code they find useful and why, what aspects of code sharing are important to them, and how satisfied they are with their ability to complete these tasks. Respondents were asked to look at a prototype code notebook and give feedback on its features. Respondents were also asked how much time they spent preparing code and if they would be willing to increase this to use a code sharing tool, such as a notebook. As a reader of research articles the most common reason (70\%) for looking at code was to gain a better understanding of the article. The most commonly encountered method for code sharing–linking articles to a code repository–was also the most useful method of accessing code from the reader's perspective. As authors, the respondents were largely satisfied with their ability to carry out tasks related to code sharing. The most important of these tasks were ensuring that the code was running in the correct environment, and sharing code with good documentation. The average researcher, according to our results, is unwilling to incur additional costs (in time, effort or expenditure) that are currently needed to use code sharing tools alongside a publication. We infer this means we need different models for funding and producing interactive or executable research outputs if they are to reach a large number of researchers. For the purpose of increasing the amount of code shared by authors, PLOS Computational Biology is, as a result, focusing on policy rather than tools.}, author = {Cadwallader, Lauren and Hrynaszkiewicz, Iain}, copyright = {https://creativecommons.org/licenses/by/4.0/}, doi = {10.7717/peerj.13933}, issn = {2167-8359}, journal = {PeerJ}, language = {en}, month = {August}, pages = {e13933}, title = {A survey of researchers' code sharing and code reuse practices, and assessment of interactive notebook prototypes}, url = {https://peerj.com/articles/13933}, urldate = {2024-11-27}, volume = {10}, year = {2022} } @article{cantelli_european_2022, author = {Cantelli, Gaia and Bateman, Alex and Brooksbank, Cath and Petrov, Anton I. and Malik-Sheriff, Rahuman S. and Ide-Smith, Michele and Hermjakob, Henning and Flicek, Paul and Apweiler, Rolf and Birney, Ewan and McEntyre, Johanna}, doi = {10.1093/nar/gkab1127}, journal = {Nucleic Acids Research}, month = {January}, number = {D1}, pages = {D11--D19}, title = {The {European} {Bioinformatics} {Institute} ({EMBL}-{EBI}) in 2021}, volume = {50}, year = {2022} } @article{carleton_architecting_2022, author = {Carleton, Anita and Shull, Forrest and Harper, Erin}, doi = {10.1109/MC.2022.3187912}, journal = {Computer}, number = {9}, pages = {89--93}, title = {Architecting the future of software engineering}, volume = {55}, year = {2022} } @article{carver_survey_2022, author = {Carver, Jeffrey C. and Weber, Nic and Ram, Karthik and Gesing, Sandra and Katz, Daniel S.}, doi = {10.7717/peerj-cs.963}, journal = {PeerJ Computer Science}, keywords = {US}, month = {May}, pages = {e963}, title = {A survey of the state of the practice for research software in the {United} {States}}, volume = {8}, year = {2022} } @inproceedings{castiel_best_2022, author = {{CASTIEL} and {EuroCC Network}}, booktitle = {Training {Best} {Practice} {Seminar} ({CASTIEL})}, month = {January}, publisher = {EuroCC}, title = {Best {Practice} {Guide}: {How} to {Find} {New} {Attendees} for {Training} {Courses}}, url = {https://www.eurocc-access.eu/wp-content/uploads/2022/04/20220401\%5FBest\%5FPractice\%5FGuide-Training\%5FBest\%5FPractice\%5FSeminar\%5Ffinal.pdf}, year = {2022} } @inproceedings{chaudhry_understanding_2022, author = {Chaudhry, Shafaq and Pazouki, Arman and Schmitz, Patrick and Hillery, Elizabett and Kee, Kerk}, doi = {10.1145/3491418.3530292}, keywords = {human resource, research data}, month = {July}, publisher = {ACM}, title = {Understanding {Factors} that {Influence} {Research} {Computing} and {Data} {Careers}}, year = {2022} } @article{conference_osec2022_2022, author = {Conference, Open Science European}, doi = {10.4000/books.oep.15829}, keywords = {Open Science}, title = {{OSEC2022}. {Proceedings} of the {Paris} {Open} {Science} {EuropeanConference}}, year = {2022} } @misc{Cosden_2022, abstract = {As software has become more essential to research across disciplines, and as the recognition of this fact has grown, the importance of professionalizing the development and maintenance of this software has also increased. The community of software professionals who work on this software have come together under the title Research Software Engineer (RSE) over the last decade. This has led to the formalization of RSE roles and organized RSE groups in universities, national labs, and industry. This, in turn, has created the need to understand how RSEs come into this profession and into these groups, how to further promote this career path to potential members, as well as the need to understand what training gaps need to be filled for RSEs coming from different entry points. We have categorized three main classifications of entry paths into the RSE profession and identified key elements, both advantages and disadvantages, that should be acknowledged and addressed by the broader research community in order to attract and retain a talented and diverse pool of future RSEs.}, archiveprefix = {arXiv}, author = {Ian A. Cosden and Kenton McHenry and Daniel S. Katz}, eprint = {2210.04275}, primaryclass = {cs.SE}, title = {Research Software Engineers: Career Entry Points and Training Gaps}, url = {https://arxiv.org/abs/2210.04275}, year = {2022} } @misc{Cosden_2022b, abstract = {The Princeton Research Software Engineering Group has grown rapidly since its inception in late 2016. The group, housed in the central Research Computing Department, comprised of professional Research Software Engineers (RSEs), works directly with researchers to create high quality research software to enable new scientific advances. As the group has matured so has the need for formalizing operational details and procedures. The RSE group uses an RSE partnership model, where Research Software Engineers work long-term with a designated academic department, institute, center, consortium, or individual principal investigator (PI). This article describes the operation of the central Princeton RSE group including funding, partner \& project selection, and best practices for defining expectations for a successful partnership with researchers.}, archiveprefix = {arXiv}, author = {Ian A. Cosden}, eprint = {2210.16261}, primaryclass = {cs.SE}, title = {An RSE Group Model: Operational and Organizational Approaches From Princeton University's Central Research Software Engineering Group}, url = {https://arxiv.org/abs/2210.16261}, year = {2022} } @article{cosden_princeton_2022, author = {Cosden, Ian A.}, doi = {10.1109/mcse.2023.3264113}, journal = {Computing in Science \& Engineering}, month = {September}, number = {5}, pages = {24--31}, title = {The {Princeton} {University} {Research} {Software} {Engineering} {Group} {Model}: {Operational} and {Organizational} {Approaches}}, volume = {24}, year = {2022} } @article{cosden_research_2022, abstract = {As software has become more essential to research across disciplines, and as the recognition of this fact has grown, the importance of professionalizing the development and maintenance of this software has also increased. The community of software professionals who work on this software have come together under the title Research Software Engineer (RSE) over the last decade. This has led to the formalization of RSE roles and organized RSE groups in universities, national labs, and industry. This, in turn, has created the need to understand how RSEs come into this profession and into these groups, how to further promote this career path to potential members, as well as the need to understand what training gaps need to be filled for RSEs coming from different entry points. We have categorized three main classifications of entry paths into the RSE profession and identified key elements, both advantages and disadvantages, that should be acknowledged and addressed by the broader research community in order to attract and retain a talented and diverse pool of future RSEs.}, author = {Cosden, Ian A. and McHenry, Kenton and Katz, Daniel S.}, keywords = {career}, month = {October}, title = {Research {Software} {Engineers}: {Career} {Entry} {Points} and {Training} {Gaps}}, year = {2022} } @article{cosden_rse_2022, abstract = {The Princeton Research Software Engineering Group has grown rapidly since its inception in late 2016. The group, housed in the central Research Computing Department, comprised of professional Research Software Engineers (RSEs), works directly with researchers to create high quality research software to enable new scientific advances. As the group has matured so has the need for formalizing operational details and procedures. The RSE group uses an RSE partnership model, where Research Software Engineers work long-term with a designated academic department, institute, center, consortium, or individual principal investigator (PI). This article describes the operation of the central Princeton RSE group including funding, partner \& project selection, and best practices for defining expectations for a successful partnership with researchers.}, author = {Cosden, Ian A.}, doi = {10.48550/ARXIV.2210.16261}, keywords = {organization}, month = {October}, title = {An {RSE} {Group} {Model}: {Operational} and {Organizational} {Approaches} {From} {Princeton} {University}'s {Central} {Research} {Software} {Engineering} {Group}}, year = {2022} } @article{davies_creation_2022, author = {Davies, Alan and Hassey, Alan and Williams, John and Moulton, Georgina}, doi = {10.1016/j.ijmedinf.2022.104905}, journal = {International Journal of Medical Informatics}, month = {December}, pages = {104905}, title = {Creation of a core competency framework for clinical informatics: {From} genesis to maintaining relevance}, volume = {168}, year = {2022} } @article{del_pico_fairsoft-practical_2022, author = {del Pico, Eva Mart\i{}\'n and Gelp\i{}\', Josep Llu\i{}\'s and Capella-Guti\'{e}rrez, Salvador}, journal = {bioRxiv}, keywords = {FAIR}, pages = {2022--05--2022--05}, title = {{FAIRsoft}-{A} practical implementation of {FAIR} principles for research software}, year = {2022} } @article{druskat_software_2022, abstract = {To satisfy the principles of FAIR software, software sustainability and software citation, research software must be formally published. Publication repositories make this possible and provide published software versions with unique and persistent identifiers. However, software publication is still a tedious, mostly manual process. To streamline software publication, HERMES, a project funded by the Helmholtz Metadata Collaboration, develops automated workflows to publish research software with rich metadata. The tooling developed by the project utilizes continuous integration solutions to retrieve, collate, and process existing metadata in source repositories, and publish them on publication repositories, including checks against existing metadata requirements. To accompany the tooling and enable researchers to easily reuse it, the project also provides comprehensive documentation and templates for widely used CI solutions. In this paper, we outline the concept for these workflows, and describe how our solution advance the state of the art in research software publication.}, author = {Druskat, Stephan and Bertuch, Oliver and Juckeland, Guido and Knodel, Oliver and Schlauch, Tobias}, keywords = {metadata}, month = {January}, title = {Software publications with rich metadata: state of the art, automated workflows and {HERMES} concept}, year = {2022} } @article{ebert_testing_2022, author = {Ebert, Christof and Bajaj, Divith and Weyrich, Michael}, doi = {10.1109/MS.2022.3166755}, journal = {IEEE Software}, number = {4}, pages = {8--17}, title = {Testing {Software} {Systems}}, volume = {39}, year = {2022} } @article{eisty_testing_2022, abstract = {Background: Research software plays an important role in solving real-life problems, empowering scientific innovations, and handling emergency situations. Therefore, the correctness and trustworthiness of research software are of absolute importance. Software testing is an important activity for identifying problematic code and helping to produce high-quality software. However, testing of research software is difficult due to the complexity of the underlying science, relatively unknown results from scientific algorithms, and the culture of the research software community. Aims: The goal of this paper is to better understand current testing practices, identify challenges, and provide recommendations on how to improve the testing process for research software development. Method: We surveyed members of the research software developer community to collect information regarding their knowledge about and use of software testing in their projects. Results: We analysed 120 responses and identified that even though research software developers report they have an average level of knowledge about software testing, they still find it difficult due to the numerous challenges involved. However, there are a number of ways, such as proper training, that can improve the testing process for research software. Conclusions: Testing can be challenging for any type of software. This difficulty is especially present in the development of research software, where software engineering activities are typically given less attention. To produce trustworthy results from research software, there is a need for a culture change so that testing is valued and teams devote appropriate effort to writing and executing tests.}, author = {Eisty, Nasir U. and Carver, Jeffrey C.}, keywords = {survey, testing}, month = {May}, title = {Testing {Research} {Software}: {A} {Survey}}, year = {2022} } @article{erdmann_rosa22_2022, author = {Erdmann, Christopher}, doi = {10.5281/ZENODO.6536628}, keywords = {Citation, Open Science, Astrophysics, Reproducibility, Discovery, Astronomy}, title = {{ROSA22} - {Citing} and {Improving} the {Discoverability} of {Your} {Research} {Software}}, year = {2022} } @article{fagerholm_cognition_2022, author = {Fagerholm, Fabian and Felderer, Michael and Fucci, Davide and Unterkalmsteiner, Michael and Marculescu, Bogdan and Martini, Markus and Tengberg, Lars G\"{o}ran Wallgren and Feldt, Robert and Lehtel\"{a}, Bettina and Nagyv\'{a}radi, Bal\'{a}zs and Khattak, Jehan}, doi = {10.1145/3508359}, issn = {0360-0300}, journal = {ACM Computing Surveys}, month = {September}, number = {11s}, title = {Cognition in software engineering: a taxonomy and survey of a half-century of research}, volume = {54}, year = {2022} } @article{fangohr_ai4sd_2022, author = {Fangohr, Hans}, doi = {10.5258/SOTON/AI3SD0269}, keywords = {reproducibility, Jupyter notebooks, Reproducible Research}, title = {{AI4SD} {Video}: {Reproducibility}, {Jupyter} notebooks and associated research software engineering}, year = {2022} } @article{filter_towards_2022, author = {Filter, Matthias and Nauta, Maarten and Pires, Sara M. and Guillier, Laurent and Buschhardt, Tasja}, doi = {10.1016/j.cofs.2022.100834}, journal = {Current Opinion in Food Science}, keywords = {microbiology, Research data}, month = {March}, pages = {100834}, title = {Towards efficient use of data, models and tools in food microbiology}, year = {2022} } @inproceedings{fischer_digital_2022, address = {Bebek Istanbul, Turkey}, author = {Fischer, Thomas and Niederlander, Ursula and Stabauer, Martin}, booktitle = {2022 20{\textbackslash}textsuperscriptth {International} {Conference} on {Information} {Technology} {Based} {Higher} {Education} and {Training} ({ITHET})}, doi = {10.1109/ithet56107.2022.10031743}, isbn = {978-1-6654-8908-9}, month = {November}, publisher = {IEEE}, title = {Digital {Badges} in {Higher} {Education}: {The} {Perspective} of {Employers} in {Upper} {Austria}}, year = {2022} } @inproceedings{fritzsch_hidden_2022, abstract = {Der Film "Hidden Figures" basiert auf historischen Tatsachen und zeigte 2017 einem breiten Publikum, dass bereits bei der Einf\"{u}hrung von Computern bei der NASA in den 50er Jahren Frauen an deren Programmierung beteiligt waren, deren Leistung aber weitgehend unbekannt blieb. Heute blicken wir auf eine immer weiter erstarkende Community der Research Software Engineers und fragen nach Diversit\"{a}t und nach Sichtbarkeit von Frauen bei der Entwicklung von Forschungssoftware.}, author = {Fritzsch, Bernadette}, booktitle = {{CampusSource} {Tagung} 2022}, keywords = {software engineering, Research software, woman}, month = {March}, title = {Hidden {Figures} - wo sind sie? {Frauen} in der {Entwicklung} von {Forschungssoftware}}, year = {2022} } @article{fritzsch_research_2022, author = {Fritzsch, Bernadette}, doi = {10.5281/ZENODO.7092505}, keywords = {human relations}, title = {Research {Software} and the people behind it}, year = {2022} } @article{fur_informationsinfrastrukturen_rfii_datenpolitik_2022, author = {f\"{u}r Informationsinfrastrukturen RfII, Rat}, keywords = {research data}, title = {Datenpolitik, {Open} {Science} und {Dateninfrastrukturen}: {Aktuelle} {Entwicklungen} im europ\"{a}ischen {Raum}}, year = {2022} } @article{garijo_nine_2022, author = {Garijo, Daniel and M\'{e}nager, Herv\'{e} and Hwang, Lorraine and Trisovic, Ana and Hucka, Michael and Morrell, Thomas and Allen, Alice}, doi = {10.7717/peerj-cs.1023}, journal = {PeerJ Computer Science}, keywords = {repository, registry}, month = {August}, pages = {e1023--e1023}, title = {Nine best practices for research software registries and repositories}, volume = {8}, year = {2022} } @misc{Godoy_2022, abstract = {This paper shares a perspective for the research software engineering (RSE) community to navigate the National Laboratory landscape. The RSE role is a recent concept that led to organizational challenges to place and evaluate their impact, costs and benefits. The premise is that RSEs are a natural fit into the current landscape and can use traditional career growth strategies in science: publications, community engagements and proposals. Projects funding RSEs can benefit from this synergy and be inclusive on traditional activities. Still, a great deal of introspection is needed to close gaps between the rapidly evolving RSE landscape and the well-established communication patterns in science. This perspective is built upon interactions in industry, academia and government in high-performance computing (HPC) environments. The goal is to contribute to the conversation around RSE career growth and understand their return on investment for scientific projects and sponsors.}, archiveprefix = {arXiv}, author = {William F Godoy}, eprint = {2209.02610}, primaryclass = {cs.SE}, title = {A perspective to navigate the National Laboratory environment for RSE career growth}, url = {https://arxiv.org/abs/2209.02610}, year = {2022} } @misc{Godoy_2022b, abstract = {The Better Scientific Software Fellowship (BSSwF) was launched in 2018 to foster and promote practices, processes, and tools to improve developer productivity and software sustainability of scientific codes. BSSwF's vision is to grow the community with practitioners, leaders, mentors, and consultants to increase the visibility of scientific software production and sustainability. Over the last five years, many fellowship recipients and honorable mentions have identified as research software engineers (RSEs). This paper provides case studies from several of the program's participants to illustrate some of the diverse ways BSSwF has benefited both the RSE and scientific communities. In an environment where the contributions of RSEs are too often undervalued, we believe that programs such as BSSwF can be a valuable means to recognize and encourage community members to step outside of their regular commitments and expand on their work, collaborations and ideas for a larger audience.}, archiveprefix = {arXiv}, author = {William F. Godoy and Ritu Arora and Keith Beattie and David E. Bernholdt and Sarah E. Bratt and Daniel S. Katz and Ignacio Laguna and Amiya K. Maji and Addi Malviya Thakur and Rafael M. Mudafort and Nitin Sukhija and Damian Rouson and Cindy Rubio-Gonz\'{a}lez and Karan Vahi}, eprint = {2211.07436}, primaryclass = {cs.SE}, title = {Giving RSEs a Larger Stage through the Better Scientific Software Fellowship}, url = {https://arxiv.org/abs/2211.07436}, year = {2022} } @article{godoy_giving_2022, author = {Godoy, William F. and Arora, Ritu and Beattie, Keith and Bernholdt, David E. and Bratt, Sarah E. and Katz, Daniel S. and Laguna, Ignacio and Maji, Amiya K. and Malviya-Thakur, Addi and Mudafort, Rafael M. and Sukhija, Nitin and Rouson, Damian and Rubio-Gonz\'{a}lez, Cindy and Vahi, Karan}, doi = {10.1109/mcse.2023.3253847}, journal = {Computing in Science \& Engineering}, month = {September}, number = {5}, pages = {6--13}, title = {Giving {Research} {Software} {Engineers} a {Larger} {Stage} {Through} the {Better} {Scientific} {Software} {Fellowship}}, volume = {24}, year = {2022} } @article{godoy_giving_2022-1, abstract = {The Better Scientific Software Fellowship (BSSwF) was launched in 2018 to foster and promote practices, processes, and tools to improve developer productivity and software sustainability of scientific codes. BSSwF's vision is to grow the community with practitioners, leaders, mentors, and consultants to increase the visibility of scientific software production and sustainability. Over the last five years, many fellowship recipients and honorable mentions have identified as research software engineers (RSEs). This paper provides case studies from several of the program's participants to illustrate some of the diverse ways BSSwF has benefited both the RSE and scientific communities. In an environment where the contributions of RSEs are too often undervalued, we believe that programs such as BSSwF can be a valuable means to recognize and encourage community members to step outside of their regular commitments and expand on their work, collaborations and ideas for a larger audience.}, author = {Godoy, William F. and Arora, Ritu and Beattie, Keith and Bernholdt, David E. and Bratt, Sarah E. and Katz, Daniel S. and Laguna, Ignacio and Maji, Amiya K. and Thakur, Addi Malviya and Mudafort, Rafael M. and Sukhija, Nitin and Rouson, Damian and Rubio-Gonz\'{a}lez, Cindy and Vahi, Karan}, doi = {10.48550/ARXIV.2211.07436}, keywords = {funding, promotion}, month = {November}, title = {Giving {RSEs} a {Larger} {Stage} through the {Better} {Scientific} {Software} {Fellowship}}, year = {2022} } @article{gomez-diaz_research_2022, author = {Gomez-Diaz, Teresa and Recio, Tomas}, doi = {10.12688/f1000research.78195.1}, journal = {F1000Research}, keywords = {open science, research data}, month = {January}, pages = {118}, title = {Research {Software} vs. {Research} {Data} {I}: {Towards} a {Research} {Data} definition in the {Open} {Science} context}, volume = {11}, year = {2022} } @article{gomez-diaz_research_2022-1, author = {Gomez-Diaz, Teresa and Recio, Tomas}, doi = {10.5281/ZENODO.6778872}, keywords = {open science, research data, reusability}, title = {Research {Software} and {Research} {Data}: dissemination, evaluation and reusability in the {Open} {Science} context}, year = {2022} } @article{gomez-diaz_research_2022-2, author = {Gomez-Diaz, Teresa and Recio, Tomas}, doi = {10.12688/f1000research.78459.1}, journal = {F1000Research}, keywords = {open science, research data, protocols}, month = {January}, pages = {117--117}, title = {Research {Software} vs. {Research} {Data} {II}: {Protocols} for {Research} {Data} dissemination and evaluation in the {Open} {Science} context}, volume = {11}, year = {2022} } @article{gonzalez-barahona_software_2022, author = {Gonzalez-Barahona, Jesus M. and Izquierdo-Cortazar, Daniel and Robles, Gregorio}, doi = {10.1109/mc.2022.3145680}, issn = {1558-0814}, journal = {Computer}, month = {April}, number = {4}, pages = {66--73}, title = {Software {Development} {Metrics} {With} a {Purpose}}, volume = {55}, year = {2022} } @article{grossfield_how_2022, author = {Grossfield, Alan}, doi = {10.33011/livecoms.3.1.1473}, journal = {Living Journal of Computational Molecular Science}, month = {January}, number = {1}, pages = {1473}, title = {How to be a {Good} {Member} of a {Scientific} {Software} {Community} [{Article} v1.0]}, volume = {3}, year = {2022} } @inproceedings{hacker_building_2022, author = {Hacker, Thomas and Smith, Preston and Brunson, Dana and Arafune, Lisa and Cheatham, Thomas and Deelman, Ewa}, doi = {10.1145/3491418.3530288}, keywords = {human resource, open science, research data}, month = {July}, publisher = {ACM}, title = {Building the {Research} {Innovation} {Workforce}: {Challenges} and {Recommendations} from a {Virtual} {Workshop} to {Advance} the {Research} {Computing} {Community}}, year = {2022} } @article{haller_ten_2022, author = {Haller, Benjamin C.}, doi = {10.1371/journal.pcbi.1010540}, journal = {PLOS Computational Biology}, month = {October}, number = {10}, pages = {e1010540}, title = {Ten simple rules for reporting a bug}, volume = {18}, year = {2022} } @inproceedings{haupt_research-software-entwicklung_2022, abstract = {Software wird mehr und mehr von Menschen entwickelt, welche keine klassische Programmier-Ausbildung erhalten haben. In der Forschung ist diese Entwicklung besonders deutlich. Im DLR haben wir die Software Engineering Initiative gestartet um Forschende dabei zu unterst\"{u}tzen Software nachhaltig zu entwickeln. Die Initiative umfasst eine Software Engineering Guideline, Trainings, Wissensaustauschworkshops, Consultings sowie das Erstellen einer f\"{u}r allen zug\"{a}nglichen Wissensbasis.}, author = {Haupt, Carina}, booktitle = {{OOP} {Digital} 2022}, keywords = {software engineering}, month = {February}, title = {({Research}-){Software}-{Entwicklung} f\"{u}r {Non}-{IT}'ler}, url = {https://elib.dlr.de/148656/}, year = {2022} } @article{hermann_documenting_2022, author = {Hermann, Sibylle and Fehr, J\"{o}rg}, doi = {10.1038/s41598-022-10376-9}, journal = {Scientific Reports}, keywords = {documentation}, month = {April}, number = {1}, title = {Documenting research software in engineering science}, volume = {12}, year = {2022} } @article{hermann_documenting_2022-1, author = {Hermann, Sibylle and Fehr, J\"{o}rg}, doi = {10.21203/rs.3.rs-1239393/v1}, keywords = {documentation}, month = {January}, title = {Documenting {Research} {Software} in {Engineering} {Science}}, year = {2022} } @misc{Heroux_2022, abstract = {Software plays a central role in scientific discovery. Improving how we develop and use software for research can have both broad and deep impacts on a spectrum of challenges and opportunities society faces today. The emergence of Research Software Engineer (RSE) as a role correlates with the growing complexity of scientific challenges and diversity of software team skills. In this paper, we describe research software science (RSS), an idea related to RSE, and particularly suited to research software teams. RSS promotes the use of scientific methodologies to explore and establish broadly applicable knowledge. Using RSS, we can pursue sustainable, repeatable, and reproducible software improvements that positively impact research software toward improved scientific discovery.}, archiveprefix = {arXiv}, author = {Michael A. Heroux}, eprint = {2211.09034}, primaryclass = {cs.SE}, title = {Research Software Science: Expanding the Impact of Research Software Engineering}, url = {https://arxiv.org/abs/2211.09034}, year = {2022} } @article{heroux_research_2022, abstract = {Software plays a central role in scientific discovery. Improving how we develop and use software for research can have both broad and deep impacts on a spectrum of challenges and opportunities society faces today. The emergence of Research Software Engineer (RSE) as a role correlates with the growing complexity of scientific challenges and diversity of software team skills. In this paper, we describe research software science (RSS), an idea related to RSE, and particularly suited to research software teams. RSS promotes the use of scientific methodologies to explore and establish broadly applicable knowledge. Using RSS, we can pursue sustainable, repeatable, and reproducible software improvements that positively impact research software toward improved scientific discovery.}, author = {Heroux, Michael A.}, doi = {10.48550/ARXIV.2211.09034}, keywords = {science}, month = {November}, title = {Research {Software} {Science}: {Expanding} the {Impact} of {Research} {Software} {Engineering}}, year = {2022} } @article{heroux_research_2022-1, author = {Heroux, Michael A.}, doi = {10.1109/mcse.2023.3260475}, journal = {Computing in Science \& Engineering}, month = {November}, number = {6}, pages = {22--27}, title = {Research {Software} {Science}: {Expanding} the {Impact} of {Research} {Software} {Engineering}}, volume = {24}, year = {2022} } @article{hirsch_resus_2022, author = {Hirsch, Markus and Iglezakis, Dorothea and Leymann, Frank and Zimmermann, Michael}, doi = {10.11588/HEIBOOKS.979.C13737}, keywords = {FAIR}, title = {The {ReSUS} {Project} - {Infrastructure} for {Sharing} {Research} {Software}}, year = {2022} } @book{hirvela_right_2022, author = {Hirvel\"{a}, P\"{a}ivi and Heikkil\"{a}, Satu}, doi = {10.1017/9781839703232}, isbn = {978-1-83970-323-2}, month = {October}, publisher = {Intersentia}, title = {Right to {Respect} for {Private} and {Family} {Life}, {Home} and {Correspondence}: {A} {Practical} {Guide} to the {Article} 8 {Case}-{Law} of the {European} {Court} of {Human} {Rights}}, year = {2022} } @inproceedings{jabrayilzade_bus_2022, address = {New York, USA}, author = {Jabrayilzade, Elgun and Evtikhiev, Mikhail and T\"{u}z\"{u}n, Eray and Kovalenko, Vladimir}, booktitle = {Proceedings of the 44{\textbackslash}textsuperscriptth {International} {Conference} on {Software} {Engineering}: {Software} {Engineering} in {Practice} ({ICSE}-{SEIP} '22)}, doi = {10.1145/3510457.3513082}, isbn = {978-1-4503-9226-6}, month = {October}, pages = {97--106}, publisher = {Association for Computing Machinery}, title = {Bus factor in practice}, year = {2022} } @inproceedings{jansen_fairseco_2022, author = {Jansen, Slinger and Baninemeh, Elena and Farshidi, Siamak}, title = {{FAIRSECO}: {An} infrastructure for measuring impact of research software}, year = {2022} } @article{kiesler_lack_2022, author = {Kiesler, Natalie and Schiffner, Daniel}, doi = {10.18420/DELFI2022-034}, keywords = {management, Open Science, FAIR, research data, software}, title = {On the {Lack} of {Recognition} of {Software} {Artifacts} and {IT} {Infrastructure} in {Educational} {Technology} {Research}}, year = {2022} } @inproceedings{konrad_research_2022, author = {Konrad, Uwe}, keywords = {HGF}, title = {Research {Software} {Development} at {Helmholtz}}, year = {2022} } @inproceedings{koopman_sustrainable_2022, author = {Oprescu, Ana and Koedijk, Lukas and van Oostveen, Sander and Kok, Stephan}, booktitle = {Teacher {Training}}, doi = {10.48550/arXiv.2204.13993}, editor = {Koopman, Pieter and Lubbers, Mart and Fernandes, Jo\~{a}o Paulo}, month = {April}, pages = {27--35}, publisher = {arXiv}, title = {{SusTrainable}: {Promoting} {Sustainability} as a {Fundamental} {Driver} in {Software} {Development} {Training} and {Education}}, year = {2022} } @inproceedings{laginja_connecting_2022, address = {Bellingham, Washington, USA}, author = {Laginja, Iva and Robles, Pablo and Barjot, Kevin and Leboulleux, Lucie and Jensen-Clem, Rebecca and Brooks, Keira J. and Moriarty, Christopher}, booktitle = {Adaptive {Optics} {Systems} {VIII}}, doi = {10.1117/12.2629483}, editor = {Schreiber, Laura and Schmidt, Dirk and Vernet, Elise}, isbn = {978-1-5106-5352-8}, month = {August}, pages = {121853A}, publisher = {SPIE}, title = {Connecting the astronomical testbed community - the {CAOTIC} project: optimized teaching methods for software version control concepts}, volume = {12185}, year = {2022} } @article{lamprecht_what_2022, abstract = {As recognition of the vital importance of software for contemporary research is increasing, Research Software Engineering (RSE) is emerging as a discipline in its own right. We present an inventory of relevant research questions about RSE as a basis for future research and initiatives to advance the field, highlighting selected literature and initiatives. This work is the outcome of a RSE community workshop held as part of the 2020 International Series of Online Research Software Events (SORSE) which identified and prioritized key questions across three overlapping themes: people, policy and infrastructure. Almost half of the questions focus on the people theme, which addresses issues related to career paths, recognition and motivation; recruitment and retention; skills; and diversity, equity and inclusion. However, the people and policy themes have the same number of prioritized questions. We recommend that different types of stakeholders, such as RSE employers and policy makers, take responsibility for supporting or encouraging answering of these questions by organizations that have an interest. Initiatives such as the International Council of RSE Associations should also be engaged in this work.}, author = {Lamprecht, Anna-Lena and Martinez-Ortiz, Carlos and Barker, Michelle and Bartholomew, Sadie L. and Barton, Justin and Hong, Neil Chue and Cohen, Jeremy and Druskat, Stephan and Forest, Jeremy and Grad, Jean-No\"{e}l and Katz, Daniel S. and Richardson, Robin and Rosca, Robert and Schulte, Douwe and Struck, Alexander and Weinzierl, Marion}, doi = {10.5334/jors.384}, journal = {Journal of Open Research Software}, keywords = {future, science}, title = {What {Do} {We} ({Not}) {Know} {About} {Research} {Software} {Engineering}?}, volume = {10}, year = {2022} } @inproceedings{lefebvre_always-sustainable_2022, author = {Lefebvre, Vincent and Santinelli, Gianni}, doi = {10.1109/netsoft54395.2022.9844077}, keywords = {sustainability, security}, month = {June}, publisher = {IEEE}, title = {Always-{Sustainable} {Software} {Security}}, year = {2022} } @article{liu_provbench_2022, author = {Liu, Fang (Cherry) and Belgin, Mehmet and Zhang, Nuyun and Manalo, Kevin and Lara, Ruben and Stone, Christopher P. and Manno, Paul}, doi = {10.1002/cpe.6820}, journal = {Concurrency and Computation: Practice and Experience}, keywords = {provenance}, month = {January}, title = {{ProvBench}: {A} performance provenance capturing framework for heterogeneous research computing environments}, year = {2022} } @inproceedings{maimone_characterizing_2022, author = {Maimone, Christina and Yockel, Scott and Middelkoop, Timothy and Stauffer, Ashley and Reidy, Chris}, doi = {10.1145/3491418.3530289}, keywords = {human resource, research data, US}, month = {July}, publisher = {ACM}, title = {Characterizing the {US} {Research} {Computing} and {Data} ({RCD}) {Workforce}}, year = {2022} } @article{malviya-thakur_research_2022, author = {Malviya-Thakur, Addi and Bernholdt, David E. and Godoy, William F. and Watson, Gregory R. and Doucet, Mathieu and Coletti, Mark A. and Rogers, David M. and McDonnell, Marshall and Billings, Jay Jay and Maccabe, Barney}, doi = {10.1109/mcse.2023.3260211}, journal = {Computing in Science \& Engineering}, month = {September}, number = {5}, pages = {14--23}, title = {Research {Software} {Engineering} at {Oak} {Ridge} {National} {Laboratory}}, volume = {24}, year = {2022} } @misc{Maric_2022, abstract = {University research groups in Computational Science and Engineering (CSE) generally lack dedicated funding and personnel for Research Software Engineering (RSE), which, combined with the pressure to maximize the number of scientific publications, shifts the focus away from sustainable research software development and reproducible results. The neglect of RSE in CSE at University research groups negatively impacts the scientific output: research data - including research software - related to a CSE publication cannot be found, reproduced, or re-used, different ideas are not combined easily into new ideas, and published methods must very often be re-implemented to be investigated further. This slows down CSE research significantly, resulting in considerable losses in time and, consequentially, public funding. We propose a RSE workflow for Computational Science and Engineering (CSE) that addresses these challenges, that improves the quality of research output in CSE. Our workflow applies established software engineering practices adapted for CSE: software testing, result visualization, and periodical cross-linking of software with reports/publications and data, timed by milestones in the scientific publication process. The workflow introduces minimal work overhead, crucial for university research groups, and delivers modular and tested software linked to publications whose results can easily be reproduced. We define research software quality from a perspective of a pragmatic researcher: the ability to quickly find the publication, data, and software related to a published research idea, quickly reproduce results, understand or re-use a CSE method, and finally extend the method with new research ideas.}, archiveprefix = {arXiv}, author = {Tomislav Maric and Dennis Gl\"{a}ser and Jan-Patrick Lehr and Ioannis Papagiannidis and Benjamin Lambie and Christian Bischof and Dieter Bothe}, eprint = {2208.07460}, primaryclass = {cs.SE}, title = {A Research Software Engineering Workflow for Computational Science and Engineering}, url = {https://arxiv.org/abs/2208.07460}, year = {2022} } @article{maric_research_2022, abstract = {University research groups in Computational Science and Engineering (CSE) generally lack dedicated funding and personnel for Research Software Engineering (RSE), which, combined with the pressure to maximize the number of scientific publications, shifts the focus away from sustainable research software development and reproducible results. The neglect of RSE in CSE at University research groups negatively impacts the scientific output: research data - including research software - related to a CSE publication cannot be found, reproduced, or re-used, different ideas are not combined easily into new ideas, and published methods must very often be re-implemented to be investigated further. This slows down CSE research significantly, resulting in considerable losses in time and, consequentially, public funding. We propose a RSE workflow for Computational Science and Engineering (CSE) that addresses these challenges, that improves the quality of research output in CSE. Our workflow applies established software engineering practices adapted for CSE: software testing, result visualization, and periodical cross-linking of software with reports/publications and data, timed by milestones in the scientific publication process. The workflow introduces minimal work overhead, crucial for university research groups, and delivers modular and tested software linked to publications whose results can easily be reproduced. We define research software quality from a perspective of a pragmatic researcher: the ability to quickly find the publication, data, and software related to a published research idea, quickly reproduce results, understand or re-use a CSE method, and finally extend the method with new research ideas.}, author = {Maric, Tomislav and Gl\"{a}ser, Dennis and Lehr, Jan-Patrick and Papagiannidis, Ioannis and Lambie, Benjamin and Bischof, Christian and Bothe, Dieter}, keywords = {software engineering, workflow}, month = {August}, title = {A {Research} {Software} {Engineering} {Workflow} for {Computational} {Science} and {Engineering}}, year = {2022} } @article{martinez-ortiz_fair4rs_2022, abstract = {In September 2021, the FAIR4RS WG formed subgroups to address milestones for the adoption of the FAIR4RS principles. This document is the output of subgroup 6, focused on adoption support.}, author = {Martinez-Ortiz, Carlos and Katz, Daniel S. and Lamprecht, Anna-Lena and Barker, Michelle and Loewe, Axel and Fouilloux, Anne and Wyngaard, Jane and Garijo, Daniel and Moldon, Javier and Castro, Leyla Jael and Wheeler, Daniel and Albers, Joost Rutger Demian and Lee, Allen}, copyright = {Creative Commons Attribution 4.0 International, Open Access}, doi = {10.5281/ZENODO.6258365}, keywords = {FAIR software}, language = {en}, month = {February}, shorttitle = {{FAIR4RS}}, title = {{FAIR4RS}: {Adoption} support}, url = {https://zenodo.org/record/6258365}, urldate = {2022-11-22}, year = {2022} } @article{martinez-ortiz_how_2022, author = {Martinez-Ortiz, Carlos and Goble, Carole and Katz, Daniel and Honeyman, Tom and Martinez, Paula and Barker, Michelle and Castro, Leyla Jael and Hong, Neil Chue and Gruenpeter, Morane and Harrow, Jennifer and Lamprecht, Anna-Lena and Psomopoulos, Fotis}, doi = {10.3897/rio.8.e95724}, journal = {Research Ideas and Outcomes}, keywords = {FAIR}, month = {October}, title = {How does software fit into the {FDO} landscape?}, volume = {8}, year = {2022} } @inproceedings{meinel_revisiting_2022, abstract = {In the past years, guidelines for a good practice in Research Software Engineering were established in many research facilities. Examples are applied guidelines at the German Aerospace Center (DLR) or the NL eScience Center. Recently, these guidelines were acknowledged as important by the European Union, the Helmholtz Association, and the Max-Planck Society as well as in their strive to support Open Science. But, most guidelines lack information on how to apply Secure Software Engineering (SSE) methods in Scientific Software. More importantly, it is not even clear what aspects of SSE are of particular interest in Research Software Development. In 2018 we published a position and vision paper at the "1ˢᵗ International Workshop on Security Awareness from Design to Deployment" called "DLR Secure Software Engineering". In this paper we drew an ambitious roadmap towards a structured approach for identification and evaluation of relevant aspects and processes. Since then we gained some insights about what is already possible, what could be done, and what is (yet) beyond our reach. In this talk we want to discuss and raise awareness why Secure Software Engineering is an important factor that needs to be acknowledged in the Research Software Engineering Community. We also want to review certain aspects of our previous work and evaluate on how things could be done (differently).}, author = {Meinel, Michael and Stoffers, Martin}, keywords = {Secure Software Engineering}, month = {September}, title = {Revisiting {Secure} {Software} {Engineering} for {Research} {Software}}, url = {https://elib.dlr.de/188479/}, year = {2022} } @article{milewicz_secure_2022, abstract = {Journalists, public policy analysts, and economists have called attention to the growing importance that high-performance and scientific computing have to national security and industrial leadership. As computing continues to power scientific advances in virtually every discipline, so too does it improve our economic productivity and quality of life. The increasing social, political, and economic importance of research software, however, has also brought the question of software security to the fore. Just as unintentional software errors can threaten the integrity of scientific studies, malicious actors could leverage vulnerabilities to alter results, exfiltrate data, and sabotage computing resources. In this editorial, the authors argue for the need to incorporate security practices and perspectives throughout the research software lifecycle, and they propose directions for future work in this space.}, author = {Milewicz, Reed and Carver, Jeffrey and Grayson, Samuel and Atkison, Travis}, doi = {10.48550/ARXIV.2211.06343}, keywords = {open source, software engineering}, month = {November}, title = {A {Secure} {Future} for {Open}-{Source} {Computational} {Science} and {Engineering}}, year = {2022} } @article{mischke_automated_2022, abstract = {Research software is often developed by individual researchers or small teams in parallel to their research work. The more people and research projects rely on the software in question, the more important it is that software updates implement new features correctly and do not introduce regressions. Thus, developers of research software must balance their limited resources between implementing new features and thoroughly testing any code changes. We present the processes we use for developing the distributed integration framework RCE at DLR. These processes aim to strike a balance between automation and manual testing, reducing the testing overhead while addressing issues as early as possible. We furthermore briefly describe how these testing processes integrate with the surrounding processes for development and releasing.}, author = {Mischke, Robert and Schaffert, Kathrin and Schneider, Dominik and Weinert, Alexander}, keywords = {software engineering, testing}, month = {April}, title = {Automated and manual testing as part of the research software development process of {RCE}}, year = {2022} } @article{monks_open_2022, author = {Monks, Thomas and Harper, Alison and Anagnostou, Anastasia and Taylor, Simon J. E.}, doi = {10.31219/osf.io/zpxtm}, keywords = {open science}, month = {July}, title = {Open {Science} for {Computer} {Simulation}}, year = {2022} } @article{morgan_socioeconomic_2022, author = {Morgan, Allison C. and LaBerge, Nicholas and Larremore, Daniel B. and Galesic, Mirta and Brand, Jennie E. and Clauset, Aaron}, doi = {10.1038/s41562-022-01425-4}, journal = {Nature Human Behaviour}, month = {August}, number = {12}, pages = {1625--1633}, title = {Socioeconomic roots of academic faculty}, volume = {6}, year = {2022} } @article{mundt_encouraging_2022, author = {Mundt, Miranda and Bisila, Jonathan and Guyer, Jonathan E. and Howard, Daniel and Katz, Daniel S. and Milewicz, Reed and Schreiner, Henry and Teves, Joshua and Wiswell, Chris}, keywords = {community of practice}, title = {Encouraging and {Enabling} {Mutual} {Ownership} in a {RSE} {Community} of {Practice}}, url = {https://tsapps.nist.gov/publication/get\%5Fpdf.cfm?pub\%5Fid=935856}, year = {2022} } @article{mundt_for_2022, author = {Mundt, Miranda R. and Beattie, Keith and Bisila, Jonathan and Ferenbaugh, Charles R. and Godoy, William F. and Gupta, Rinku and Guyer, Jonathan E. and Kiran, Miriam and Malviya-Thakur, Addi and Milewicz, Reed and Sims, Benjamin H. and Sochat, Vanessa and Teves, Joshua B.}, doi = {10.1109/mcse.2023.3256759}, journal = {Computing in Science \& Engineering}, month = {November}, number = {6}, pages = {6--13}, title = {For the {Public} {Good}: {Connecting}, {Retaining}, and {Recognizing} {Current} and {Future} {RSEs} at {U}.{S}. {National} {Research} {Laboratories} and {Agencies}}, volume = {24}, year = {2022} } @article{mundt_working_2022, abstract = {Within the rapidly diversifying field of computational science and engineering (CSE), research software engineers (RSEs) represent a shift towards the adoption of mainstream software engineering tools and practices into scientific software development. An unresolved challenge is the need to effectively integrate RSEs and their expertise into multi-disciplinary scientific software teams. There has been a long-standing "chasm" between the domains of CSE and software engineering, and the emergence of RSEs as a professional identity within CSE presents an opportunity to finally bridge that divide. For this reason, we argue there is an urgent need for systematic investigation into multi-disciplinary teaming strategies which could promote a more productive relationship between the two fields.}, author = {Mundt, Miranda and Milewicz, Reed}, keywords = {software engineering, teams}, month = {January}, title = {Working in {Harmony}: {Towards} {Integrating} {RSEs} into {Multi}-{Disciplinary} {CSE} {Teams}}, year = {2022} } @book{national_academies_of_sciences_engineering_and_medicine_transforming_2022, address = {Washington, D.C., USA}, author = {{National Academies of Sciences, Engineering, and Medicine}}, doi = {10.17226/26345}, editor = {Hammonds, Evelynn and Taylor, Valerie and Hutton, Rebekah}, isbn = {978-0-309-26908-7}, publisher = {The National Academies Press}, title = {Transforming {Trajectories} for {Women} of {Color} in {Tech}}, year = {2022} } @article{noor_improving_2022, author = {Noor, Adeeb}, doi = {10.7717/peerj-cs.839}, journal = {PeerJ Computer Science}, month = {January}, pages = {e839}, title = {Improving bioinformatics software quality through incorporation of software engineering practices}, volume = {8}, year = {2022} } @article{oladipo_curriculum_2022, author = {Oladipo, Francisca and Folorunso, Sakinat and Ogundepo, Ezekiel and Osigwe, Obinna and Akindele, Akinyinka}, doi = {10.1162/dint_a_00183}, journal = {Data Intelligence}, number = {4}, pages = {991--1012}, title = {Curriculum {Development} for {FAIR} {Data} {Stewardship}}, volume = {4}, year = {2022} } @article{orviz_quality-based_2022, author = {Orviz, Pablo and Bernardo, Samuel and David, Mario and Naranjo, Diana and Molt\'{o}, Germ\'{a}n and Caballer, Miguel and Campos, Isabel and Gomes, Jorge and Kozlov, Valentin and Esteban Sanchis, Borja and Hardt, Marcus and Braesicke, Peter and Kerzenmacher, Tobias and Blanquer, Ignacio}, keywords = {software, pipelines, quality assurance, service}, title = {A quality-based approach for research software and services}, year = {2022} } @article{parker_evidence_2022, author = {Parker, Wendy S.}, doi = {10.1007/s10670-020-00260-1}, issn = {1572-8420}, journal = {Erkenntnis}, month = {August}, number = {4}, pages = {1521--1538}, title = {Evidence and {Knowledge} from {Computer} {Simulation}}, volume = {87}, year = {2022} } @article{pfeil_fair_2022, author = {Pfeil, Andreas and Jejkal, Thomas and Chelbi, Sabrine and Blumenr\"{o}hr, Nicolas}, doi = {10.3897/rio.8.e94408}, journal = {Research Ideas and Outcomes}, keywords = {FAIR}, month = {October}, title = {A {FAIR} {Digital} {Object} {Lab} {Software} {Stack}}, volume = {8}, year = {2022} } @misc{Pierce_2022, abstract = {The Science Gateways Community Institute (SGCI) is an NSF Software Infrastructure for Sustained Innovation (S2I2) funded project that leads and supports the science gateway community. Major activities for SGCI include a) sustainability training, including the Focus Week week-long course designed to help science gateway operators develop sustainability plans, and the Jumpstart virtual short-course; b) usability and user experience consulting; c) a community catalog of science gateways and science gateway software; d) workforce development activities, including a coding institute for students, internship opportunities, and hackathons; e) an annual conference; and f) in-depth technical support for client gateway projects. The goals of SGCI's Embedded Technical Support component are to help the institute's clients to create new science gateways or to significantly enhance existing science gateways. Examples of the latter include helping to implement major new capabilities and to implement significant usability improvements suggested by SGCI's usability consultants. The Embedded Technical Support component was managed by Indiana University and involved research software engineers at San Diego Supercomputer Center, Texas Advanced Computing Center, Indiana University, and Purdue University (through 2019). Since 2016, the component has involved 20 research software engineers as consultants and has conducted 59 client consultations. This short paper provides a summary of lessons learned from the Embedded Technical Support program that may be useful for the research software engineering community.}, archiveprefix = {arXiv}, author = {Marlon Pierce and Michael Zentner and Maytal Dahan and Sandra Gesing and Claire Stirm and Linda Bailey Hayden}, eprint = {2209.03958}, primaryclass = {cs.SE}, title = {The Science Gateway Community Institute's Consulting Services Program: Lessons for Research Software Engineering Organizations}, url = {https://arxiv.org/abs/2209.03958}, year = {2022} } @article{pierce_science_2022, abstract = {The Science Gateways Community Institute (SGCI) is an NSF Software Infrastructure for Sustained Innovation (S2I2) funded project that leads and supports the science gateway community. Major activities for SGCI include a) sustainability training, including the Focus Week week-long course designed to help science gateway operators develop sustainability plans, and the Jumpstart virtual short-course; b) usability and user experience consulting; c) a community catalog of science gateways and science gateway software; d) workforce development activities, including a coding institute for students, internship opportunities, and hackathons; e) an annual conference; and f) in-depth technical support for client gateway projects. The goals of SGCI's Embedded Technical Support component are to help the institute's clients to create new science gateways or to significantly enhance existing science gateways. Examples of the latter include helping to implement major new capabilities and to implement significant usability improvements suggested by SGCI's usability consultants. The Embedded Technical Support component was managed by Indiana University and involved research software engineers at San Diego Supercomputer Center, Texas Advanced Computing Center, Indiana University, and Purdue University (through 2019). Since 2016, the component has involved 20 research software engineers as consultants and has conducted 59 client consultations. This short paper provides a summary of lessons learned from the Embedded Technical Support program that may be useful for the research software engineering community.}, author = {Pierce, Marlon and Zentner, Michael and Dahan, Maytal and Gesing, Sandra and Stirm, Claire and Hayden, Linda Bailey}, keywords = {consulting}, month = {September}, title = {The {Science} {Gateway} {Community} {Institute}'s {Consulting} {Services} {Program}: {Lessons} for {Research} {Software} {Engineering} {Organizations}}, year = {2022} } @article{plomp_taking_2022, author = {Plomp, Esther and Tsang, Emmy and Lavanchy, Paula M. Martinez}, doi = {10.7191/jeslib.2022.1221}, issn = {2161-3974}, journal = {Journal of eScience Librarianship}, month = {May}, number = {1}, title = {Taking the {TU} {Delft} {Carpentries} {Workshops} {Online}}, volume = {11}, year = {2022} } @article{ringuette_advocating_2022, author = {Ringuette, Rebecca and Murphy, Nicholas and Petrenko, Maksym and Reardon, Kevin and Rigler, Josh and Mays, Leila and Guidoni, Silvina and De Zeeuw, Darren and Weigel, Robert and Chen, Thomas Y. and {others}}, journal = {Solar and Space Physics (Heliophysics) Decadal Survey}, title = {Advocating for {Equality} of {Contribution}: {The} {Research} {Software} {Engineer} ({RSE})}, year = {2022} } @inproceedings{rochlin_evaluating_2022, author = {Rochlin, Nick and Gardner, Jeff and Kinney, Elizabeth}, doi = {10.1145/3491418.3530295}, keywords = {training, infrastructure}, month = {July}, publisher = {ACM}, title = {Evaluating research computing training and support as part of a broader digital research infrastructure needs assessment}, year = {2022} } @article{schindler_role_2022, author = {Schindler, David and Bensmann, Felix and Dietze, Stefan and Kr\"{u}ger, Frank}, doi = {10.7717/peerj-cs.835}, journal = {PeerJ Computer Science}, keywords = {knowledge graph, PubMed}, month = {January}, pages = {e835}, title = {The role of software in science: a knowledge graph-based analysis of software mentions in {PubMed} {Central}}, volume = {8}, year = {2022} } @article{sethuraman_teaching_2022, author = {Sethuraman, Arun}, doi = {10.1093/biomethods/bpac032}, journal = {Biology Methods and Protocols}, month = {January}, number = {1}, title = {Teaching computational genomics and bioinformatics on a high performance computing cluster--a primer}, volume = {7}, year = {2022} } @incollection{smith_digging_2022, author = {Smith, Spencer and Michalski, Peter}, booktitle = {Computational {Science} – {ICCS} 2022}, doi = {10.1007/978-3-031-08760-8_45}, keywords = {practice, software engineering}, pages = {545--559--545--559}, publisher = {Springer International Publishing}, title = {Digging {Deeper} into the {State} of the {Practice} for {Domain} {Specific} {Research} {Software}}, year = {2022} } @inproceedings{smith_digging_2022-1, address = {Cham}, author = {Smith, Spencer and Michalski, Peter}, booktitle = {Computational {Science} – {ICCS} 2022}, editor = {Groen, Derek and de Mulatier, Cl\'{e}lia and Paszynski, Maciej and Krzhizhanovskaya, Valeria V. and Dongarra, Jack J. and Sloot, Peter M. A.}, isbn = {978-3-031-08760-8}, pages = {545--559}, publisher = {Springer International Publishing}, series = {Lecture {Notes} in {Computer} {Science}}, title = {Digging deeper into the state of the practice for domain specific research software}, volume = {13353}, year = {2022} } @article{sochat_citelang_2022, author = {Sochat, Vanessa}, doi = {10.21105/joss.04458}, journal = {Journal of Open Source Software}, keywords = {citation}, month = {September}, number = {77}, pages = {4458--4458}, title = {{CiteLang}: {Modeling} the {Research} {Software} {Ecosystem}}, volume = {7}, year = {2022} } @article{sochat_research_2022, author = {Sochat, Vanessa and May, Nicholas and Cosden, Ian and Martinez-Ortiz, Carlos and Bartholomew, Sadie}, doi = {10.5334/jors.359}, journal = {Journal of Open Research Software}, keywords = {research software}, title = {The {Research} {Software} {Encyclopedia}: {A} {Community} {Framework} to {Define} {Research} {Software}}, volume = {10}, year = {2022} } @article{strasser_ten_2022, author = {Strasser, Carly and Hertweck, Kate and Greenberg, Josh and Taraborelli, Dario and Vu, Elizabeth}, doi = {10.1371/journal.pcbi.1010627}, journal = {PLOS Computational Biology}, keywords = {funding, open source}, month = {November}, number = {11}, pages = {e1010627--e1010627}, title = {Ten simple rules for funding scientific open source software}, volume = {18}, year = {2022} } @article{thakur_towards_2022, author = {Thakur, Addi Malviya and Hitefield, Seth and McDonnell, Marshall and Wolf, Matthew and Archibald, Richard and Drane, Lance and Roccapriore, Kevin and Ziatdinov, Maxim and McGaha, Jesse and Smith, Robert and {others}}, keywords = {open science}, title = {Towards a {Software} {Development} {Framework} for {Interconnected} {Science} {Ecosystems}}, year = {2022} } @article{trinkenreich_pots_2022, author = {Trinkenreich, Bianca and Guizani, Mariam and Wiese, Igor and Conte, Tayana and Gerosa, Marco and Sarma, Anita and Steinmacher, Igor}, doi = {10.1109/tse.2021.3108032}, journal = {IEEE Transactions on Software Engineering}, month = {October}, number = {10}, pages = {3940--3953}, title = {Pots of {Gold} at the {End} of the {Rainbow}: {What} is {Success} for {Open} {Source} {Contributors}?}, volume = {48}, year = {2022} } @article{vallet_toward_2022, author = {Vallet, Nicolas and Michonneau, David and Tournier, Simon}, doi = {10.1038/s41597-022-01720-9}, journal = {Scientific Data}, keywords = {open science, reproducibility}, month = {October}, number = {1}, title = {Toward practical transparent verifiable and long-term reproducible research using {Guix}}, volume = {9}, year = {2022} } @article{van_eijnatten_amsterdam_2022, author = {Van Eijnatten, Joris and Barker, Michelle and Azzar\`{a}, Valentina and Bakker, Tom and Katz, Daniel S. and Martinez-Ortiz, Carlos and Cruz, Maria J. and Pang, Veronica}, doi = {10.5281/ZENODO.7330542}, keywords = {open science, software sustainability, declaration, funding}, title = {Amsterdam {Declaration} on {Funding} {Research} {Software} {Sustainability}}, year = {2022} } @inproceedings{venigalla_gitq-_2022, address = {New York, New York, USA}, author = {Venigalla, Akhila Sri Manasa and Boyalakuntla, Kowndinya and Chimalakonda, Sridhar}, booktitle = {Proceedings of the 30{\textbackslash}textsuperscriptth {IEEE}/{ACM} {International} {Conference} on {Program} {Comprehension} ({ICPC} 2022)}, doi = {10.1145/3524610.3527876}, isbn = {978-1-4503-9298-3}, month = {May}, pages = {157--161}, publisher = {ACM}, title = {{GitQ}- towards using badges as visual cues for {GitHub} projects}, year = {2022} } @article{weber_research_2022, abstract = {Research software is increasingly recognized as a vital component of the scholarly record. Journals offer authors the opportunity to publish research software papers, but often have different requirements for how these publications should be structured and how code should be verified. In this short case study we gather data from 20 Physical Science journals to trace the frequency, quality control, and publishing criteria for software papers. Our goal with the case study is to provide a proof-of-concept for doing descriptive empirical work with software publication policies across numerous domains of science and engineering. In the narrative we therefore provide descriptive statistics showing how these journals differ in criteria required for archiving, linking, verifying, and documenting software as part of a formal publication. The contribution of this preliminary work is twofold: 1. We provide case study of Physical Science research software publications over time; 2. We demonstrate the use of a new survey method for analyzing research software publication policies. In our conclusion, we describe how comparative research into software publication policies can provide better criteria and requirements for an emerging software publication landscape.}, author = {Weber, Nic}, keywords = {policy, publication}, month = {June}, title = {Research {Software} {Publication} {Policy} {Case} {Study}}, year = {2022} } @article{willenbring_evaluating_2022, author = {Willenbring, James and Walia, Gursimran}, keywords = {Sustainability, Software Engineering, Empirical Study}, title = {Evaluating the {Sustainability} of {Computational} {Science} and {Engineering} {Software}: {Empirical} {Observations}}, year = {2022} } @article{woolston_why_2022, author = {Woolston, Chris}, copyright = {https://www.springer.com/tdm}, doi = {10.1038/d41586-022-01516-2}, issn = {0028-0836, 1476-4687}, journal = {Nature}, language = {en}, month = {May}, pages = {d41586--022--01516--2}, title = {Why science needs more research software engineers}, url = {https://www.nature.com/articles/d41586-022-01516-2}, urldate = {2024-11-29}, year = {2022} } @article{wuttke_guidelines_2022, author = {Wuttke, Joachim and Cottrell, Stephen and Gonzalez, Miguel A. and Kaestner, Anders and Markvardsen, Anders and Rod, Thomas H. and Rozyczko, Piotr and Vardanyan, Gagik}, doi = {10.3233/jnr-220002}, journal = {Journal of Neutron Research}, keywords = {guidelines, development}, month = {March}, number = {1}, pages = {33--72}, title = {Guidelines for collaborative development of sustainable data treatment software}, volume = {24}, year = {2022} } @article{yehudi_why_2022, author = {Yehudi, Yo}, doi = {10.5281/ZENODO.6545452}, keywords = {open source, community}, title = {Why open source community building makes your research software better (and what to expect when you get started)}, year = {2022} } @article{acker_emulation_2021, author = {Acker, Amelia}, doi = {10.1002/asi.24482}, journal = {Journal of the Association for Information Science and Technology}, keywords = {research software, preservation}, number = {9}, pages = {1148--1160--1148--1160}, title = {Emulation practices for software preservation in libraries, archives, and museums}, volume = {72}, year = {2021} } @article{akhmerov_tu_2021, author = {Akhmerov, Anton and Bazuine, Merlijn and Beardsell, Julie and van den Bogerd, Rianne and Branchett, Susan and Dunning, Alastair and Keijzer-de Ruijter, Meta and Cruz, Maria and Martinez-Lavanchy, Paula and Schenk, Mark and Spaargaren, Margot and Teperek, Marta}, doi = {10.5281/ZENODO.4629661}, keywords = {FAIR software, Open Science, Policy, RDM, TU Delft}, title = {{TU} {Delft} {Research} {Software} {Policy}}, year = {2021} } @article{allen_scicodes_2021, abstract = {The Astrophysics Source Code Library (ASCL ascl.net), started in 1999, is a free open registry of software used in refereed astronomy research. Over the past few years, it has spearheaded an effort to form a consortium of scientific software registries and repositories. In 2019 and 2020, ASCL contacted editors and maintainers of discipline and institutional software registries and repositories in math, biology, neuroscience, geophysics, remote sensing, and other fields to develop a list of best practices for these research software resources. At the completion of that project, performed as a Task Force for a FORCE11 working group, members decided to form SciCodes as an ongoing consortium. This presentation covered the consortium's work so far, what it is currently working on, what it hopes to achieve for making scientific research software more discoverable across disciplines, and how the consortium can benefit astronomers.}, author = {Allen, Alice}, doi = {https://doi.org/10.48550/arXiv.2111.14278}, keywords = {repository}, month = {November}, title = {{SciCodes}: {Astronomy} {Research} {Software} and {Beyond}}, year = {2021} } @article{alsudais_-code_2021, author = {Alsudais, Abdulkareem}, doi = {10.1016/j.joi.2021.101139}, journal = {Journal of Informetrics}, keywords = {open source, research software, citation}, number = {2}, pages = {101139--101139}, title = {In-code citation practices in open research software libraries}, volume = {15}, year = {2021} } @article{alt_who_2021, author = {Alt, Dorit}, doi = {10.1007/s12144-021-02002-0}, journal = {Current Psychology}, month = {June}, number = {8}, pages = {6629--6640}, title = {Who benefits from digital badges? {Motivational} precursors of digital badge usages in higher education}, volume = {42}, year = {2021} } @article{ambite_bd2k_2021, author = {Ambite, Jos\'{e} Luis and Fierro, Lily and Gordon, Jonathan and Burns, Gully A. P. C. and Geigl, Florian and Lerman, Kristina and Van Horn, John D.}, doi = {10.1109/tetc.2019.2903466}, journal = {IEEE Transactions on Emerging Topics in Computing}, month = {January}, number = {1}, pages = {316--328}, title = {{BD2K} {Training} {Coordinating} {Center}'s {ERuDIte}: {The} {Educational} {Resource} {Discovery} {Index} for {Data} {Science}}, volume = {9}, year = {2021} } @article{anzt_crediting_2021, author = {Anzt, Hartwig and Kuehn, Eileen and Flegar, Goran}, doi = {10.1016/j.jocs.2020.101278}, journal = {Journal of Computational Science}, keywords = {Research Software, Open Source}, month = {February}, pages = {101278--101278}, title = {Crediting pull requests to open source research software as an academic contribution}, volume = {49}, year = {2021} } @article{anzt_environment_2021, author = {Anzt, Hartwig and Bach, Felix and Druskat, Stephan and L\"{o}ffler, Frank and Loewe, Axel and Renard, Bernhard Y. and Seemann, Gunnar and Struck, Alexander and Achhammer, Elke and Aggarwal, Piush and Appel, Franziska and Bader, Michael and Brusch, Lutz and Busse, Christian and Chourdakis, Gerasimos and Dabrowski, Piotr Wojciech and Ebert, Peter and Flemisch, Bernd and Friedl, Sven and Fritzsch, Bernadette and Funk, Maximilian D. and Gast, Volker and Goth, Florian and Grad, Jean-No\"{e}l and Hegewald, Jan and Hermann, Sibylle and Hohmann, Florian and Janosch, Stephan and Kutra, Dominik and Linxweiler, Jan and Muth, Thilo and Peters-Kottig, Wolfgang and Rack, Fabian and Raters, Fabian H.C. and Rave, Stephan and Reina, Guido and Rei\ss{}ig, Malte and Ropinski, Timo and Schaarschmidt, Joerg and Seibold, Heidi and Thiele, Jan P. and Uekermann, Benjamin and Unger, Stefan and Weeber, Rudolf}, doi = {10.12688/f1000research.23224.2}, journal = {F1000Research}, number = {295}, title = {An environment for sustainable research software in {Germany} and beyond: current state, open challenges, and call for action [version 2; peer review: 2 approved]}, volume = {9}, year = {2021} } @article{bahaidarah_toward_2021, abstract = {An essential part of research and scientific communication is researchers' ability to reproduce the results of others. While there have been increasing standards for authors to make data and code available, many of these files are hard to re-execute in practice, leading to a lack of research reproducibility. This poses a major problem for students and researchers in the same field who cannot leverage the previously published findings for study or further inquiry. To address this, we propose an open-source platform named RE3 that helps improve the reproducibility and readability of research projects involving R code. Our platform incorporates assessing code readability with a machine learning model trained on a code readability survey and an automatic containerization service that executes code files and warns users of reproducibility errors. This process helps ensure the reproducibility and readability of projects and therefore fast-track their verification and reuse.}, author = {Bahaidarah, Layan and Hung, Ethan and Oliveira, Andreas F. De Melo and Penumaka, Jyotsna and Rosario, Lukas and Trisovic, Ana}, keywords = {reproducibility, reusability}, month = {September}, title = {Toward {Reusable} {Science} with {Readable} {Code} and {Reproducibility}}, year = {2021} } @article{balaban_ten_2021, author = {Balaban, Gabriel and Grytten, Ivar and Rand, Knut Dagestad and Scheffer, Lonneke and Sandve, Geir Kjetil}, doi = {10.1371/journal.pcbi.1008549}, journal = {PLOS Computational Biology}, keywords = {research software, software engineering}, month = {March}, number = {3}, pages = {e1008549--e1008549}, title = {Ten simple rules for quick and dirty scientific programming}, volume = {17}, year = {2021} } @incollection{bani_baker_design_2021, author = {Bani Baker, Qanita and Nuser, Maryam S.}, booktitle = {Your {Passport} to a {Career} in {Bioinformatics}}, doi = {10.1007/978-981-15-9544-8_10}, edition = {2}, editor = {Suravajhala, Prashanth N.}, isbn = {978-981-15-9544-8}, pages = {91--102}, publisher = {Springer Singapore}, title = {Design {Bioinformatics} {Curriculum} {Guidelines}: {Perspectives}}, year = {2021} } @article{barakhshan_exchanging_2021, abstract = {We present best practices and tools for professionals who support computational and data intensive (CDI) research projects. The practices resulted from an initiative that brings together national projects and university teams that include individual or groups of such professionals. We focus particularly on practices that differ from those in a general software engineering context. The paper also describes the initiative , the Xpert Network , where participants exchange successes, challenges, and general information about their activities, leading to increased productivity, efficiency, and coordination in the ever growing community of scientists that use computational and data-intensive research methods.}, author = {Barakhshan, Parinaz and Eigenmann, Rudolf}, keywords = {research software, Research data, infrastructures}, month = {February}, title = {Exchanging {Best} {Practices} and {Tools} for {Supporting} {Computational} and {Data}-{Intensive} {Research}, {The} {Xpert} {Network}}, year = {2021} } @article{bazuine_tu_2021, author = {Bazuine, Merlijn}, doi = {10.5281/ZENODO.4629635}, keywords = {FAIR software, Open Science, Policy, RDM, TU Delft, Guidelines}, title = {{TU} {Delft} {Guidelines} on {Research} {Software}: {Licensing}, {Registration} and {Commercialisation}}, year = {2021} } @article{beckman_implementing_2021, author = {Beckman, Matthew D. and \c{C}etinkaya-Rundel, Mine and Horton, Nicholas J. and Rundel, Colin W. and Sullivan, Adam J. and Tackett, Maria}, doi = {10.1080/10691898.2020.1848485}, journal = {Journal of Statistics and Data Science Education}, month = {January}, number = {sup1}, pages = {S132--S144}, title = {Implementing {Version} {Control} {With} {Git} and {GitHub} as a {Learning} {Objective} in {Statistics} and {Data} {Science} {Courses}}, volume = {29}, year = {2021} } @article{bertuch_research_2021, author = {Bertuch, Oliver}, doi = {10.5446/55276}, keywords = {RSE, RDM, Reproducibility, Research Data Management, Research Software Engineering, Reproducible Research, Credibility, FDM, Information Science}, title = {Research {Software} {Engineering} und {Forschungsdatenmanagement} - eine himmlische {Kombination}}, year = {2021} } @article{bokulich_data_2021, author = {Bokulich, Alisa and Parker, Wendy}, doi = {10.1007/s13194-020-00345-2}, issn = {1879-4920}, journal = {European Journal for Philosophy of Science}, month = {January}, number = {1}, pages = {31}, title = {Data models, representation and adequacy-for-purpose}, volume = {11}, year = {2021} } @article{boline_best_2021, author = {Boline, Jyl and Das, Samir and Faye, Ibrahima and Goscinski, Wojtek and Hellgren-Kotaleski, Jeanette and Hicks, Ramona and Kennedy, David and Leergaard, Trygve and Martone, Maryann and Mou\v{c}ek, Roman and Venugopal, Sharmila and Wachtler, Thomas and Abrams, Mathew}, doi = {10.7490/F1000RESEARCH.1118518.1}, keywords = {FAIR, research software}, title = {Best practices review of five recommendations for {FAIR} software}, year = {2021} } @inproceedings{carver_sustaining_2021, abstract = {Research software is a class of software developed to support research. Today a wealth of such software is created daily in universities, government, and commercial research enterprises worldwide. The sustainability of this software faces particular challenges due, at least in part, to the type of people who develop it. These Research Software Engineers (RSEs) face challenges in developing and sustaining software that differ from those faced by the developers of traditional software. As a result, professional associations have begun to provide support, advocacy, and resources for RSEs. These benefits are critical to sustaining RSEs, especially in environments where their contributions are often undervalued and not rewarded. This paper focuses on how professional associations, such as the United States Research Software Engineer Association (US-RSE), can provide this.}, address = {Los Alamitos, California, USA}, author = {Carver, Jeffrey C. and Cosden, Ian A. and Hill, Chris and Gesing, Sandra and Katz, Daniel S.}, booktitle = {Proceedings of the 2021 {IEEE}/{ACM} {International} {Workshop} on {Body} of {Knowledge} for {Software} {Sustainability} ({BoKSS})}, doi = {10.1109/bokss52540.2021.00016}, isbn = {978-1-6654-4460-6}, keywords = {sustainability, Research software, institutionalization}, month = {June}, publisher = {IEEE}, title = {Sustaining {Research} {Software} via {Research} {Software} {Engineers} and {Professional} {Associations}}, year = {2021} } @article{carver_us-rse_2021, author = {Carver, Jeff and Cosden, Ian and Damerow, Julia and Ferenbaugh, Charles and Gesing, Sandra and Hill, Chris and Katz, Daniel S. and Maimone, Christina and Parsons, Lance}, copyright = {All Rights Reserved}, doi = {10.17613/B7GT-VV31}, keywords = {RSE, association}, language = {en}, title = {The {US}-{RSE} {Association}: {Bringing} {Together} {Research} {Software} {Engineers}}, year = {2021} } @article{chalstrey_developing_2021, abstract = {This report discusses 3 distinct, but overlapping topics. Firstly, it recommends the tools and best practices for research software engineering and data science that are most relevant to the researchers working on the Wales Multimorbidity Machine Learning (WMML) project. Secondly, it expands upon these recommendations for the specific use case of Trusted Research Environments (TREs), with development workflows for computational research in TREs offered that respect and complement existing best practices. Finally, it discusses the considerations around publishing research code that is developed to run within a TRE on sensitive data, offering practical advice that researchers using TREs can follow.}, author = {Chalstrey, Ed}, doi = {10.5281/zenodo.5675093}, keywords = {workflows}, month = {November}, title = {Developing and {Publishing} {Code} for {Trusted} {Research} {Environments}: {Best} {Practices} and {Ways} of {Working}}, year = {2021} } @article{chang_practical_2021, author = {Chang, Hui-Yin and Colby, Sean M. and Du, Xiuxia and Gomez, Javier D. and Helf, Maximilian J. and Kechris, Katerina and Kirkpatrick, Christine R. and Li, Shuzhao and Patti, Gary J. and Renslow, Ryan S. and Subramaniam, Shankar and Verma, Mukesh and Xia, Jianguo and Young, Jamey D.}, doi = {10.1021/acs.analchem.0c03581}, journal = {Analytical Chemistry}, month = {January}, number = {4}, pages = {1912--1923}, title = {A {Practical} {Guide} to {Metabolomics} {Software} {Development}}, volume = {93}, year = {2021} } @inproceedings{chiodini_curated_2021, address = {New York, New York, USA}, author = {Chiodini, Luca and Moreno Santos, Igor and Gallidabino, Andrea and Tafliovich, Anya and Santos, Andr\'{e} L. and Hauswirth, Matthias}, booktitle = {Proceedings of the 26{\textbackslash}textsuperscriptth {ACM} {Conference} on {Innovation} and {Technology} in {Computer} {Science} {Education}}, doi = {10.1145/3430665.3456343}, isbn = {978-1-4503-8214-4}, month = {June}, pages = {380--386}, publisher = {ACM}, title = {A {Curated} {Inventory} of {Programming} {Language} {Misconceptions}}, volume = {1}, year = {2021} } @article{chue_hong_fair_2021, author = {Chue Hong, Neil P. and Katz, Daniel S. and Barker, Michelle and Lamprecht, Anna-Lena and Martinez, Carlos and Psomopoulos, Fotis E. and Harrow, Jen and Castro, Leyla Jael and Gruenpeter, Morane and Martinez, Paula Andrea and Honeyman, Tom}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.15497/RDA00068}, keywords = {FAIR}, language = {en}, title = {{FAIR} {Principles} for {Research} {Software} ({FAIR4RS} {Principles})}, year = {2021} } @article{clausen_learning_2021, author = {Clausen, Jon M.}, doi = {10.1007/s11528-021-00673-x}, journal = {TechTrends}, month = {October}, number = {2}, pages = {276--286}, title = {Learning to {Fly}: {Development} and {Design} of a {Micro}-{Credentialing} {System} for an {Educator} {Preparation} {Program} in the {Absence} of a {Required} {Educational} {Technology} {Course}}, volume = {66}, year = {2021} } @article{cohen_four_2021, author = {Cohen, Jeremy and Katz, Daniel S. and Barker, Michelle and Chue Hong, Neil and Haines, Robert and Jay, Caroline}, copyright = {https://ieeexplore.ieee.org/Xplorehelp/downloads/license-information/IEEE.html}, doi = {10.1109/MS.2020.2973362}, issn = {0740-7459, 1937-4194}, journal = {IEEE Software}, month = {January}, number = {1}, pages = {97--105}, title = {The {Four} {Pillars} of {Research} {Software} {Engineering}}, url = {https://ieeexplore.ieee.org/document/8994167/}, urldate = {2024-11-29}, volume = {38}, year = {2021} } @inproceedings{demchenko_research_2021, address = {Red Hook, New York, USA}, author = {Demchenko, Yuri and Stoy, Lennart}, booktitle = {Proceedings of the 2001 {IEEE} {Global} {Engineering} {Education} {Conference} ({EDUCON})}, doi = {10.1109/educon46332.2021.9453956}, editor = {Klinger, Thomas and Kollmitzer, Christian and Pester, Andreas}, isbn = {978-1-7281-8478-4}, month = {April}, publisher = {IEEE}, title = {Research {Data} {Management} and {Data} {Stewardship} {Competences} in {University} {Curriculum}}, year = {2021} } @article{diewald_lessons_2021, author = {Diewald, Nils and Margaretha, Eliza and Kupietz, Marc}, copyright = {Creative Commons - CC BY - Namensnennung 4.0 International}, doi = {10.14618/IDS-PUB-10469}, keywords = {linguistics}, language = {en}, title = {Lessons learned in quality management for online research software tools in linguistics}, year = {2021} } @article{druskat_research_2021, abstract = {Software citation contributes to achieving software sustainability in two ways: It provides an impact metric to incentivize stakeholders to make software sustainable. It also provides references to software used in research, which can be reused and adapted to become sustainable. While software citation faces a host of technical and social challenges, community initiatives have defined the principles of software citation and are working on implementing solutions.}, author = {Druskat, Stephan and Katz, Daniel S. and Todorov, Ilian T.}, doi = {10.1109/BoKSS52540.2021.00008}, keywords = {sustainability, research software, citation}, month = {March}, title = {Research {Software} {Sustainability} and {Citation}}, year = {2021} } @inproceedings{du_citeas_2021, author = {Du, Caifan and Cohoon, Johanna and Priem, Jason and Piwowar, Heather and Meyer, Casey and Howison, James}, booktitle = {Companion {Publication} of the 2021 {Conference} on {Computer} {Supported} {Cooperative} {Work} and {Social} {Computing}}, doi = {10.1145/3462204.3482889}, keywords = {citation}, month = {October}, publisher = {ACM}, title = {{CiteAs}: {Better} {Software} through {Sociotechnical} {Change} for {Better} {Software} {Citation}}, year = {2021} } @article{eisty_developers_2021, abstract = {Background: Research software is software developed by and/or used by researchers, across a wide variety of domains, to perform their research. Because of the complexity of research software, developers cannot conduct exhaustive testing. As a result, researchers have lower confidence in the correctness of the output of the software. Peer code review, a standard software engineering practice, has helped address this problem in other types of software. Aims: Peer code review is less prevalent in research software than it is in other types of software. In addition, the literature does not contain any studies about the use of peer code review in research software. Therefore, through analyzing developers perceptions, the goal of this work is to understand the current practice of peer code review in the development of research software, identify challenges and barriers associated with peer code review in research software, and present approaches to improve the peer code review in research software. Method: We conducted interviews and a community survey of research software developers to collect information about their current peer code review practices, difficulties they face, and how they address those difficulties. Results: We received 84 unique responses from the interviews and surveys. The results show that while research software teams review a large amount of their code, they lack formal process, proper organization, and adequate people to perform the reviews. Conclusions: Use of peer code review is promising for improving the quality of research software and thereby improving the trustworthiness of the underlying research results. In addition, by using peer code review, research software developers produce more readable and understandable code, which will be easier to maintain.}, author = {Eisty, Nasir U. and Carver, Jeffrey C.}, doi = {10.1007/s10664-021-10053-x}, journal = {Empirical Software Engineering, 27(1), 2022}, keywords = {engineering, code review}, month = {September}, title = {Developers {Perception} of {Peer} {Code} {Review} in {Research} {Software} {Development}}, year = {2021} } @article{fehr_sustainable_2021, author = {Fehr, J. and Himpe, C. and Rave, S. and Saak, J.}, doi = {10.5334/jors.307}, journal = {Journal of Open Research Software}, month = {April}, number = {1}, pages = {5}, title = {Sustainable {Research} {Software} {Hand}-{Over}}, volume = {9}, year = {2021} } @inproceedings{fritzsch_forschungssoftware_2021, abstract = {Research software plays a crucial role in scientific working process. The talk relates the topic to the new rules for good scientific practice and the current developments in Open Science. In addition, the importance of research software in the context of the digitization strategy of Helmholtz association is considered.}, author = {Fritzsch, Bernadette and Konrad, Uwe}, title = {Forschungssoftware im {Kontext} von guter wissenschaftlicher {Praxis}, {Open} {Science} und der {Helmholtz} {Digitalisierungsstrategie}}, year = {2021} } @article{goggins_making_2021, author = {Goggins, Sean P. and Germonprez, Matt and Lumbard, Kevin}, doi = {10.1109/mc.2021.3084015}, issn = {1558-0814}, journal = {Computer}, month = {August}, number = {8}, pages = {104--111}, title = {Making {Open} {Source} {Project} {Health} {Transparent}}, volume = {54}, year = {2021} } @inproceedings{goggins_open_2021, author = {Goggins, Sean and Lumbard, Kevin and Germonprez, Matt}, booktitle = {Proceedings of the 2021 {IEEE}/{ACM} 4{\textbackslash}textsuperscriptth {International} {Workshop} on {Software} {Health} in {Projects}, {Ecosystems} and {Communities} ({SoHeal})}, doi = {10.1109/soheal52568.2021.00010}, isbn = {978-1-6654-4557-3}, month = {May}, pages = {25--33}, publisher = {IEEE}, title = {Open {Source} {Community} {Health}: {Analytical} {Metrics} and {Their} {Corresponding} {Narratives}}, year = {2021} } @article{gomez-diaz_open_2021, author = {Gomez-Diaz, Teresa and Recio, Tomas}, journal = {Research Ideas and Outcomes}, keywords = {Research Software, Infrastructure}, pages = {e63872--e63872}, title = {Open comments on the {Task} {Force} {SIRS} report: {Scholarly} {Infrastructures} for {Research} {Software} ({EOSC} {Executive} {Board}, {EOSCArchitecture})}, volume = {7}, year = {2021} } @article{gruenpeter_defining_2021, author = {Gruenpeter, Morane and Katz, Daniel S. and Lamprecht, Anna-Lena and Honeyman, Tom and Garijo, Daniel and Struck, Alexander and Niehues, Anna and Martinez, Paula Andrea and Castro, Leyla Jael and Rabemanantsoa, Tovo and Chue Hong, Neil P. and Martinez-Ortiz, Carlos and Sesink, Laurents and Liffers, Matthias and Fouilloux, Anne Claire and Erdmann, Chris and Peroni, Silvio and Martinez Lavanchy, Paula and Todorov, Ilian and Sinha, Manodeep}, doi = {10.5281/ZENODO.5504015}, keywords = {academic software, definition, FAIR principles, scientific software, software source code}, title = {Defining {Research} {Software}: a controversial discussion}, year = {2021} } @inproceedings{gutica_fostering_2021, address = {New York, New York, USA}, author = {Gutica, Mirela}, booktitle = {Proceedings of the 26{\textbackslash}textsuperscriptth {ACM} {Conference} on {Innovation} and {Technology} in {Computer} {Science} {Education}}, doi = {10.1145/3430665.3456353}, isbn = {978-1-4503-8214-4}, month = {June}, pages = {471--477}, publisher = {ACM}, title = {Fostering {High} {School} {Girls}' {Interest} and {Attainment} in {Computer} {Science}}, volume = {1}, year = {2021} } @article{haider_realization_2021, author = {Haider, Michael and Riesch, Michael and Jirauschek, Christian}, doi = {10.1007/s11082-021-03192-4}, journal = {Optical and Quantum Electronics}, month = {September}, number = {10}, title = {Realization of best practices in software engineering and scientific writing through ready-to-use project skeletons}, volume = {53}, year = {2021} } @article{haim_gutekriterien_2021, author = {Haim, Mario}, doi = {10.5771/1615-634x-2021-1-65}, journal = {Medien \& Kommunikationswissenschaft}, number = {1}, pages = {65--79}, title = {G\"{u}tekriterien und {Handlungsempfehlungen} f\"{u}r die {Entwicklung} von {Forschungssoftware} in der {Kommunikations}- und {Medienwissenschaft}}, volume = {69}, year = {2021} } @article{harriet_impact_2021, author = {Harriet, Sorrel and Groen, Derek and Crouch, Stephen}, keywords = {management}, month = {July}, title = {On the {Impact} of {Management} and {Process} on {Academic} {Research} {Software}}, year = {2021} } @article{hata_science-software_2021, abstract = {Although computer science papers are often accompanied by software artifacts, connecting research papers to their software artifacts and vice versa is not always trivial. First of all, there is a lack of well-accepted standards for how such links should be provided. Furthermore, the provided links, if any, often become outdated: they are affected by link rot when pre-prints are removed, when repositories are migrated, or when papers and repositories evolve independently. In this paper, we summarize the state of the practice of linking research papers and associated source code, highlighting the recent efforts towards creating and maintaining such links. We also report on the results of several empirical studies focusing on the relationship between scientific papers and associated software artifacts, and we outline challenges related to traceability and opportunities for overcoming these challenges.}, author = {Hata, Hideaki and Guo, Jin L. C. and Kula, Raula Gaikovina and Treude, Christoph}, journal = {arXiv:2104.05891 [cs]}, keywords = {Computer Science - Digital Libraries, Computer Science - Software Engineering}, month = {April}, shorttitle = {Science-{Software} {Linkage}}, title = {Science-{Software} {Linkage}: {The} {Challenges} of {Traceability} between {Scientific} {Knowledge} and {Software} {Artifacts}}, url = {http://arxiv.org/abs/2104.05891}, urldate = {2021-11-20}, year = {2021} } @article{hepp_jenseits_2021, author = {Hepp, Andreas and Loosen, Wiebke and Hasebrink, Uwe}, doi = {10.5771/1615-634x-2021-1-3-1}, journal = {Medien \& Kommunikationswissenschaft}, keywords = {research software, communication science, methods}, number = {1}, pages = {3--24--3--24}, title = {Jenseits des {Computational} {Turn}: {Methodenentwicklung} und {Forschungssoftware} in der {Kommunikations}- und {Medienwissenschaft} – zur {Einf\"{u}hrung} in das {Themenheft}}, volume = {69}, year = {2021} } @article{hong_understanding_2021, abstract = {Research software – specialist software used to support or undertake research – is of huge importance to researchers. It contributes to significant advances in the wider world and requires collaboration between people with diverse skills and backgrounds. Analysis of recent survey data provides evidence for a lack of diversity in the Research Software Engineer community. We identify interventions which could address challenges in the wider research software community and highlight areas where the community is becoming more diverse. There are also lessons that are applicable, more generally, to the field of software development around recruitment from other disciplines and the importance of welcoming communities.}, author = {Hong, Neil P. Chue and Cohen, Jeremy and Jay, Caroline}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.48550/ARXIV.2104.01712}, keywords = {FOS: Computer and information sciences, Software Engineering (cs.SE)}, title = {Understanding {Equity}, {Diversity} and {Inclusion} {Challenges} {Within} the {Research} {Software} {Community}}, url = {https://arxiv.org/abs/2104.01712}, urldate = {2024-11-29}, year = {2021} } @article{hunter-zinck_ten_2021, author = {Hunter-Zinck, Haley and Siqueira, Alexandre Fioravante de and V\'{a}squez, V\'{a}leri N. and Barnes, Richard and Martinez, Ciera C.}, doi = {10.1371/journal.pcbi.1009481}, editor = {Markel, Scott}, journal = {PLOS Computational Biology}, keywords = {open source}, month = {November}, number = {11}, pages = {e1009481}, title = {Ten simple rules on writing clean and reliable open-source scientific software}, volume = {17}, year = {2021} } @incollection{imran_impact_2021, author = {Imran, Asif and Kosar, Tevfik}, booktitle = {Software {Sustainability}}, doi = {10.1007/978-3-030-69970-3_12}, keywords = {people, sustainability}, pages = {287--300}, publisher = {Springer International Publishing}, title = {The {Impact} of {Human} {Factors} on {Software} {Sustainability}}, year = {2021} } @book{irving_research_2021, author = {Irving, Damien and Hertweck, Kate and Johnston, Luke and Ostblom, Joel and Wickham, Charlotte and Wilson, Greg}, doi = {10.1201/9781003143482}, isbn = {978-1-003-14348-2}, keywords = {Python, Research Software, RSE}, publisher = {CRC Press}, title = {Research {Software} {Engineering} with {Python}: {Building} software that makes research possible}, year = {2021} } @article{kasprzak_six_2021, abstract = {The use of Shiny in research publications is investigated. From the appearance of this popular web application framework for R through to 2018, it has been utilised in many diverse research areas. While it can be shown that the complexity of Shiny applications is limited by the background architecture, and real security concerns exist for novice app developers, the collaborative benefits are worth attention from the wider research community. Shiny simplifies the use of complex methodologies for users of different specialities, at the level of proficiency appropriate for the end user. This enables a diverse community of users to interact efficiently, utilising cutting-edge methodologies. The literature reviewed demonstrates that complex methodologies can be put into practice without the necessity for investment in professional training. It would appear that Shiny opens up concurrent benefits in communication between those who analyse data and those in other disciplines, thereby potentially enriching research through this technology.}, author = {Kasprzak, Peter and Mitchell, Lachlan and Kravchuk, Olena and Timmins, Andy}, keywords = {R}, month = {January}, title = {Six {Years} of {Shiny} in {Research} – {Collaborative} {Development} of {Web} {Tools} in {R}}, year = {2021} } @article{katz_addressing_2021, abstract = {Research software is essential to modern research, but it requires ongoing human effort to sustain: to continually adapt to changes in dependencies, to fix bugs, and to add new features. Software sustainability institutes, amongst others, develop, maintain, and disseminate best practices for research software sustainability, and build community around them. These practices can both reduce the amount of effort that is needed and create an environment where the effort is appreciated and rewarded. The UK SSI is such an institute, and the US URSSI and the Australian AuSSI are planning to become institutes, and this extended abstract discusses them and the strengths and weaknesses of this approach.}, author = {Katz, Daniel S. and Carver, Jeffrey C. and Hong, Neil P. Chue and Gesing, Sandra and Hettrick, Simon and Honeyman, Tom and Ram, Karthik and Weber, Nicholas}, doi = {10.1109/BoKSS52540.2021.00013}, keywords = {sustainability, research software, institutionalization}, month = {March}, title = {Addressing {Research} {Software} {Sustainability} via {Institutes}}, year = {2021} } @article{katz_fair4rs_2021, abstract = {The FAIR For Research Software Working Group (FAIR4RS WG) is leading the research software community in the crucial step of agreeing how to apply the FAIR principles to research software, including defining the principles and adoption guidelines. This group was convened under the Research Software Alliance (ReSA), the Research Data Alliance (RDA), and FORCE11 (the Future of Research Communication and Escholarship). This paper explains how the community collaboration to enable this has been built, as an example of a model for teamwork across the research software community, and which could potentially be used in other fields and domains as well, as this is an interdisciplinary and global effort}, author = {Katz, Daniel S. and Barker, Michelle and Chue Hong, Neil P. and Castro, Leyla Jael and Martinez, Paula Andrea}, copyright = {Creative Commons Attribution 4.0 International, Open Access}, doi = {10.5281/ZENODO.5037157}, keywords = {FAIR software, FAIR, collaboration, community, research software}, language = {en}, month = {June}, shorttitle = {The {FAIR4RS} team}, title = {The {FAIR4RS} team: {Working} together to make research software {FAIR}}, url = {https://zenodo.org/record/5037157}, urldate = {2021-11-20}, year = {2021} } @article{katz_fresh_2021, abstract = {This document captures the discussion and deliberation of the FAIR for Research Software (FAIR4RS) subgroup that took a fresh look at the applicability of the FAIR Guiding Principles for scientific data management and stewardship for research software. We discuss the vision of research software as ideally reproducible, open, usable, recognized, sustained and robust, and then review both the characteristic and practiced differences of research software and data. This vision and understanding of initial conditions serves as a backdrop for an attempt at translating and interpreting the guiding principles to more fully align with research software. We have found that many of the principles remained relatively intact as written, as long as considerable interpretation was provided. This was particularly the case for the "Findable" and "Accessible" foundational principles. We found that "Interoperability" and "Reusability" are particularly prone to a broad and sometimes opposing set of interpretations as written. We propose two new principles modeled on existing ones, and provide modified guiding text for these principles to help clarify our final interpretation. A series of gaps in translation were captured during this process, and these remain to be addressed. We finish with a consideration of where these translated principles fall short of the vision laid out in the opening.}, author = {Katz, Daniel S. and Gruenpeter, Morane and Honeyman, Tom and Hwang, Lorraine and Wilkinson, Mark D. and Sochat, Vanessa and Anzt, Hartwig and Goble, Carole and 1, for FAIR4RS Subgroup}, keywords = {FAIR, Open Science}, language = {en}, month = {January}, title = {A {Fresh} {Look} at {FAIR} for {Research} {Software}}, url = {https://arxiv.org/abs/2101.10883v3}, urldate = {2021-02-10}, year = {2021} } @article{katz_recognizing_2021, author = {Katz, Daniel S. and Hong, Neil P. Chue and Clark, Tim and Muench, August and Stall, Shelley and Bouquin, Daina and Cannon, Matthew and Edmunds, Scott and Faez, Telli and Feeney, Patricia and Fenner, Martin and Friedman, Michael and Grenier, Gerry and Harrison, Melissa and Heber, Joerg and Leary, Adam and MacCallum, Catriona and Murray, Hollydawn and Pastrana, Erika and Perry, Katherine and Schuster, Douglas and Stockhause, Martina and Yeston, Jake}, doi = {10.12688/f1000research.26932.2}, journal = {F1000Research}, keywords = {Citation}, month = {January}, pages = {1257--1257}, title = {Recognizing the value of software: a software citation guide}, volume = {9}, year = {2021} } @inproceedings{katz_research_2021, author = {Katz, Daniel and Mchenry, Kenton}, doi = {10.24251/hicss.2021.873}, keywords = {Research Software, Sutainability}, publisher = {Hawaii International Conference on System Sciences}, title = {Research {Software} {Sustainability}: {Lessons} {Learned} at {NCSA}}, year = {2021} } @article{katz_taking_2021, author = {Katz, Daniel S. and Gruenpeter, Morane and Honeyman, Tom}, doi = {10.1016/j.patter.2021.100222}, journal = {Patterns}, keywords = {FAIR, research software}, month = {March}, number = {3}, pages = {100222--100222}, title = {Taking a fresh look at {FAIR} for research software}, volume = {2}, year = {2021} } @article{kendall-morwick_open-source_2021, abstract = {The shared values between free and open source software (FOSS) and those of the academic community have led to increasing adoption of FOSS projects by researchers and instructors in computing fields. Many papers have been written evaluating the pedagogical value of individual FOSS projects and FOSS as a whole. More recently the scholarly value of FOSS has also been explored. This paper bridges the conversations on the scholarly and pedagogical merits of FOSS development and identifies the value of FOSS to helping computing departments in small and regional colleges and universities better support the mission of their institution.}, author = {Kendall-Morwick, Joseph}, issn = {1937-4771}, journal = {J. Comput. Sci. Coll.}, keywords = {open source, open science, research software}, month = {April}, number = {6}, pages = {37--44}, title = {Open-{Source} {Scholarship} at {Teaching}-{Oriented} {Institutions}}, volume = {36}, year = {2021} } @article{khan_future_2021, author = {Khan, Firoz and Kumar, R. Lakshmana and Kadry, Seifedine and Nam, Yunyoung}, doi = {10.11591/ijece.v11i4.pp3443-3450}, issn = {2088-8708}, journal = {International Journal of Electrical and Computer Engineering (IJECE)}, month = {August}, number = {4}, pages = {3443--3450}, title = {The future of software engineering: visions of 2025 and beyond}, volume = {11}, year = {2021} } @article{kim_effects_2021, author = {Kim, Jihoon and Castelli, Darla M.}, doi = {10.3390/ijerph18073550}, issn = {1660-4601}, journal = {International Journal of Environmental Research and Public Health}, month = {March}, number = {7}, pages = {3550}, title = {Effects of {Gamification} on {Behavioral} {Change} in {Education}: {A} {Meta}-{Analysis}}, volume = {18}, year = {2021} } @article{knowles_we_2021, author = {Knowles, Rebecca and Mateen, Bilal A. and Yehudi, Yo}, doi = {10.1038/s43588-021-00048-5}, keywords = {open science, research data, research software}, month = {March}, number = {3}, pages = {169--171--169--171}, title = {We need to talk about the lack of investment in digital research infrastructure}, volume = {1}, year = {2021} } @article{lannelongue_green_2021, abstract = {Abstract Climate change is profoundly affecting nearly all aspects of life on earth, including human societies, economies, and health. Various human activities are responsible for significant greenhouse gas (GHG) emissions, including data centers and other sources of large-scale computation. Although many important scientific milestones are achieved thanks to the development of high-performance computing, the resultant environmental impact is underappreciated. In this work, a methodological framework to estimate the carbon footprint of any computational task in a standardized and reliable way is presented and metrics to contextualize GHG emissions are defined. A freely available online tool, Green Algorithms ( www.green-algorithms.org ) is developed, which enables a user to estimate and report the carbon footprint of their computation. The tool easily integrates with computational processes as it requires minimal information and does not interfere with existing code, while also accounting for a broad range of hardware configurations. Finally, the GHG emissions of algorithms used for particle physics simulations, weather forecasts, and natural language processing are quantified. Taken together, this study develops a simple generalizable framework and freely available tool to quantify the carbon footprint of nearly any computation. Combined with recommendations to minimize unnecessary CO 2 emissions, the authors hope to raise awareness and facilitate greener computation.}, author = {Lannelongue, Lo\"{\i}c and Grealey, Jason and Inouye, Michael}, doi = {10.1002/advs.202100707}, issn = {2198-3844, 2198-3844}, journal = {Advanced Science}, language = {en}, month = {June}, number = {12}, pages = {2100707}, shorttitle = {Green {Algorithms}}, title = {Green {Algorithms}: {Quantifying} the {Carbon} {Footprint} of {Computation}}, url = {https://onlinelibrary.wiley.com/doi/10.1002/advs.202100707}, urldate = {2025-03-01}, volume = {8}, year = {2021} } @article{laporte_not_2021, author = {Laporte, Claude Y. and Munoz, Mirna}, doi = {10.1109/MC.2021.3064438}, journal = {Computer}, number = {5}, pages = {81--88}, title = {Not teaching software engineering standards to future software engineers – malpractice?}, volume = {54}, year = {2021} } @article{lawlor_roles_2021, author = {Lawlor, Brendan and Sleator, Roy D.}, doi = {10.1177/00368504211010570}, journal = {Science Progress}, keywords = {research software, biology}, month = {April}, number = {2}, pages = {003685042110105--003685042110105}, title = {The roles of code in biology}, volume = {104}, year = {2021} } @article{lee_barely_2021, author = {Lee, Graham and Bacon, Sebastian and Bush, Ian and Fortunato, Laura and Gavaghan, David and Lestang, Thibault and Morton, Caroline and Robinson, Martin and Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Webb, Helena}, doi = {10.1016/j.patter.2021.100206}, journal = {Patterns}, keywords = {open science, research software}, month = {February}, number = {2}, pages = {100206--100206}, title = {Barely sufficient practices in scientific computing}, volume = {2}, year = {2021} } @article{leroy_when_2021, author = {Leroy, Dorian and Sallou, June and Bourcier, Johann and Combemale, Benoit}, doi = {10.1109/mc.2021.3102299}, journal = {Computer}, keywords = {engineering}, month = {December}, number = {12}, pages = {60--71}, title = {When {Scientific} {Software} {Meets} {Software} {Engineering}}, volume = {54}, year = {2021} } @article{levet_developing_2021, author = {Levet, Florian and Carpenter, Anne E. and Eliceiri, Kevin W. and Kreshuk, Anna and Bankhead, Peter and Haase, Robert}, doi = {10.12688/f1000research.52531.1}, journal = {F1000Research}, keywords = {open source, research software, biology}, month = {April}, pages = {302--302}, title = {Developing open-source software for bioimage analysis: opportunities and challenges}, volume = {10}, year = {2021} } @incollection{liu_humanities_2021, author = {Liu, Rui and McKay, Dana and Buchanan, George}, booktitle = {Linking {Theory} and {Practice} of {Digital} {Libraries}}, doi = {10.1007/978-3-030-86324-1_25}, keywords = {Digital Humanities}, pages = {215--226--215--226}, publisher = {Springer International Publishing}, title = {Humanities {Scholars} and {Digital} {Humanities} {Projects}: {Practice} {Barriers} in {Tools} {Usage}}, year = {2021} } @inproceedings{lloret-llinares_permedcoe_2021, author = {Lloret-Llinares, Marta and Calb\'{o}, Joaquim and Carbonell-Caballero, Jose and Conejero, Javier and Dorado-Ladera, Esther and Kastelic, Damjana and Matser, Vera and Morales, Ana Mar\'{\i}a and Nortamo, Henrik and Thomas-Lopez, Daniel and Vazquez, Miguel and Villa, Alessandra}, month = {July}, title = {The {PerMedCoE} competency framework to guide the training programme}, url = {https://permedcoe.eu/publication/the-permedcoe-competency-framework-to-guide-the-training-programme/}, year = {2021} } @article{malviya_thakur_dynamics_2021, author = {Malviya Thakur, Addi and Watson, Greg}, doi = {10.13140/RG.2.2.14117.63201}, keywords = {RSE, software engineering}, month = {June}, title = {Dynamics of {Scientific} {Software} {Teams}}, year = {2021} } @inproceedings{maull_expanding_2021, author = {Maull, Keith E. and Mayernik, Matt}, keywords = {Citation}, pages = {23--23}, title = {Expanding {Impact} {Metrics} {Contexts} {With} {Software} {Citation}}, year = {2021} } @article{messerschmidt_checkliste_2021, author = {Messerschmidt, Reinhard and Pampel, Heinz and Bach, Felix and zu Castell, Wolfgang and Denker, Michael and Finke, Ants and Fritzsch, Bernadette and Hammitzsch, Martin and Konrad, Uwe and Leifels, Yvonne and M\"{o}hl, Christoph and Nolden, Marco and Scheinert, Markus and Schlauch, Tobias and Schnicke, Thomas and Steglich, Dirk}, doi = {10.48440/OS.HELMHOLTZ.031}, keywords = {Research Software, Policy}, title = {Checkliste zur {Unterst\"{u}tzung} der {Helmholtz}-{Zentren} bei der {Implementierung} von {Richtlinien} f\"{u}r nachhaltige {Forschungssoftware}}, year = {2021} } @article{milewicz_exploration_2021, abstract = {As a newly designated professional title, research software engineers (RSEs) link the two worlds of software engineering and research science. They lack clear development and training opportunities, particularly in the realm of mentoring. In this paper, we discuss mentorship as it pertains to the unique needs of RSEs and propose ways in which organizations and institutions can support mentor/mentee relationships for RSEs}, author = {Milewicz, Reed and Mundt, Miranda}, keywords = {education, mentoring}, month = {October}, title = {An {Exploration} of the {Mentorship} {Needs} of {Research} {Software} {Engineers}}, year = {2021} } @inproceedings{moldon_how_2021, author = {Moldon, Lukas and Strohmaier, Markus and Wachs, Johannes}, booktitle = {Proceedings of the 2021 {IEEE}/{ACM} 43{\textbackslash}textsuperscriptrd {International} {Conference} on {Software} {Engineering} ({ICSE})}, doi = {10.1109/icse43902.2021.00058}, isbn = {978-1-6654-0296-5}, month = {May}, publisher = {IEEE}, title = {How {Gamification} {Affects} {Software} {Developers}: {Cautionary} {Evidence} from a {Natural} {Experiment} on {GitHub}}, year = {2021} } @article{moore_ten_2021, author = {Moore, Benjamin and Carvajal-L\'{o}pez, Patricia and Chauke, Paballo Abel and Cristancho, Marco and Dominguez Del Angel, Victoria and Fernandez-Valverde, Selene L. and Ghouila, Amel and Gopalasingam, Piraveen and Guerfali, Fatma Zahra and Matimba, Alice and Morgan, Sarah L. and Oliveira, Guilherme and Ras, Verena and Reyes, Alejandro and De Las Rivas, Javier and Mulder, Nicola}, doi = {10.1371/journal.pcbi.1009218}, editor = {Markel, Scott}, journal = {PLOS Computational Biology}, month = {August}, number = {8}, pages = {e1009218}, title = {Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries}, volume = {17}, year = {2021} } @article{nust_codecheck_2021, author = {N\"{u}st, Daniel and Eglen, Stephen J.}, doi = {10.12688/f1000research.51738.2}, journal = {F1000Research}, keywords = {reproducibility, research software, peer review}, month = {July}, pages = {253--253}, title = {{CODECHECK}: an {Open} {Science} initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility}, volume = {10}, year = {2021} } @article{orduna-malea_link-based_2021, author = {Ordu\~{n}a-Malea, Enrique and Costas, Rodrigo}, doi = {10.1007/s11192-021-04082-y}, journal = {Scientometrics}, keywords = {usage}, month = {July}, number = {9}, pages = {8153--8186}, title = {Link-based approach to study scientific software usage: the case of {VOSviewer}}, volume = {126}, year = {2021} } @article{ozkaya_future_2021, author = {Ozkaya, Ipek}, doi = {10.1109/MS.2021.3089729}, journal = {IEEE Software}, number = {5}, pages = {3--6}, title = {The future of software engineering work}, volume = {38}, year = {2021} } @article{pereira_ranking_2021, author = {Pereira, Rui and Couto, Marco and Ribeiro, Francisco and Rua, Rui and Cunha, J\'{a}come and Fernandes, Jo\~{a}o Paulo and Saraiva, Jo\~{a}o}, doi = {10.1016/j.scico.2021.102609}, journal = {Science of Computer Programming}, month = {May}, pages = {102609}, title = {Ranking programming languages by energy efficiency}, volume = {205}, year = {2021} } @article{poirier_exploring_2021, author = {Poirier, Therese I. and Weis, Logan}, doi = {10.1016/j.cptl.2021.01.004}, journal = {Currents in Pharmacy Teaching and Learning}, month = {May}, number = {5}, pages = {506--511}, title = {Exploring pharmacy students' interest in digital badges}, volume = {13}, year = {2021} } @article{reinecke_community_2021, author = {Reinecke, Robert and Trautmann, Tim and Wagener, Thorsten and Sch\"{u}ler, Katja}, doi = {10.5194/egusphere-egu21-801}, keywords = {research software, hydrology}, month = {March}, title = {A {Community} {Perspective} on {Research} {Software} in the {Hydrological} {Sciences}}, year = {2021} } @article{reinhart_expanding_2021, author = {Reinhart, Alex and Genovese, Christopher R.}, doi = {10.1080/10691898.2020.1845109}, journal = {Journal of Statistics and Data Science Education}, month = {January}, number = {sup1}, pages = {S7--S15}, title = {Expanding the {Scope} of {Statistical} {Computing}: {Training} {Statisticians} to {Be} {Software} {Engineers}}, volume = {29}, year = {2021} } @article{sanchez_best_2021, abstract = {The world is becoming increasingly complex, both in terms of the rich sources of data we have access to as well as in terms of the statistical and computational methods we can use on those data. These factors create an ever-increasing risk for errors in our code and sensitivity in our findings to data preparation and execution of complex statistical and computing methods. The consequences of coding and data mistakes can be substantial. Openness (e.g., providing others with data code) and transparency (e.g., requiring that data processing and code follow standards) are two key solutions to help alleviate concerns about replicability and errors. In this paper, we describe the key steps for implementing a code quality assurance (QA) process for researchers to follow to improve their coding practices throughout a project to assure the quality of the final data, code, analyses and ultimately the results. These steps include: (i) adherence to principles for code writing and style that follow best practices, (ii) clear written documentation that describes code, workflow and key analytic decisions; (iii) careful version control, (iv) good data management; and (iv) regular testing and review. Following all these steps will greatly improve the ability of a study to assure results are accurate and reproducible. The responsibility for code QA falls not only on individual researchers but institutions, journals, and funding agencies as well.}, author = {Sanchez, Ricardo and Griffin, Beth Ann and Pane, Joseph and McCaffrey, Daniel}, keywords = {Statistics}, month = {January}, title = {Best {Practices} in {Statistical} {Computing}}, year = {2021} } @inproceedings{saraiva_bringing_2021, address = {New York, New York, USA}, author = {Saraiva, Jo\~{a}o and Zong, Ziliang and Pereira, Rui}, booktitle = {Proceedings of the 26{\textbackslash}textsuperscriptth {ACM} {Conference} on {Innovation} and {Technology} in {Computer} {Science} {Education}}, doi = {10.1145/3430665.3456386}, isbn = {978-1-4503-8214-4}, month = {June}, pages = {498--504}, publisher = {ACM}, title = {Bringing {Green} {Software} to {Computer} {Science} {Curriculum}: {Perspectives} from {Researchers} and {Educators}}, volume = {1}, year = {2021} } @article{schmitz_advancing_2021, author = {Schmitz, Patrick and Yockel, Scott and Mizumoto, Claire and Cheatham, Thomas and Brunson, Dana}, doi = {10.1109/mcse.2021.3098421}, journal = {Computing in Science \& Engineering}, keywords = {human resource, RSE}, month = {September}, number = {5}, pages = {19--27}, title = {Advancing the {Workforce} {That} {Supports} {Computationally} and {Data} {Intensive} {Research}}, volume = {23}, year = {2021} } @article{shanahan_progress_2021, author = {Shanahan, Hugh and Hoebelheinrich, Nancy and Whyte, Angus}, doi = {10.1016/j.patter.2021.100324}, issn = {2666-3899}, journal = {Patterns}, month = {October}, number = {10}, pages = {100324}, title = {Progress toward a comprehensive teaching approach to the {FAIR} data principles}, volume = {2}, year = {2021} } @article{sharma_appraisal_2021, author = {Sharma, Smriti and Bhatia, Vinayak}, doi = {10.2174/1574893616666210609094743}, journal = {Current Bioinformatics}, month = {November}, number = {9}, pages = {1117--1125}, title = {An {Appraisal} of {Skill} {Gaps} in {Bioinformatics} {Education}}, volume = {16}, year = {2021} } @article{smith_raising_2021, author = {Smith, Spencer and Sayari Nejad, Mojdeh and Wassyng, Alan}, doi = {10.1109/mcse.2020.3019770}, issn = {1558-366X}, journal = {Computing in Science \& Engineering}, month = {January}, number = {1}, pages = {47--57}, title = {Raising the {Bar}: {Assurance} {Cases} for {Scientific} {Software}}, volume = {23}, year = {2021} } @article{sufi_rise_2021, abstract = {Research Software Engineering is the application of professional software skills to research problems. Those who do this are called Research Software Engineers or RSEs for short. RSEs work closely with researchers in a collaborative fashion rather than just offering a standalone function (c.f. the traditional IT workforce or Librarians working to provide a general set of services to the University community such as research, teaching or administrative functions). It is this overlap with academic researchers that make the RSE and the RSE management a new type of third space professional in the higher education sector. We explore aspects of knowledge, relationships, legitimacies and language in relation to the model constructed by Whitchurch in Reconstructing Identities in Higher Education to explore how these relate to the RSE role and go on to highlight open problems that need resolving to put RSEs on a firmer organisational footing.}, author = {Sufi, Shoaib}, keywords = {research software, institutionalization}, month = {March}, title = {The {Rise} of a {New} {Digital} {Third} {Space} {Professional} in {Higher} {Education}: {Recognising} {Research} {Software} {Engineering}}, year = {2021} } @inproceedings{venters_software_2021, author = {Venters, Colin C. and Kocak, Sedef Akinli and Betz, Stefanie and Brooks, Ian and Capilla, Rafael and Chitchyan, Ruzanna and Duboc, Leticia and Heldal, Rogardt and Moreira, Ana and Oyedeji, Shola and Penzenstadler, Birgit and Porras, Jari and Seyff, Norbert}, booktitle = {2021 {IEEE}/{ACM} {International} {Workshop} on {Body} of {Knowledge} for {Software} {Sustainability} ({BoKSS})}, doi = {10.1109/bokss52540.2021.00009}, keywords = {sustainability}, month = {June}, publisher = {IEEE}, title = {Software {Sustainability}: {Beyond} the {Tower} of {Babel}}, year = {2021} } @article{von_nordheim_entwicklung_2021, author = {von Nordheim, Gerret and Koppers, Lars and Boczek, Karin and Rieger, Jonas and Jentsch, Carsten and M\"{u}ller, Henrik and Rahnenf\"{u}hrer, J\"{o}rg}, doi = {10.5771/1615-634x-2021-1-80}, journal = {Medien \& Kommunikationswissenschaft}, number = {1}, pages = {80--96}, title = {Die {Entwicklung} von {Forschungssoftware} als praktische {Interdisziplinarit\"{a}t}}, volume = {69}, year = {2021} } @article{vrana_aquarium_2021, author = {Vrana, Justin and de Lange, Orlando and Yang, Yaoyu and Newman, Garrett and Saleem, Ayesha and Miller, Abraham and Cordray, Cameron and Halabiya, Samer and Parks, Michelle and Lopez, Eriberto and Goldberg, Sarah and Keller, Benjamin and Strickland, Devin and Klavins, Eric}, doi = {10.1093/synbio/ysab006}, journal = {Synthetic Biology}, keywords = {open source, research software, data management}, month = {January}, number = {1}, title = {Aquarium: open-source laboratory software for design, execution and data management}, volume = {6}, year = {2021} } @article{woodley_cscce_2021, abstract = {{\textbackslash}textlessstrong{\textbackslash}textgreaterContext for this profile{\textbackslash}textless/strong{\textbackslash}textgreater CSCCE Community Profiles provide a snapshot of scientific communities. The data for these profiles were collected by surveying scientific community managers as part of a research project conducted by CSCCE staff. This profile showcases the FAIR for Research Software (FAIR4RS) Working Group, and is part of a second collection of profiles published in July 2021. You can view and download all of the CSCCE Community Profiles, including those in the first collection that was published in 2020, here. If you would like CSCCE to create a profile for your scientific community or organization, please contact us: info\@cscce.org. {\textbackslash}textlessstrong{\textbackslash}textgreaterAbout CSCCE{\textbackslash}textless/strong{\textbackslash}textgreater The Center for Scientific Collaboration and Community Engagement (CSCCE) champions the importance of human infrastructure for effective collaboration in STEM. We provide training and support for the people who make scientific collaborations succeed at scale - and we also research the impact of these emerging roles. Find out more about us on our website: CSCCE.org}, author = {Woodley, Lou and Pratt, Katie and Kobilka, Sara and Martinez, Paula Andrea}, copyright = {Open Access}, doi = {10.5281/ZENODO.5019939}, keywords = {FAIR, FAIR4RS, CSCCE, CSCCE Community Profile, Describing STEM Communities}, month = {July}, shorttitle = {{CSCCE} {Community} {Profile}}, title = {{CSCCE} {Community} {Profile}: {The} {FAIR} for {Research} {Software} ({FAIR4RS}) {Working} {Group}}, url = {https://zenodo.org/record/5019939}, urldate = {2021-11-20}, year = {2021} } @article{yoshii_what_2021, abstract = {We are entering the post-Moore era where we no longer enjoy the free ride of the performance growth from simply shrinking the transistor features. However, this does not necessarily mean that we are entering a dark era of computing. On the contrary, sustaining the performance growth of computing in the post-Moore era itself is cutting-edge research. Concretely, heterogeneity and hardware specialization are becoming promising approaches in hardware designs. However, these are paradigm shifts in computer architecture. So what does the post-Moore era mean for research software engineering? This position paper addresses such a question by summarizing possible challenges and opportunities for research software engineering in the post-Moore era. We then briefly discuss what is missing and how we prepare to tackle such challenges and exploit opportunities for the future of computing.}, author = {Yoshii, Kazutomo}, keywords = {sustainability}, month = {November}, title = {What {Does} the {Post}-{Moore} {Era} {Mean} for {Research} {Software} {Engineering}?}, year = {2021} } @inproceedings{acker_emulation_2020, author = {Acker, Amelia}, keywords = {Digital Archive}, title = {Emulation {Encounters}: {Software} {Preservation} in {Libraries}, {Archives}, and {Museums}}, year = {2020} } @article{albani_ever-est_2020, author = {Albani, Mirko and Leone, Rosemarie and Foglini, Federica and De Leo, Francesco and Marelli, Fulvio and Maggio, Iolanda}, doi = {10.5334/dsj-2020-021}, issn = {1683-1470}, journal = {Data Science Journal}, keywords = {FAIR other contexts}, language = {en}, month = {May}, pages = {21}, shorttitle = {{EVER}-{EST}}, title = {{EVER}-{EST}: {The} {Platform} {Allowing} {Scientists} to {Cross}-{Fertilize} and {Cross}-{Validate} {Data}}, url = {http://datascience.codata.org/articles/10.5334/dsj-2020-021/}, urldate = {2020-10-25}, volume = {19}, year = {2020} } @inproceedings{allen_best_2020, abstract = {Software citation is good for research transparency and reproducibility, and maybe, if you work it right, for your CV, too. You can get credit and recognition through citations for your code! This presentation highlights several powerful methods for increasing the probability that use of your research software will be cited, and cited correctly. The presentation covers how to create codemeta.json and CITATION.cff automagically from Astrophysics Source Code Library (ASCL ascl.net) entries, edit, and use these files, the value of including such files on your code site(s), and efforts underway in astronomy and other fields to improve software citation and credit.}, author = {Allen, A. and Nemiroff, R. and Ryan, P. and Schmidt, J. and Teuben, P.}, keywords = {Citation}, month = {January}, pages = {10912--10912}, title = {Best ways to let others know how to cite your research software}, year = {2020} } @article{allen_making_2020, abstract = {Software is the most used instrument in astronomy, and organizations such as NASA and the Heidelberg Institute for Theoretical Physics (HITS) fund, develop, and release research software. NASA, for example, has created sites such as code.nasa.gov to share its software with the world, but how easy is it to see what NASA has? Until recently, searching NASA's Astrophysics Data System (ADS) for NASA astronomy research software has not been fruitful. Through its ADAP program, NASA funded the Astrophysics Source Code Library to improve the discoverability of these codes. Adding institutional tags to ASCL entries makes it easy to find this software not only in the ASCL but also in ADS and other services that index the ASCL. This presentation covered the changes the ASCL made as a result of this funding and how you can use the results of this work to better find organizational software in ASCL and ADS.}, author = {Allen, Alice and Mavuram, Siddha and Nemiroff, Robert J. and Schmidt, Judy and Teuben, Peter}, doi = {https://doi.org/10.48550/arXiv.2012.12526}, keywords = {Research Software, Seeking}, month = {December}, title = {Making organizational software easier to find in {ASCL} and {ADS}}, year = {2020} } @article{alliez_attributing_2020, abstract = {Software is a fundamental pillar of modern scientific research, across all fields and disciplines. However, there is a lack of adequate means to cite and reference software due to the complexity of the problem in terms of authorship, roles, and credits. This complexity is further increased when it is considered over the lifetime of a software that can span up to several decades. Building upon the internal experience of Inria, the French research institute for digital sciences, we provide in this article a contribution to the ongoing efforts in order to develop proper guidelines and recommendations for software citation and reference. Namely, we recommend: first, a richer taxonomy for software contributions with a qualitative scale; second, to put humans at the heart of the evaluation; and third, to distinguish citation from reference.}, author = {Alliez, Pierre and Cosmo, Roberto Di and Guedj, Benjamin and Girault, Alain and Hacid, Mohand-Sa\"{\i}d and Legrand, Arnaud and Rougier, Nicolas}, doi = {10.1109/MCSE.2019.2949413}, issn = {1558-366X}, journal = {Computing in Science Engineering}, keywords = {software engineering, Guidelines, Metadata, Libraries, attributing software, authorship, Best practices, citation analysis, Complexity theory, development process, digital sciences, French research institute, Inria, reference software, Research and development, software citation, Software citation, Software packages, software reference}, month = {October}, number = {1}, pages = {39--52}, shorttitle = {Attributing and {Referencing} ({Research}) {Software}}, title = {Attributing and {Referencing} ({Research}) {Software}: {Best} {Practices} and {Outlook} {From} {Inria}}, volume = {22}, year = {2020} } @article{anzt_environment_2020, abstract = {Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.}, author = {Anzt, Hartwig and Bach, Felix and Druskat, Stephan and L\"{o}ffler, Frank and Loewe, Axel and Renard, Bernhard Y. and Seemann, Gunnar and Struck, Alexander and Achhammer, Elke and Aggarwal, Piush and Appel, Franziska and Bader, Michael and Brusch, Lutz and Busse, Christian and Chourdakis, Gerasimos and Dabrowski, Piotr W. and Ebert, Peter and Flemisch, Bernd and Friedl, Sven and Fritzsch, Bernadette and Funk, Maximilian D. and Gast, Volker and Goth, Florian and Grad, Jean-No\"{e}l and Hermann, Sibylle and Hohmann, Florian and Janosch, Stephan and Kutra, Dominik and Linxweiler, Jan and Muth, Thilo and Peters-Kottig, Wolfgang and Rack, Fabian and Raters, Fabian H. C. and Rave, Stephan and Reina, Guido and Rei\ss{}ig, Malte and Ropinski, Timo and Schaarschmidt, Joerg and Seibold, Heidi and Thiele, Jan P. and Uekerman, Benjamin and Unger, Stefan and Weeber, Rudolf}, doi = {10/ggx4z2}, journal = {F1000Research 2020}, keywords = {Germany, Sustainability}, month = {April}, title = {An {Environment} for {Sustainable} {Research} {Software} in {Germany} and {Beyond}: {Current} {State}, {Open} {Challenges}, and {Call} for {Action}}, year = {2020} } @article{arvanitou_software_2020, author = {Arvanitou, Elvira-Maria and Ampatzoglou, Apostolos and Chatzigeorgiou, Alexander and Carver, Jeffrey C.}, journal = {Journal of Systems and Software}, keywords = {Software Engineering}, pages = {110848--110848}, title = {Software engineering practices for scientific software development: {A} systematic mapping study}, year = {2020} } @article{bain_design_2020, author = {Bain, Stevie A. and Meagher, Thomas R. and Barker, Daniel}, doi = {10.1080/00219266.2020.1858932}, journal = {Journal of Biological Education}, month = {December}, number = {5}, pages = {570--580}, title = {Design, delivery and evaluation of a bioinformatics education workshop for 13-16-year-olds}, volume = {56}, year = {2020} } @article{barnhart_short_2020, author = {Barnhart, Katherine R. and Hutton, Eric W. H. and Tucker, Gregory E. and Gasparini, Nicole M. and Istanbulluoglu, Erkan and Hobley, Daniel E. J. and Lyons, Nathan J. and Mouchene, Margaux and Nudurupati, Sai Siddhartha and Adams, Jordan M. and Bandaragoda, Christina}, doi = {10.5194/esurf-2020-12}, keywords = {Python, Geo Science}, month = {March}, title = {Short communication: {Landlab} v2.0: {A} software package for {Earth} surface dynamics}, year = {2020} } @article{beard_tess_2020, author = {Beard, Niall and Bacall, Finn and Nenadic, Aleksandra and Thurston, Milo and Goble, Carole A. and Sansone, Susanna-Assunta and Attwood, Teresa K.}, doi = {10.1093/bioinformatics/btaa047}, editor = {Wren, Jonathan}, journal = {Bioinformatics}, month = {February}, number = {10}, pages = {3290--3291}, title = {{TeSS}: a platform for discovering life-science training opportunities}, volume = {36}, year = {2020} } @inproceedings{behroozi_does_2020, address = {New York, USA}, author = {Behroozi, Mahnaz and Shirolkar, Shivani and Barik, Titus and Parnin, Chris}, booktitle = {Proceedings of the 28{\textbackslash}textsuperscriptth {ACM} joint meeting on {European} {Software} {Engineering} {Conference} and symposium on the {Foundations} of {Software} {Engineering} ({ESEC}/{FSE} 2020)}, doi = {10.1145/3368089.3409712}, isbn = {978-1-4503-7043-1}, month = {November}, pages = {481--492}, publisher = {Association for Computing Machinery}, title = {Does stress impact technical interview performance?}, year = {2020} } @inproceedings{benthall_software_2020, author = {Benthall, Sebastian and Seth, Mridul}, keywords = {Python}, title = {Software {Engineering} as {Research} {Method}: {Aligning} {Roles} in {Econ}-{ARK}}, year = {2020} } @article{bercic_deep_2020, abstract = {{\textbackslash}textlesssection class="abstract"{\textbackslash}textgreater{\textbackslash}textlessh2 class="abstractTitle text-title my-1" id="d705e2"{\textbackslash}textgreaterAbstract{\textbackslash}textless/h2{\textbackslash}textgreater{\textbackslash}textlessp{\textbackslash}textgreaterIn this article, we analyze the state of research data in mathematics. We find that while the mathematical community embraces the notion of open data, the FAIR principles are not yet sufficiently realized. Indeed, we claim that the case of mathematical data is special, since the objects of interest are abstract (all properties can be known) and complex (they have a rich inner structure that must be represented). We present a novel classification of mathematical data and derive an extended set of FAIR requirements, which accomodate the special needs of math datasets. We summarize these as {\textbackslash}textlessstrong{\textbackslash}textgreaterdeep FAIR{\textbackslash}textless/strong{\textbackslash}textgreater. Finally, we show a prototypical system infrastructure, which can realize deep FAIRness for one category (tabular data) of mathematical datasets.{\textbackslash}textless/p{\textbackslash}textgreater{\textbackslash}textless/section{\textbackslash}textgreater}, author = {Ber\v{c}i\v{c}, Katja and Kohlhase, Michael and Rabe, Florian}, doi = {10.1515/itit-2019-0028}, issn = {1611-2776, 2196-7032}, journal = {it - Information Technology}, keywords = {FAIR practice}, language = {en}, month = {February}, number = {1}, pages = {7--17}, title = {({Deep}) {FAIR} mathematics}, url = {https://www.degruyter.com/view/journals/itit/62/1/article-p7.xml}, urldate = {2020-05-12}, volume = {62}, year = {2020} } @article{bezuidenhout_varying_2020, author = {Bezuidenhout, Louise and Havemann, Johanna}, doi = {10.12688/f1000research.26615.1}, journal = {F1000Research}, keywords = {Open Science, Open Source}, month = {November}, pages = {1292--1292}, title = {The varying openness of digital open science tools}, volume = {9}, year = {2020} } @article{bierwirth_leipzig-berlin-erklarung_2020, author = {Bierwirth, Maik and Gl\"{o}ckner, Frank Oliver and Grimm, Christian and Schimmler, Sonja and Boehm, Franziska and Busse, Christian and Degkwitz, Andreas and Koepler, Oliver and Neuroth, Heike}, doi = {10.5281/ZENODO.3895209}, keywords = {Forschungsdaten, NFDI}, title = {Leipzig-{Berlin}-{Erkl\"{a}rung} zu {NFDI}-{Querschnittsthemen} der {Infrastrukturentwicklung}}, year = {2020} } @inproceedings{bird_software_2020, author = {Bird, Ian and Campana, Simone and Vila, Pere Mato and Roiser, Stefan and Schulz, Markus and Stewart, Graeme A. and Valassi, Andrea}, keywords = {Research Software, Data Management, Software sustainability institute}, pages = {08020--08020}, title = {A {Software} {Institute} for {Data}-{Intensive} {Sciences}, {Joining} {Computer} {Science} {Academia} and {Natural} {Science} {Research}}, volume = {245}, year = {2020} } @article{bobra_survey_2020, abstract = {The SunPy Project developed a 13-question survey to understand the software and hardware usage of the solar physics community. 364 members of the solar physics community, across 35 countries, responded to our survey. We found that 99\pm{}0.5\% of respondents use software in their research and 66\% use the Python scientific software stack. Students are twice as likely as faculty, staff scientists, and researchers to use Python rather than Interactive Data Language (IDL). In this respect, the astrophysics and solar physics communities differ widely: 78\% of solar physics faculty, staff scientists, and researchers in our sample uses IDL, compared with 44\% of astrophysics faculty and scientists sampled by Momcheva and Tollerud (2015). 63\pm{}4\% of respondents have not taken any computer-science courses at an undergraduate or graduate level. We also found that most respondents utilize consumer hardware to run software for solar-physics research. Although 82\% of respondents work with data from space-based or ground-based missions, some of which (e.g. the Solar Dynamics Observatory and Daniel K. Inouye Solar Telescope) produce terabytes of data a day, 14\% use a regional or national cluster, 5\% use a commercial cloud provider, and 29\% use exclusively a laptop or desktop. Finally, we found that 73\pm{}4\% of respondents cite scientific software in their research, although only 42\pm{}3\% do so routinely.}, author = {Bobra, Monica G. and Mumford, Stuart J. and Hewett, Russell J. and Christe, Steven D. and Reardon, Kevin and Savage, Sabrina and Ireland, Jack and Pereira, Tiago M. D. and Chen, Bin and P\'{e}rez-Su\'{a}rez, David}, doi = {10.1007/s11207-020-01622-2}, journal = {Solar Physics}, keywords = {Physik, Survey}, month = {April}, number = {4}, pages = {57--57}, title = {A {Survey} of {Computational} {Tools} in {Solar} {Physics}}, volume = {295}, year = {2020} } @article{brian_place_2020, abstract = {This paper aims to bridge Digital Humanities (DH) and Research Software Engineering (RSE) communities. It argues that the production of models is the core contribution of RSE to the epistemology of DH. We adopt an inclusive definition of models and modelling (Ciula et al. 2018) which spans the whole range from {\textbackslash}textbackslashtextquoteleftdeformative{\textbackslash}textbackslashtextquoteright to empirical modelling (Smithies 2017: 168), including formal or predictive modelling (Joslyn and Turchin 1993), and the technical solutions produced in the process as well as the know-how, languages and documentation which accompany this production. From this wide perspective, models are also artefacts which can be studied across the history of science and of the humanities tradition (Bod 2018) and in comparison with other modelling practices in science. RSE practice is grounded on a strong conscience of the experimental apparatus and the iterative critique of models built (and often deflated) for a purpose. The challenge is to recognise the idiosyncrasy and situatedness of modelling practices and artefacts while devising methods to expose the scalability of the underlying workflows and modelling processes. We reflect on the epistemology of DH from the practical perspective of our RSE lab - King{\textbackslash}textbackslashtextquoterights Digital Lab (KDL) - and the research processes embedded in our Software Development Lifecycle. The human element is at the core of the technical ecosystem we research and operate in. We acknowledge that KDL models and modelling are co-constitutive of human expertise, technical systems and operational methods, all aspiring to an environment conducive of open knowledge. We use project-specific examples, including data modelling and knowledge representation practices, to demonstrate how some of our research into model-making processes challenge the perception of the technical work of RSE within DH as a stale, mechanistic and uncritical procedural activity.}, author = {Brian, Maher and Ciula, Arianna and Geoffroy, No\"{e}l and Ginestra, Ferraro and Miguel, Vieira and Paul, Caton}, doi = {10.17613/789Z-9P59}, keywords = {Digital Humanities, Modellierung}, title = {The place of models and modelling in {Digital} {Humanities}: {Intersections} with a {Research} {Software} {Engineering} perspective}, year = {2020} } @article{brito_recommendations_2020, author = {Brito, Jaqueline J. and Li, Jun and Moore, Jason H. and Greene, Casey S. and Nogoy, Nicole A. and Garmire, Lana X. and Mangul, Serghei}, doi = {10.1093/gigascience/giaa056}, journal = {GigaScience}, month = {June}, number = {6}, title = {Recommendations to enhance rigor and reproducibility in biomedical research}, volume = {9}, year = {2020} } @article{busse_fair_2020, author = {Busse, Christian E.}, doi = {10.5281/ZENODO.3947104}, keywords = {FAIR}, title = {{FAIR}, {FLOSS} and {Sustainable}: {Complementary} {Paradigms} for {Research} {Software}}, year = {2020} } @article{canales-negron_principios_2020, author = {Canales-Negr\'{o}n, Ismael}, doi = {10.19083/ridu.2020.1170}, issn = {2223-2516}, journal = {Revista Digital de Investigaci\'{o}n en Docencia Universitaria}, month = {November}, number = {2}, pages = {e1170}, title = {Principios de dise\~{n}o de insignias digitales en programas de educaci\'{o}n continua profesional: una revisi\'{o}n exploratoria}, volume = {14}, year = {2020} } @inproceedings{carvalho_discussion_2020, author = {Carvalho, Rui and Silva, A.}, keywords = {Sustainability}, title = {Discussion {Towards} a {Library} of {Software} {Sustainability} {Requirements}}, year = {2020} } @inproceedings{castro_software_2020, author = {Castro, Leyla Jael Garcia and Barker, Michelle and Hong, Neil P. Chue and Psomopoulos, Fotis and Harrow, Jennifer and Katz, Daniel S. and Kuzak, Mateusz and Martinez, Paula Andrea and Via, Allegra}, keywords = {Research Software, Institutionalization}, title = {Software as a first-class citizen in research}, year = {2020} } @article{cereceda_graduate_2020, author = {Cereceda, Oihane and Quinn, Danielle E. A.}, doi = {10.1139/facets-2019-0020}, editor = {Clendinneng, Debra}, journal = {FACETS}, month = {January}, number = {1}, pages = {289--303}, title = {A graduate student perspective on overcoming barriers to interacting with open-source software}, volume = {5}, year = {2020} } @article{chassanoff_curation_2020, author = {Chassanoff, Alexandra and Altman, Micah}, doi = {10.1002/asi.24244}, issn = {2330-1635, 2330-1643}, journal = {Journal of the Association for Information Science and Technology}, language = {en}, month = {March}, number = {3}, pages = {325--337}, shorttitle = {Curation as ``{Interoperability} {With} the {Future}''}, title = {Curation as ``{Interoperability} {With} the {Future}'': {Preserving} {Scholarly} {Research} {Software} in {Academic} {Libraries}}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/asi.24244}, urldate = {2020-10-25}, volume = {71}, year = {2020} } @article{cheung_figure_2020, author = {Cheung, Foo}, doi = {10/ggzwsf}, journal = {Journal of Open Research Software}, keywords = {Experiments, Visualization}, title = {A {Figure} {One} {Web} {Tool} for {Visualization} of {Experimental} {Designs}}, volume = {8}, year = {2020} } @article{cohen_rses_2020, abstract = {The term Research Software Engineer (RSE) was first used in the UK research community in 2012 to refer to individuals based in research environments who focus on the development of software to support and undertake research. Since then, the term has gained wide adoption and many RSE groups and teams have been set up at institutions within the UK and around the world. There is no "manual" for establishing an RSE group! These groups are often set up in an ad hoc manner based on what is practical within the context of each institution. Some of these groups are based in a central IT environment, others are based in research groups in academic departments. Is one option better than another? What are the pros and cons of different options? In this position paper we look at some arguments for where RSE teams fit best within academic institutions and research organisations and consider whether there is an ideal "home" for RSEs.}, author = {Cohen, Jeremy and Woodbridge, Mark}, keywords = {Research Software, Professionalization}, month = {October}, title = {{RSEs} in {Research}? {RSEs} in {IT}?: {Finding} a suitable home for {RSEs}}, year = {2020} } @article{cosmo_announcing_2020, author = {Cosmo, Roberto Di}, doi = {10.1145/3417564.3417570}, journal = {ACM SIGSOFT Software Engineering Notes}, keywords = {Citation}, month = {October}, number = {4}, pages = {22--23--22--23}, title = {Announcing biblatex-software}, volume = {45}, year = {2020} } @article{cosmo_referencing_2020, author = {Cosmo, Roberto Di and Gruenpeter, Morane and Zacchiroli, Stefano}, doi = {10/ggzwsg}, journal = {Computing in Science \& Engineering}, keywords = {Citation, Citation analysis, Cryptography, data citation toolchains, digital identifiers, digital objects, external third parties, integrity checking, Object recognition, program verification, reference source code, scientific reproducibility, Semantics, software citation, Software Heritage project, software source code artifacts, software tools, Software tools, source code (software), source code files, Source coding, Syntactics, Uniform resource locators}, month = {March}, number = {2}, pages = {33--43--33--43}, title = {Referencing {Source} {Code} {Artifacts}: {A} {Separate} {Concern} in {Software} {Citation}}, volume = {22}, year = {2020} } @inproceedings{couto_energy_2020, address = {New York, New York, USA}, author = {Couto, Marco and Maia, Daniel and Saraiva, Jo\~{a}o and Pereira, Rui}, booktitle = {Proceedings of the 3{\textbackslash}textsuperscriptrd {International} {Conference} on {Technical} {Debt}}, doi = {10.1145/3387906.3388628}, isbn = {978-1-4503-7960-1}, month = {September}, pages = {62--66}, publisher = {Association for Computing Machinery}, title = {On {Energy} {Debt}: {Managing} {Consumption} on {Evolving} {Software}}, year = {2020} } @article{davenport_data_2020, author = {Davenport, James Harold and Grant, James and Jones, Catherine Mary}, doi = {10/ggzwsh}, journal = {Data Science Journal}, keywords = {Research Data}, title = {Data {Without} {Software} {Are} {Just} {Numbers}}, volume = {19}, year = {2020} } @article{davidson_d33_2020, abstract = {FAIRsFAIR's analysis of the data policy landscape in 2019 (D3.1 FAIR Policy Landscape Analysis) has shown that the priority and supporting actions outlined in the Turning FAIR into Reality (TFiR) report are being reflected in the policies of funding bodies, publishers/journals and Research Performing Organisations (RPOs) to some extent. However, as crucial components in the FAIR ecosystem, there is still much that needs to be done to foster and harmonise policies to support the aims of the European Open Science Cloud and realise the vision of TFiR. Based on this initial landscape assessment and the work of related initiatives, FAIRsFAIR has prepared a series of practical recommendations for policy enhancement to support the realisation of a FAIR ecosystem. These recommendations are released as a living document that will be refined to reflect the forthcoming work of other projects funded under the INFRAEOSC-05-2018-2019 call and other relevant initiatives. This is the draft version of the deliverable not yet approved by the European Commission. Though we can't undertake to respond to every comment directly, we are seeking wide feedback on this deliverable which will inform discussions and further work within FAIRsFAIR as well as collaborations with other relevant projects. Comments and suggestions can be added until 17 April 2020 at: https://drive.google.com/file/d/1haEU9D-VPJkG7uwxvFBOVFZCxl7NK6wR/view?usp=sharing}, author = {Davidson, Joy and Grootveld, Marjan and Whyte, Angus and Herterich, Patricia and Engelhardt, Claudia and Stoy, Lennart and Proudman, Vanessa}, doi = {10.5281/zenodo.3686901}, keywords = {policy, FAIR data, recommendations}, month = {February}, title = {D3.3 {Policy} {Enhancement} {Recommendations}}, url = {https://zenodo.org/record/3686901}, urldate = {2020-05-11}, year = {2020} } @article{davies_core_2020, author = {Davies, Alan and Mueller, Julia and Moulton, Georgina}, doi = {10.1016/j.ijmedinf.2020.104237}, journal = {International Journal of Medical Informatics}, month = {September}, pages = {104237}, title = {Core competencies for clinical informaticians: {A} systematic review}, volume = {141}, year = {2020} } @article{dekker_social_2020, abstract = {The European Commission report ``Turning FAIR into reality'' provides an index of 27 FAIR Action Plan recommendations. This index is used for a self-assessment on CESSDA, the Consortium of European Social Science Data Archives. CESSDA is performing well on ``Concepts for FAIR implementation'', ``Skills for FAIR'', and ``Investment in FAIR''; there is work in progress on ``FAIR culture'', and work to start up on ``FAIR ecosystem'' and especially on ``Incentives and metrics for FAIR data and services''. Next, an analysis on the FAIR components, reveals that CESSDA has accomplished the ``F'', is working on the ``A'' – considering the sensitivity and security requirements of social data, just started on ``I'', and that there is lack of clarity on what should be in ``R''. On Findability, the CESSDA Data Catalogue is explained, showing the building blocks that need to be in place before one can produce a catalogue. The article ends with a forward look on CESSDA's deployment on the FAIR principles.}, author = {Dekker, Ron}, doi = {10.1162/dint_a_00044}, issn = {2641-435X}, journal = {Data Intelligence}, keywords = {FAIR practice}, language = {en}, month = {January}, number = {1-2}, pages = {220--229}, shorttitle = {Social {Data}}, title = {Social {Data}: {CESSDA} {Best} {Practices}}, url = {https://www.mitpressjournals.org/doi/abs/10.1162/dint\%5Fa\%5F00044}, urldate = {2020-05-12}, volume = {2}, year = {2020} } @article{der_velden_reproducibility_2020, author = {der Velden, Yasemin Turkyilmaz-van and Dintzner, Nicolas and Teperek, Marta}, doi = {10.1016/j.patter.2020.100099}, journal = {Patterns}, keywords = {Open Science}, month = {September}, number = {6}, pages = {100099--100099}, title = {Reproducibility {Starts} from {You} {Today}}, volume = {1}, year = {2020} } @article{di_cosmo_archiving_2020, author = {Di Cosmo, Roberto}, doi = {10.1007/978-3-030-52200-1_36}, journal = {Mathematical Software – ICMS 2020}, keywords = {Citation, Archive}, pages = {362--373--362--373}, title = {Archiving and {Referencing} {Source} {Code} with {Software} {Heritage}}, url = {http://dx.doi.org/10.1007/978-3-030-52200-1\%5F36}, year = {2020} } @article{di_cosmo_bibl_2020, author = {Di Cosmo, Roberto}, keywords = {Citation, LaTeX}, title = {{BibL} {A} {TEX} style extension for {Software}}, year = {2020} } @incollection{eisty_testing_2020, author = {Eisty, Nasir U. and Perez, Danny and Carver, Jeffrey C. and Moulton, J. David and Nam, Hai Ah}, booktitle = {Lecture {Notes} in {Computer} {Science}}, doi = {10.1007/978-3-030-50436-6_33}, keywords = {Testing}, pages = {457--463--457--463}, publisher = {Springer International Publishing}, title = {Testing {Research} {Software}: {A} {Case} {Study}}, year = {2020} } @article{fecher_making_2020, author = {Fecher, Benedikt and Sokolovska, Nataliia and V\"{o}lker, Teresa and Nebe, Philip and Kahn, Rebecca}, journal = {Journal of the Association for Information Science and Technology (JASIST)}, keywords = {Forschungsinfrastruktur}, title = {Making a {Research} {Infrastructure}: {Conditions} and {Strategies} to {Transform} a {Service} into an {Infrastructure}}, year = {2020} } @article{flemisch_umgang_2020, author = {Flemisch, Bernd and Hermann, Sibylle and Holm, Christian and Mehl, Miriam and Reina, Guido and Uekermann, Benjamin and Boehringer, David and Ertl, Thomas and Grad, Jean-No\"{e}l and Iglezakis, Dorothea and {others}}, keywords = {Research Software, Policy}, title = {Umgang mit {Forschungssoftware} an der {Universit\"{a}t} {Stuttgart}}, year = {2020} } @techreport{flemisch_umgang_2020-1, author = {Flemisch, Bernd and Hermann, Sibylle and Holm, Christian and Mehl, Miriam and Reina, Guido and Uekermann, Benjamin and Boehringer, David and Ertl, Thomas and Grad, Jean-No\"{e}l and Iglezakis, Dorothea and Jaust, Alexander and Koch, Timo and Seeland, Anett and Weeber, Rudolf and Weik, Florian and Weishaupt, Kilian}, doi = {10.18419/OPUS-11178}, institution = {Universit\"{a}t Stuttgart}, language = {de}, title = {Umgang mit {Forschungssoftware} an der {Universit\"{a}t} {Stuttgart}}, year = {2020} } @article{fortunato_case_2020, author = {Fortunato, Laura and Galassi, Mark}, doi = {10.31235/osf.io/ye7sx}, keywords = {Open Source}, month = {August}, title = {The case for free and open source software in research and scholarship}, year = {2020} } @article{garcia_ten_2020, author = {Garcia, Leyla and Batut, B\'{e}r\'{e}nice and Burke, Melissa L. and Kuzak, Mateusz and Psomopoulos, Fotis and Arcila, Ricardo and Attwood, Teresa K. and Beard, Niall and Carvalho-Silva, Denise and Dimopoulos, Alexandros C. and Dominguez del Angel, Victoria and Dumontier, Michel and Gurwitz, Kim T. and Krause, Roland and McQuilton, Peter and Le Pera, Loredana and Morgan, Sarah L. and Rauste, P\"{a}ivi and Via, Allegra and Kahlem, Pascal and Rustici, Gabriella and van Gelder, Celia W.G. and Palagi, Patricia M.}, doi = {10.1371/journal.pcbi.1007854}, editor = {Markel, Scott}, journal = {PLOS Computational Biology}, keywords = {FAIR other contexts}, month = {May}, number = {5}, pages = {e1007854}, title = {Ten simple rules for making training materials {FAIR}}, volume = {16}, year = {2020} } @article{garijo_towards_2020, author = {Garijo, Daniel and Gil, Yolanda and Osorio, Maximiliano and Ratnakar, Varun and Khider, Deborah}, doi = {10.5281/ZENODO.3977916}, keywords = {Research Software, Metadata}, title = {Towards {Knowledge} {Graphs} of {Research} {Software} metadata}, year = {2020} } @article{garousi_experience_2020, abstract = {Development of scientific and engineering software is usually different and could be more challenging than the development of conventional enterprise software. The authors were involved in a technology-transfer project between academia and industry which focused on engineering, development and testing of a software for optimization of pumping energy costs for oil pipelines. Experts with different skillsets (mechanical, power and software engineers) were involved. Given the complex nature of the software (a sophisticated underlying optimization model) and having experts from different fields, there were challenges in various software engineering aspects of the software system (e.g., requirements and testing). We report our observations and experience in addressing those challenges during our technology-transfer project, and aim to add to the existing body of experience and evidence in engineering of scientific and engineering software. We believe that our observations, experience and lessons learnt could be useful for other researchers and practitioners in engineering of other scientific and engineering software systems.}, author = {Garousi, Vahid and Abbasi, Ehsan and Tekinerdogan, Bedir}, keywords = {⛔ No DOI found, Software Engineering}, month = {March}, title = {Experience in engineering of scientific software: {The} case of an optimization software for oil pipelines}, year = {2020} } @article{grannan_understanding_2020, author = {Grannan, A. and Sood, K. and Norris, B. and Dubey, A.}, doi = {10/ggnd4b}, journal = {The International Journal of High Performance Computing Applications}, keywords = {High Performance Computing}, month = {January}, pages = {109434201989945--109434201989945}, title = {Understanding the landscape of scientific software used on high-performance computing platforms}, year = {2020} } @article{gruenpeter_m215_2020, abstract = {Software has an important place in academia and as such it has an important place in the FAIR ecosystem. Software can be used throughout the research process; however it can also be an outcome of the research process. Distinguishing between these different roles is essential for any assessment of the `FAIRness of software'. This is the first milestone of the FAIRsFAIR project focused specifically on software as a digital object. In this report we discuss the state-of-the-art of software in the scholarly ecosystem in general and in the FAIR literature in particular. We identify the challenges of different stakeholders when it comes to finding and reusing software. Furthermore, we present an analysis of nine resources that call for the recognition of software in academia and that present guidelines or recommendations to improve its status - either by becoming more FAIR or by improving the curation of software in general. With this analysis we demonstrate to what extent each of the FAIR principles is seen as relevant, achievable and measurable; and in what sense it benefits software artifacts. Finally, we present 10 high-level recommendations for organizations that seek to define FAIR principles or other requirements for research software in the scholarly domain. Feedback and suggestions will be most welcome as comments on the public Google Doc version of this report https://docs.google.com/document/d/1yvdLSP6oH3XozVy4CJtThzGNHkseCBdvmxfruDYLB6Q/edit?usp=sharing}, author = {Gruenpeter, Morane and Di Cosmo, Roberto and Koers, Hylke and Herterich, Patricia and Hooft, Rob and Parland-von Essen, Jessica and Tana, Jonas and Aalto, Tero and Jones, Sarah}, doi = {10.5281/zenodo.4095092}, keywords = {FAIR, EOSC, FAIR Software, Software guidelines, Software in academia}, month = {October}, title = {M2.15 {Assessment} report on '{FAIRness} of software'}, url = {https://zenodo.org/record/4095092#.YCHNkMIRXs0}, urldate = {2021-02-08}, year = {2020} } @article{gurwitz_framework_2020, author = {Gurwitz, Kim T. and Singh Gaur, Prakash and Bellis, Louisa J. and Larcombe, Lee and Alloza, Eva and Balint, Balint Laszlo and Botzki, Alexander and Dimec, Jure and Angel, Victoria Dominguez del and Fernandes, Pedro L. and Korpelainen, Eija and Krause, Roland and Kuzak, Mateusz and Le Pera, Loredana and Lesko\v{s}ek, Brane and Lindvall, Jessica M. and Marek, Diana and Martinez, Paula A. and Muyldermans, Tuur and Nyg\aa{}rd, St\aa{}le and Palagi, Patricia M. and Peterson, Hedi and Psomopoulos, Fotis and Spiwok, Vojtech and van Gelder, Celia W. G. and Via, Allegra and Vidak, Marko and Wibberg, Daniel and Morgan, Sarah L. and Rustici, Gabriella}, doi = {10.1371/journal.pcbi.1007976}, editor = {Ouellette, Francis}, journal = {PLOS Computational Biology}, month = {July}, number = {7}, pages = {e1007976}, title = {A framework to assess the quality and impact of bioinformatics training across {ELIXIR}}, volume = {16}, year = {2020} } @article{harjes_fair_2020, abstract = {Abstract. Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract model}, author = {Harjes, Janno and Link, Anton and Weibulat, Tanja and Triebel, Dagmar and Rambold, Gerhard}, doi = {10.1093/database/baaa059}, journal = {Database}, keywords = {FAIR other contexts}, language = {en}, month = {January}, title = {{FAIR} digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results}, url = {https://academic.oup.com/database/article/doi/10.1093/database/baaa059/5894776}, urldate = {2020-10-25}, volume = {2020}, year = {2020} } @inproceedings{harzenetter_analysis_2020, author = {Harzenetter, Lukas and Breitenb\"{u}cher, Johanna Barzen Uwe and Leymann, Frank and Mathiak, Brigitte and Schildkamp, Philip and Neuefeind, Claes}, keywords = {Research Software, Digital Humanities}, month = {July}, publisher = {ADHO}, title = {Analysis and {Categorisation} of {Research} {Software} in the {Digital} {Humanities}}, year = {2020} } @article{hasselbring_fair_2020, abstract = {The Open Science agenda holds that science advances faster when we can build on existing results. Therefore, research data must be FAIR (Findable, Accessible, Interoperable, and Reusable) in order to advance the findability, reproducibility and reuse of research results. Besides the research data, all the processing steps on these data – as basis of scientific publications – have to be available, too. For good scientific practice, the resulting research software should be both open and adhere to the FAIR principles to allow full repeatability, reproducibility, and reuse. As compared to research data, research software should be both archived for reproducibility and actively maintained for reusability. The FAIR data principles do not require openness, but research software should be open source software. Established open source software licenses provide sufficient licensing options, such that it should be the rare exception to keep research software closed. We review and analyze the current state in this area in order to give recommendations for making research software FAIR and open.}, author = {Hasselbring, Wilhelm and Carr, Leslie and Hettrick, Simon and Packer, Heather and Tiropanis, Thanassis}, doi = {10.1515/itit-2019-0040}, issn = {2196-7032}, journal = {it - Information Technology}, keywords = {FAIR, FAIR principles, Open Source, open source software, research software}, language = {en}, month = {February}, number = {1}, pages = {39--47}, title = {From {FAIR} research data toward {FAIR} and open research software}, url = {https://www.degruyter.com/document/doi/10.1515/itit-2019-0040/html?lang=en}, urldate = {2023-01-23}, volume = {62}, year = {2020} } @article{hasselbring_kieker_2020, author = {Hasselbring, Wilhelm and van Hoorn, Andr\'{e}}, doi = {10.1016/j.simpa.2020.100019}, journal = {Software Impacts}, keywords = {Software Engineering}, month = {August}, pages = {100019--100019}, title = {Kieker: {A} monitoring framework for software engineering research}, volume = {5}, year = {2020} } @article{hasselbring_open_2020, author = {Hasselbring, Wilhelm and Carr, Leslie and Hettrick, Simon and Packer, Heather and Tiropanis, Thanassis}, doi = {10.1109/mc.2020.2998235}, journal = {Computer}, keywords = {Open Source}, month = {August}, number = {8}, pages = {84--88--84--88}, title = {Open {Source} {Research} {Software}}, volume = {53}, year = {2020} } @inproceedings{hermann_community_2020, author = {Hermann, Ben and Winter, Stefan and Siegmund, Janet}, keywords = {Software Engineering}, pages = {469--480--469--480}, title = {Community expectations for research artifacts and evaluation processes}, year = {2020} } @article{higashi_perceived_2020, author = {Higashi, Ross and Schunn, Christian D.}, doi = {10.1037/edu0000401}, journal = {Journal of Educational Psychology}, month = {July}, number = {5}, pages = {1020--1041}, title = {Perceived relevance of digital badges predicts longitudinal change in program engagement}, volume = {112}, year = {2020} } @article{holinski_biocuration_2020, author = {Holinski, Alexandra and Burke, Melissa L. and Morgan, Sarah L. and McQuilton, Peter and Palagi, Patricia M.}, doi = {10.12688/f1000research.25413.2}, journal = {F1000Research}, month = {December}, pages = {1094}, title = {Biocuration - mapping resources and needs [version 2; peer review: 2 approved]}, volume = {9}, year = {2020} } @article{jalili_galaxy_2020, author = {Jalili, Vahid and Afgan, Enis and Gu, Qiang and Clements, Dave and Blankenberg, Daniel and Goecks, Jeremy and Taylor, James and Nekrutenko, Anton}, doi = {10.1093/nar/gkaa554}, journal = {Nucleic Acids Research}, month = {June}, number = {14}, pages = {8205--8207}, title = {The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses: 2020 update}, volume = {48}, year = {2020} } @article{jalili_galaxy_2020-1, author = {Jalili, Vahid and Afgan, Enis and Gu, Qiang and Clements, Dave and Blankenberg, Daniel and Goecks, Jeremy and Taylor, James and Nekrutenko, Anton}, doi = {10.1093/nar/gkaa434}, journal = {Nucleic Acids Research}, month = {June}, number = {W1}, pages = {W395--W402}, title = {The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses: 2020 update}, volume = {48}, year = {2020} } @article{jay_software_2020, abstract = {Software now lies at the heart of scholarly research. Here we argue that as well as being important from a methodological perspective, software should, in many instances, be recognised as an output of research, equivalent to an academic paper. The article discusses the different roles that software may play in research and highlights the relationship between software and research sustainability and reproducibility. It describes the challenges associated with the processes of citing and reviewing software, which differ from those used for papers. We conclude that whilst software outputs do not necessarily fit comfortably within the current publication model, there is a great deal of positive work underway that is likely to make an impact in addressing this.}, author = {Jay, Caroline and Haines, Robert and Katz, Daniel S.}, keywords = {Research Software, Open Science, Professionalization}, month = {November}, title = {Software must be recognised as an important output of scholarly research}, year = {2020} } @article{junk_reproducibility_2020, author = {Junk, Thomas and Lyons, Louis}, doi = {10.1162/99608f92.250f995b}, journal = {Harvard Data Science Review}, month = {December}, number = {4}, title = {Reproducibility and replication of experimental particle physics results}, volume = {2}, year = {2020} } @article{katz_software_2020, author = {Katz, Daniel S. and Hong, Neil P. Chue and Clark, Tim and Fenner, Martin and Martone, Maryann E.}, doi = {10/ggzwsj}, journal = {Computing in Science \& Engineering}, keywords = {Citation, Research Data}, month = {March}, number = {2}, pages = {4--7--4--7}, title = {Software and {Data} {Citation}}, volume = {22}, year = {2020} } @article{khalifeh_incorporating_2020, author = {Khalifeh, Amin and Farrell, Peter and Alrousan, Mohammad and Alwardat, Shaima and Faisal, Masar}, doi = {10.1108/ijmpb-12-2019-0289}, journal = {International Journal of Managing Projects in Business}, keywords = {Sustainability}, month = {July}, number = {6}, pages = {1339--1361--1339--1361}, title = {Incorporating sustainability into software projects: a conceptual framework}, volume = {13}, year = {2020} } @article{koehler_leman_better_2020, author = {Koehler Leman, Julia and Weitzner, Brian D. and Renfrew, P. Douglas and Lewis, Steven M. and Moretti, Rocco and Watkins, Andrew M. and Mulligan, Vikram Khipple and Lyskov, Sergey and Adolf-Bryfogle, Jared and Labonte, Jason W. and Krys, Justyna and {RosettaCommons Consortium} and Bystroff, Christopher and Schief, William and Gront, Dominik and Schueler-Furman, Ora and Baker, David and Bradley, Philip and Dunbrack, Roland and Kortemme, Tanja and Leaver-Fay, Andrew and Strauss, Charlie E. M. and Meiler, Jens and Kuhlman, Brian and Gray, Jeffrey J. and Bonneau, Richard}, doi = {10.1371/journal.pcbi.1007507}, editor = {Schneidman-Duhovny, Dina}, journal = {PLOS Computational Biology}, month = {May}, number = {5}, pages = {e1007507}, title = {Better together: {Elements} of successful scientific software development in a distributed collaborative community}, volume = {16}, year = {2020} } @article{koers_assessment_2020, abstract = {To realise the full potential of a FAIR ecosystem in which research can be easily shared and optimally reused, as put forward in the {\textbackslash}textlessem{\textbackslash}textgreaterTurning FAIR into reality{\textbackslash}textless/em{\textbackslash}textgreater report, we must look beyond `just' research data: on the one hand we should include research software and other digital objects, and on the other hand we should lay out a vision and a roadmap for services and supporting infrastructure that fosters an optimal interplay between digital objects and services. The latter calls for an assessment framework for service owners which can be used to gauge where change is needed, together with actionable recommendations to drive incremental improvements. However, while the development of various FAIR assessment frameworks for data and other digital objects has enjoyed substantial activity over the last few years, a FAIR assessment framework for data services is still lacking -- a fact that was recently underlined again in the interim recommendations from the EOSC FAIR Working Group. FAIRsFAIR task 2.4, entitled `FAIR services', aims to close this gap by developing a FAIR assessment framework for data services (alongside a similar framework for research software). This report marks the first milestone of the task. It presents a survey of existing FAIR assessment frameworks, a proposed set of guiding principles and desiderata for the FAIR assessment framework that will be constructed, and three `FAIR service assessment' case studies. We are seeking wide feedback on this report to inform subsequent work and, ultimately, feed into a FAIR assessment framework for data services that delivers clear direction and value to service owners and the community at large. {\textbackslash}textlessem{\textbackslash}textgreaterFeedback and suggestions will be most welcome as comments on the public Google Doc version of this report: https://docs.google.com/document/d/1VO8T8mpsp4qt-XSbcdUBTMVgOVwEf9na81Ccv56NPg4/edit{\textbackslash}textless/em{\textbackslash}textgreater}, author = {Koers, Hylke and Gruenpeter, Morane and Herterich, Patricia and Hooft, Rob and Jones, Sarah and Parland-von Essen, Jessica and Staiger, Christine}, copyright = {Creative Commons Attribution 4.0 International, Open Access}, doi = {10.5281/ZENODO.3688762}, keywords = {FAIR, FAIR other contexts, EOSC, Data Services, Research Data Management, Service Management}, language = {en}, month = {February}, title = {Assessment report on '{FAIRness} of services'}, url = {https://zenodo.org/record/3688762}, urldate = {2020-11-07}, year = {2020} } @article{koers_recommendations_2020, author = {Koers, Hylke and Bangert, Daniel and Hermans, Emilie and van Horik, Ren\'{e} and de Jong, Maaike and Mokrane, Mustapha}, doi = {10.1016/j.patter.2020.100058}, issn = {26663899}, journal = {Patterns}, keywords = {FAIR other contexts}, language = {en}, month = {August}, number = {5}, pages = {100058}, title = {Recommendations for {Services} in a {FAIR} {Data} {Ecosystem}}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2666389920300696}, urldate = {2020-10-25}, volume = {1}, year = {2020} } @article{konkol_publishing_2020, abstract = {Funding agencies increasingly ask applicants to include data and software management plans into proposals. In addition, the author guidelines of scientific journals and conferences more often include a statement on data availability, and some reviewers reject unreproducible submissions. This trend towards open science increases the pressure on authors to provide access to the source code and data underlying the computational results in their scientific papers. Still, publishing reproducible articles is a demanding task and not achieved simply by providing access to code scripts and data files. Consequently, several projects develop solutions to support the publication of executable analyses alongside articles considering the needs of the aforementioned stakeholders. The key contribution of this paper is a review of applications addressing the issue of publishing executable computational research results. We compare the approaches across properties relevant for the involved stakeholders, e.g., provided features and deployment options, and also critically discuss trends and limitations. The review can support publishers to decide which system to integrate into their submission process, editors to recommend tools for researchers, and authors of scientific papers to adhere to reproducibility principles.}, author = {Konkol, Markus and N\"{u}st, Daniel and Goulier, Laura}, keywords = {⛔ No DOI found, Literature Review, Publication}, month = {January}, title = {Publishing computational research. {A} review of infrastructures for reproducible and transparent scholarly communication}, year = {2020} } @article{konrad_digitale_2020, author = {Konrad, Uwe and F\"{o}rstner, Konrad and Reetz, Johannes and Wannemacher, Klaus and Kett, J\"{u}rgen and Mannseicher, Florian}, doi = {10.5281/ZENODO.4301924}, keywords = {Research Software, Open Science, Open Source, Allianz der deutschen Wissenschaftsorganisationen, Digital Transformation, Digitale Dienste, Information Technology}, title = {Digitale {Dienste} f\"{u}r die {Wissenschaft} - wohin geht die {Reise}?}, year = {2020} } @article{kunkel_contributing_2020, author = {Kunkel, Julian and Himstedt, Kai and Filinger, Weronika and Acquaviva, Jean-Thomas and Gerbes, Anja and Lafayette, Lev}, doi = {10.22369/issn.2153-4136/11/1/17}, issn = {2153-4136}, journal = {The Journal of Computational Science Education}, month = {January}, number = {1}, pages = {106--107}, title = {Contributing {HPC} {Skills} to the {HPC} {Certification} {Forum}}, volume = {11}, year = {2020} } @article{kunkel_hpc_2020, author = {Kunkel, Julian and Filinger, Weronika and Meesters, Christian and Gerbes, Anja}, doi = {10.1109/MCSE.2020.2996073}, issn = {1521-9615}, journal = {Computing in Science \& Engineering}, number = {4}, pages = {110--114}, title = {The {HPC} {Certification} {Forum}: {Toward} a {Globally} {Acknowledged} {HPC} {Certification}}, volume = {22}, year = {2020} } @article{kunkel_one_2020, author = {Kunkel, Julian Martin and Himstedt, Kai and Filinger, Weronika and Acquaviva, Jean-Thomas and Gerbes, Anja and Lafayette, Lev}, doi = {10.22369/issn.2153-4136/11/1/6}, issn = {2153-4136}, journal = {The Journal of Computational Science Education}, month = {January}, number = {1}, pages = {29--35}, title = {One {Year} {HPC} {Certification} {Forum} in {Retrospective}}, volume = {11}, year = {2020} } @article{kurtz_enabling_2020, abstract = {In this whitepaper we advocate that the Planetary Science (PS) community build a discipline-specific digital library, in collaboration with the existing astronomy digital library, ADS. We suggest that the PS data archives increase their level of curation to allow for direct linking between the archival data and the derived journal articles. And we suggest that a new component of the PS information infrastructure be created to collate and curate information on features and objects in our solar system, beginning with the USGS/IAU Gazetteer of Planetary Nomenclature.}, author = {Kurtz, Michael J. and Accomazzi, Alberto and Henneken, Edwin A.}, keywords = {Astrophysics}, month = {September}, title = {Enabling {Synergy}: {Improving} the {Information} {Infrastructure} for {Planetary} {Science}}, year = {2020} } @article{leaser_connecting_2020, author = {Leaser, David and Jona, Kemi and Gallagher, Sean}, doi = {10.1002/cc.20396}, issn = {1536-0733}, journal = {New Directions for Community Colleges}, month = {February}, number = {189}, pages = {39--51}, title = {Connecting {Workplace} {Learning} and {Academic} {Credentials} via {Digital} {Badges}}, volume = {2020}, year = {2020} } @article{lebeau_evolution_2020, author = {LeBeau, Brandon C. and Aloe, Ariel M.}, doi = {10.17077/pp.005273}, keywords = {Methodik, Quantitative}, month = {July}, title = {Evolution of {Statistical} {Software} and {Quantitative} {Methods}}, year = {2020} } @inproceedings{legay_usage_2020, author = {Legay, Damien and Decan, Alexandre and Mens, Tom}, booktitle = {Proceedings of the 18{\textbackslash}textsuperscriptth {Edition} of the {Belgian}-{Netherlands} {Software} {Evolution} {Symposium} ({BENEVOL} 2019)}, editor = {Di Nucci, Dario and De Roover, Coen}, month = {May}, publisher = {CEUR}, series = {{CEUR} {Workshop} {Proceedings}}, title = {On the {Usage} of {Badges} in {Open} {Source} {Packages} on {GitHub}}, url = {https://ceur-ws.org/Vol-2605/9.pdf}, year = {2020} } @article{lehra_increasing_2020, author = {Lehra, Jan-Patrick and Maricb, Tomislav and Botheb, Dieter and Bischofa, Christian}, keywords = {Software Engineering}, title = {Increasing the quality of (academic) scientific software}, year = {2020} } @article{leipzig_role_2020, abstract = {Reproducible computational research (RCR) is the keystone of the scientific method for in silico analyses, packaging the transformation of raw data to published results. In addition to its role in research integrity, RCR has the capacity to significantly accelerate evaluation and reuse. This potential and wide-support for the FAIR principles have motivated interest in metadata standards supporting RCR. Metadata provides context and provenance to raw data and methods and is essential to both discovery and validation. Despite this shared connection with scientific data, few studies have explicitly described the relationship between metadata and RCR. This article employs a functional content analysis to identify metadata standards that support RCR functions across an analytic stack consisting of input data, tools, notebooks, pipelines, and publications. Our article provides background context, explores gaps, and discovers component trends of embeddedness and methodology weight from which we derive recommendations for future work.}, author = {Leipzig, Jeremy and N\"{u}st, Daniel and Hoyt, Charles Tapley and Soiland-Reyes, Stian and Ram, Karthik and Greenberg, Jane}, keywords = {Open Science, Metadaten}, month = {June}, title = {The role of metadata in reproducible computational research}, year = {2020} } @article{malone_doing_2020, abstract = {Open source software is ubiquitous throughout data science, and enables the work of nearly every data scientist in some way or another. Open source projects, however, are disproportionately maintained by a small number of individuals, some of whom are institutionally supported, but many of whom do this maintenance on a purely volunteer basis. The health of the data science ecosystem depends on the support of open source projects, on an individual and institutional level.}, author = {Malone, Katie and Wolski, Rich}, journal = {Harvard Data Science Review}, language = {en}, month = {June}, shorttitle = {Doing {Data} {Science} on the {Shoulders} of {Giants}}, title = {Doing {Data} {Science} on the {Shoulders} of {Giants}: {The} {Value} of {Open} {Source} {Software} for the {Data} {Science} {Community}}, url = {https://hdsr.mitpress.mit.edu/pub/xsrt4zs2/release/2}, urldate = {2020-06-05}, year = {2020} } @article{manola_implementing_2020, author = {Manola, Natalia and Mutschke, Peter and Scherp, Guido and Tochtermann, Klaus and Wittenburg, Peter and Gregory, Kathleen and Hasselbring, Wilhelm and den Heijer, Kees and Manghi, Paolo and Van Uytvanck, Dieter}, doi = {10.4230/DAGMAN.8.1.1}, keywords = {FAIR}, title = {Implementing {FAIR} {Data} {Infrastructures} ({Dagstuhl} {Perspectives} {Workshop} 18472)}, year = {2020} } @article{martin_barking_2020, author = {Martin, Leslie and Sibbald, Matthew}, doi = {10.1111/medu.14178}, journal = {Medical Education}, month = {June}, number = {7}, pages = {593--595}, title = {Barking up the same tree? {Lessons} from workplace-based assessment and digital badges}, volume = {54}, year = {2020} } @article{martins_bioinformatics-based_2020, author = {Martins, Ana and Fonseca, Maria Jo\~{a}o and Lemos, Marina and Lencastre, Leonor and Tavares, Fernando}, doi = {10.3389/fmicb.2020.578099}, issn = {1664-302X}, journal = {Frontiers in Microbiology}, month = {October}, title = {Bioinformatics-{Based} {Activities} in {High} {School}: {Fostering} {Students}' {Literacy}, {Interest}, and {Attitudes} on {Gene} {Regulation}, {Genomics}, and {Evolution}}, volume = {11}, year = {2020} } @article{mcclatchy_nine_2020, author = {McClatchy, Susan and Bass, Kristin M. and Gatti, Daniel M. and Moylan, Adam and Churchill, Gary}, doi = {10.1371/journal.pcbi.1008007}, editor = {Schwartz, Russell}, journal = {PLOS Computational Biology}, month = {July}, number = {7}, pages = {e1008007}, title = {Nine quick tips for efficient bioinformatics curriculum development and training}, volume = {16}, year = {2020} } @incollection{mendez_open_2020, author = {Mendez, Daniel and Graziotin, Daniel and Wagner, Stefan and Seibold, Heidi}, booktitle = {Contemporary {Empirical} {Methods} in {Software} {Engineering}}, doi = {10.1007/978-3-030-32489-6_17}, keywords = {Open Science}, pages = {477--501--477--501}, publisher = {Springer International Publishing}, title = {Open {Science} in {Software} {Engineering}}, year = {2020} } @article{milewicz_research_2020, abstract = {At Sandia National Laboratories, the Software Engineering and Research Department seeks to provide sustainable career pathways for research software engineers (RSEs). The conceptual model for our organization follows what we call a Research, Develop, and Deploy (RDD) workflow pattern, enabling RSEs to partner with research and deployment specialists. We argue that this interdisciplinary model allows our department to act as an incubator and an accelerator for impactful ideas. We describe these tactics and our experiences as a RSE team in a scientific computing center.}, author = {Milewicz, Reed and Willenbring, James and Vigil, Dena}, keywords = {Software Engineering}, month = {October}, title = {Research, {Develop}, {Deploy}: {Building} a {Full} {Spectrum} {Software} {Engineering} and {Research} {Department}}, year = {2020} } @article{milewicz_towards_2020, author = {Milewicz, Reed}, keywords = {Software Engineering}, title = {Towards {Evidence}-{Based} {Practice} in {Scientific} {Software} {Develop}-ment}, year = {2020} } @article{monteil_nine_2020, abstract = {Scientific software registries and repositories serve various roles in their respective disciplines. These resources improve software discoverability and research transparency, provide information for software citations, and foster preservation of computational methods that might otherwise be lost over time, thereby supporting research reproducibility and replicability. However, developing these resources takes effort, and few guidelines are available to help prospective creators of registries and repositories. To address this need, we present a set of nine best practices that can help managers define the scope, practices, and rules that govern individual registries and repositories. These best practices were distilled from the experiences of the creators of existing resources, convened by a Task Force of the FORCE11 Software Citation Implementation Working Group during the years 2019-2020. We believe that putting in place specific policies such as those presented here will help scientific software registries and repositories better serve their users and their disciplines.}, author = {Monteil, Alain and Gonzalez-Beltran, Alejandra and Ioannidis, Alexandros and Allen, Alice and Lee, Allen and Bandrowski, Anita and Wilson, Bruce E. and Mecum, Bryce and Du, Cai Fan and Robinson, Carly and Garijo, Daniel and Katz, Daniel S. and Long, David and Milliken, Genevieve and M\'{e}nager, Herv\'{e} and Hausman, Jessica and Spaaks, Jurriaan H. and Fenlon, Katrina and Vanderbilt, Kristin and Hwang, Lorraine and Davis, Lynn and Fenner, Martin and Crusoe, Michael R. and Hucka, Michael and Wu, Mingfang and Hong, Neil Chue and Teuben, Peter and Stall, Shelley and Druskat, Stephan and Carnevale, Ted and Morrell, Thomas}, doi = {https://doi.org/10.48550/arXiv.2012.13117}, keywords = {Research Software, Registries}, month = {December}, title = {Nine {Best} {Practices} for {Research} {Software} {Registries} and {Repositories}: {A} {Concise} {Guide}}, year = {2020} } @article{mundt_how_2020, abstract = {We are research software engineers and team members in the Department of Software Engineering and Research at Sandia National Laboratories, an organization which aims to advance software engineering in the domain of computational science. Our team hopes to promote processes and principles that lead to quality, rigor, correctness, and repeatability in the implementation of algorithms and applications in scientific software for high consequence applications. We use our experience to argue that there is a readily achievable set of software tools and best practices with a large return on investment that can be imparted upon scientific researchers that will remarkably improve the quality of software and, as a result, the quality of research.}, author = {Mundt, Miranda and Harvey, Evan}, keywords = {Software Engineering}, month = {October}, title = {How {Research} {Software} {Engineers} {Can} {Support} {Scientific} {Software}}, year = {2020} } @incollection{nieva_de_la_hidalga_envri_2020, author = {Nieva de la Hidalga, Abraham and Hardisty, Alex and Martin, Paul and Magagna, Barbara and Zhao, Zhiming}, booktitle = {Towards {Interoperable} {Research} {Infrastructures} for {Environmental} and {Earth} {Sciences}}, doi = {10.1007/978-3-030-52829-4_4}, isbn = {978-3-030-52828-7}, month = {July}, pages = {61--81}, title = {The {ENVRI} {Reference} {Model}}, year = {2020} } @article{nust_ten_2020, author = {N\"{u}st, Daniel and Sochat, Vanessa and Marwick, Ben and Eglen, Stephen and Head, Tim and Hirst, Tony and Evans, Benjamin}, doi = {10.31219/osf.io/fsd7t}, keywords = {Open Science, Forschungsdatenmanagement, research data}, month = {April}, title = {Ten {Simple} {Rules} for {Writing} {Dockerfiles} for {Reproducible} {Data} {Science}}, year = {2020} } @article{ocais_expanding_2020, author = {O'Cais, Alan and Steinbach, Peter}, doi = {10.22369/issn.2153-4136/11/1/4}, issn = {2153-4136}, journal = {The Journal of Computational Science Education}, month = {January}, number = {1}, pages = {21--25}, title = {Expanding user communities with {HPC} {Carpentry}}, volume = {11}, year = {2020} } @article{pomann_methods_2020, author = {Pomann, Gina-Maria and Boulware, L. Ebony and Cayetano, Shari Messinger and Desai, Manisha and Enders, Felicity T. and Gallis, John A. and Gelfond, Jonathan and Grambow, Steven C. and Hanlon, Alexandra L. and Hendrix, Angelean and Kulkarni, Pandurang and Lapidus, Jodi and Lee, Hui-Jie and Mahnken, Jonathan D. and McKeel, Julie P. and Moen, Rebecca and Oster, Robert A. and Peskoe, Sarah and Samsa, Greg and Stewart, Thomas G. and Truong, Tracy and Wruck, Lisa and Thomas, Samantha M.}, doi = {10.1017/cts.2020.518}, journal = {Journal of Clinical and Translational Science}, month = {August}, number = {1}, pages = {e26}, title = {Methods for training collaborative biostatisticians}, volume = {5}, year = {2020} } @article{romano_ten_2020, author = {Romano, Joseph D. and Moore, Jason H.}, doi = {10.1371/journal.pcbi.1008390}, journal = {PLOS Computational Biology}, keywords = {Research Software, Scientific Writing}, month = {November}, number = {11}, pages = {e1008390--e1008390}, title = {Ten simple rules for writing a paper about scientific software}, volume = {16}, year = {2020} } @incollection{saini_domain-based_2020, author = {Saini, Jatinderkumar R. and Chomal, Vikas S.}, booktitle = {Advances in {Intelligent} {Systems} and {Computing}}, doi = {10.1007/978-981-15-0936-0_5}, keywords = {Software Engineering, Testing}, pages = {53--69--53--69}, publisher = {Springer Singapore}, title = {Domain-{Based} {Ranking} of {Software} {Test}--{Effort} {Estimation} {Techniques} for {Academic} {Projects}}, year = {2020} } @article{saputri_software_2020, author = {Saputri, Theresia Ratih Dewi and Lee, Seok-Won}, doi = {10/ggnd4h}, journal = {International Journal of Software Engineering and Knowledge Engineering}, keywords = {Sustainability, Software Analysis}, month = {January}, number = {01}, pages = {67--95}, title = {Software {Analysis} {Method} for {Assessing} {Software} {Sustainability}}, volume = {30}, year = {2020} } @article{schmitt_nfdi4ing_2020, author = {Schmitt, Robert H. and Anthofer, Verena and Auer, S\"{o}ren and Ba\c{s}kaya, Sait and Bischof, Christian and Bronger, Torsten and Claus, Florian and Cordes, Florian and Demandt, \'{E}variste and Eifert, Thomas and Flemisch, Bernd and Fuchs, Matthias and Fuhrmans, Marc and Gerike, Regine and Gerstner, Eva-Maria and Hanke, Vanessa and Heine, Ina and Huebser, Louis and Iglezakis, Dorothea and Jagusch, Gerald and Klinger, Axel and Krafczyk, Manfred and Kraft, Angelina and Kuckertz, Patrick and K\"{u}sters, Ulrike and Lachmayer, Roland and Langenbach, Christian and Mozgova, Iryna and M\"{u}ller, Matthias S. and Nestler, Britta and Pelz, Peter and Politze, Marius and Preu\ss{}, Nils and Przybylski-Freund, Marie-Dominique and Ri\ss{}ler-Pipka, Nanette and Robinius, Martin and Schachtner, Joachim and Schlenz, Hartmut and Schwarz, Annett and Schwibs, J\"{u}rgen and Selzer, Michael and Sens, Irina and St\"{a}cker, Thomas and Stemmer, Christian and Stille, Wolfgang and Stolten, Detlef and Stotzka, Rainer and Streit, Achim and Str\"{o}tgen, Robert and Wang, Wei Min}, doi = {10.5281/ZENODO.4015201}, keywords = {NFDI, Engineering}, title = {{NFDI4Ing} - the {National} {Research} {Data} {Infrastructure} for {Engineering} {Sciences}}, year = {2020} } @inproceedings{simao_de_deus_use_2020, address = {Los Alamitos, California, USA}, author = {Sim\~{a}o de Deus, William and Francine Barbosa, Ellen}, booktitle = {Proceedings of the 2020 {IEEE} 44{\textbackslash}textsuperscriptth {Annual} {Computers}, {Software}, and {Applications} {Conference} ({COMPSAC})}, doi = {10.1109/compsac48688.2020.00025}, editor = {Chan, W. K. and Claycomb, Bill and Takakura, Hiroki and Yang, Ji-Jiang and Teranishi, Yuuichi and Towey, Dave and Segura, Sergio and Shahriar, Hossain and Reisman, Sorel and Ahamed, Sheikh Iqbal}, isbn = {978-1-7281-7303-0}, month = {July}, publisher = {IEEE}, title = {The {Use} of {Metadata} in {Open} {Educational} {Resources} {Repositories}: {An} {Exploratory} {Study}}, year = {2020} } @article{straub_vorlesung_2020, author = {Straub, Wolfgang and St\"{u}rmer, Matthias}, keywords = {Open Source, license}, title = {Vorlesung {Digitale} {Nachhaltigkeit}:{Open} {Source} {Lizenzen}}, year = {2020} } @inproceedings{tripathi_building_2020, author = {Tripathi, Ravi and Monroe, William Stonewall and Hanby, Mike and Robinson, John-Paul}, doi = {10.1145/3311790.3399620}, keywords = {Infrastructure}, month = {July}, publisher = {ACM}, title = {Building a {Scalable} {Infrastructure}}, year = {2020} } @inproceedings{uzwyshyn_developing_2020, author = {Uzwyshyn, Ray}, keywords = {Open Source}, month = {February}, title = {Developing an {Open} {Source} {Digital} {Scholarship} {Ecosystem}}, year = {2020} } @article{uzwyshyn_open_2020, author = {Uzwyshyn, Raymond}, keywords = {Research Software, Open Source, Infrastructure}, title = {Open {Source} {Digital} {Ecosystems} for {Accelerating} {Global} {Research}, {Innovation} and {Collaboration}}, year = {2020} } @article{van_den_oord_esiwace2_2020, abstract = {We present the collaborative model of ESiWACE2 Services, where Research Software Engineers (RSEs) from the Netherlands eScience Center (NLeSC) and Atos offer their expertise to climate and earth system modeling groups across Europe. Within 6-month collaborative projects, the RSEs intend to provide guidance and advice regarding the performance, portability to new architectures, and scalability of selected applications. We present the four awarded projects as examples of this funding structure.}, author = {van den Oord, Gijs and Azizi, Victor and Sclocco, Alessio and Moulard, Georges-Emmanuel and Guibert, David and Attema, Jisk and Raffin, Erwan and van Werkhoven, Ben}, keywords = {Collaboration}, month = {September}, title = {{ESiWACE2} {Services}: {RSE} collaborations in {Weather} and {Climate}}, year = {2020} } @article{weber_finite_2020, author = {Weber, Nicholas}, doi = {10.1002/pra2.281}, journal = {Proceedings of the Association for Information Science and Technology}, keywords = {Research Software, Institutional Logics}, month = {October}, number = {1}, title = {Finite and infinite games: {An} ethnography of institutional logics in research software sustainability}, volume = {57}, year = {2020} } @inproceedings{wernitznig_cliff_2020, author = {Wernitznig, Andreas and Lipp, Jesse J. and Zichner, Thomas and Gerlach, Daniel and Bauer, Markus J. and Voss, Tilman and Schlattl, Andreas and Haslinger, Christian and Montgomery, Philip G. and Zamanighomi, Mahdi and Sellers, William R. and Kraut, Norbert}, doi = {10.1158/1538-7445.am2020-3227}, keywords = {Bioinformatik}, month = {August}, publisher = {American Association for Cancer Research}, title = {{CLIFF}, a bioinformatics software tool to explore molecular differences between two sets of cancer cell lines}, year = {2020} } @article{wittenburg_state_2020, abstract = {Since 2009 initiatives that were selected for the roadmap of the European Strategy Forum on Research Infrastructures started working to build research infrastructures for a wide range of research disciplines. An important result of the strategic discussions was that distributed infrastructure scenarios were now seen as ``complex research facilities'' in addition to, for example traditional centralised infrastructures such as CERN. In this paper we look at five typical examples of such distributed infrastructures where many researchers working in different centres are contributing data, tools/services and knowledge and where the major task of the research infrastructure initiative is to create a virtually integrated suite of resources allowing researchers to carry out state-of-the-art research. Careful analysis shows that most of these research infrastructures worked on the Findability, Accessibility, Interoperability and Reusability dimensions before the term ``FAIR'' was actually coined. The definition of the FAIR principles and their wide acceptance can be seen as a confirmation of what these initiatives were doing and it gives new impulse to close still existing gaps. These initiatives also seem to be ready to take up the next steps which will emerge from the definition of FAIR maturity indicators. Experts from these infrastructures should bring in their 10-years' experience in this definition process.}, author = {Wittenburg, Peter and de Jong, Franciska and van Uytvanck, Dieter and Cocco, Massimo and Jeffery, Keith and Lautenschlager, Michael and Thiemann, Hannes and Hellstr\"{o}m, Margareta and Asmi, Ari and Holub, Petr}, doi = {10.1162/dint_a_00045}, issn = {2641-435X}, journal = {Data Intelligence}, keywords = {FAIR practice}, language = {en}, month = {January}, number = {1-2}, pages = {230--237}, title = {State of {FAIRness} in {ESFRI} {Projects}}, url = {https://www.mitpressjournals.org/doi/abs/10.1162/dint\%5Fa\%5F00045}, urldate = {2020-05-12}, volume = {2}, year = {2020} } @article{yu_free_2020, author = {Yu, Jingyuan and Mu\~{n}oz-Justicia, Juan}, doi = {10/ggkx4f}, journal = {Social Science Computer Review}, keywords = {Social Science, Twitter}, month = {February}, pages = {089443932090431--089443932090431}, title = {Free and {Low}-{Cost} {Twitter} {Research} {Software} {Tools} for {Social} {Science}}, year = {2020} } @article{zirkelbach_collaborative_2020, author = {Zirkelbach, Christian and Krause, Alexander and Hasselbring, Wilhelm}, journal = {International Journal On Advances in Software}, keywords = {Open Source}, number = {1\&2}, pages = {34--49--34--49}, title = {The {Collaborative} {Modularization} and {Reengineering} {Approach} {CORAL} for {Open} {Source} {Research} {Software}}, volume = {13}, year = {2020} } @inproceedings{allen_receiving_2019, author = {Allen, Alice}, editor = {Teuben, Peter J. and Pound, Marc W. and Thomas, Brian A. and Warner, Elizabeth M.}, keywords = {Citation}, month = {October}, pages = {593--593}, title = {Receiving {Credit} for {Research} {Software}}, url = {https://ui.adsabs.harvard.edu/abs/2019ASPC..523..593A}, volume = {523}, year = {2019} } @article{anzt_towards_2019, author = {Anzt, Hartwig and Cojean, Terry and K\"{u}hn, Eileen}, doi = {10/ggnd39}, journal = {PAMM}, keywords = {Sustainability, Peer Review, Reproducibility}, month = {November}, number = {1}, title = {Towards a {New} {Peer} {Review} {Concept} for {Scientific} {Computing} ensuring {Technical} {Quality}, {Software} {Sustainability}, and {Result} {Reproducibility}}, volume = {19}, year = {2019} } @article{attwood_global_2019, author = {Attwood, Teresa K. and Blackford, Sarah and Brazas, Michelle D. and Davies, Angela and Schneider, Maria Victoria}, doi = {10.1093/bib/bbx100}, issn = {1477-4054}, journal = {Briefings in Bioinformatics}, month = {March}, number = {2}, pages = {398--404}, title = {A global perspective on evolving bioinformatics and data science training needs}, volume = {20}, year = {2019} } @inproceedings{badreddin_susereum_2019, author = {Badreddin, Omar and Hamou-Lhadj, Wahab and Chauhan, Swapnil}, doi = {10.1109/SE4Science.2019.00015}, keywords = {⚠️ Invalid DOI, Finance}, pages = {51--54}, publisher = {IEEE Press}, title = {Susereum: {Towards} a {Reward} {Structure} for {Sustainable} {Scientific} {Research} {Software}}, url = {https://doi.org/10.1109/SE4Science.2019.00015}, year = {2019} } @article{bast_fairer_2019, author = {Bast, Radovan}, doi = {10/gf69tq}, journal = {Nature Physics}, keywords = {FAIR}, month = {August}, number = {8}, pages = {728--730}, title = {A {FAIRer} future}, volume = {15}, year = {2019} } @article{bernard_open_2019, author = {Bernard, Christophe}, doi = {10/ggcmcn}, journal = {eNeuro}, keywords = {Open Source, Methodik}, month = {September}, number = {5}, pages = {ENEURO.0342--19.2019}, title = {Open {Source} {Tools} and {Methods}}, volume = {6}, year = {2019} } @article{brauer_online_2019, author = {Brauer, Sanna and Korhonen, Anne-Maria and Siklander, Pirkko}, doi = {10.1080/00131881.2018.1562953}, journal = {Educational Research}, month = {January}, number = {1}, pages = {53--69}, title = {Online scaffolding in digital open badge-driven learning}, volume = {61}, year = {2019} } @article{broeder_sshoc_2019, abstract = {The SSHOC project aims to build a Social Sciences and Humanities Open Cloud (SSHOC) as part of the European Open Science Cloud (EOSC) by implementing a cloud-based infrastructure. The goal is to provide a recognisable and accessible environment for data, tools, services and trainings, and to maximise data reuse through Open Science and FAIR principles. In line with these goals, this report provides an inventory of data formats and metadata standards that are currently used and relevant for the research infrastructures currently managed by the SSHOC main stakeholders, recommendations of specific formats and standards for increasing interoperability, and prioritisations for providing conversion services and planning solutions. In the context of this deliverable, selected experts from the SSHOC stakeholder's infrastructures were interviewed about research data and metadata use in their respective infrastructures. Special attention was paid to interoperability aspects. The interviews and the desk research indicated both the diversity of the SSHOC communities and the diversity of metadata standards used and needed. Therefore, this deliverable recommends a variety of metadata standards and data formats. The recommended metadata standards include domain specific metadata standards for each domain but also Dublin Core and relaxed DataCite for all domains. The diversity of SSHOC communities is also shown in their data: there is a large selection of different media types and an enormous selection of data formats. The recommended data formats include a small selection of data formats for some general media types e.g. images, text annotations. The format for controlled vocabularies was also examined and SKOS was selected as the recommended format. It is worth noting that hardly any recommendation can fulfill all the use cases, so other metadata standards, data formats and formats for controlled vocabularies may still be used when necessary. The priorities for providing conversion services and planning solutions were decided based on the interviews and on the needs from other SSHOC tasks. The challenges and solutions are analysed for each SSHOC community and both the priority and the needed actions are specified. We expect the prioritisation to change in the course of the project with the appearance of new requirements. Beyond WP3, this document is relevant to WP4, WP5, WP7 and WP9. Ongoing discussion between the work packages and tasks is needed. The authors of this report wish to thank the interviewed informants for their time and valuable contribution.}, author = {Broeder, Daan and Trippel, Thorsten and Degl'Innocenti, Emiliano and Giacomi, Roberta and Sanesi, Maurizio and Kleemola, Mari and Moilanen, Katja and Ala-Lahti, Henri and Jordan, Caspar and Alfredsson, Iris and L'Hours, Herv\'{e} and \v{D}ur\v{c}o, Matej}, copyright = {Creative Commons Attribution 4.0 International, Open Access}, doi = {10.5281/ZENODO.3569867}, keywords = {FAIR principles, data interoperability, EOSC, European Open Science Cloud, Interoperability, metadata interoperability, metadata standards, Social Sciences and Humanities Open Cloud, SSHOC}, language = {en}, month = {December}, title = {{SSHOC} {D3}.1 {Report} on {SSHOC} (meta)data interoperability problems}, url = {https://zenodo.org/record/3569867}, urldate = {2020-06-18}, year = {2019} } @article{celebi_towards_2019, abstract = {It is essential for the advancement of science that scientists and researchers share, reuse and reproduce workflows and protocols used by others. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize a number of important points regarding the means by which digital objects are found and reused by others. The question of how to apply these principles not just to the static input and output data but also to the dynamic workflows and protocols that consume and produce them is still under debate and poses a number of challenges. In this paper we describe our inclusive and overarching approach to apply the FAIR principles to workflows and protocols and demonstrate its benefits. We apply and evaluate our approach on a case study that consists of making the PREDICT workflow, a highly cited drug repurposing workflow, open and FAIR. This includes FAIRification of the involved datasets, as well as applying semantic technologies to represent and store data about the detailed versions of the general protocol, of the concrete workflow instructions, and of their execution traces. A semantic model was proposed to better address these specific requirements and were evaluated by answering competency questions. This semantic model consists of classes and relations from a number of existing ontologies, including Workflow4ever, PROV, EDAM, and BPMN. This allowed us then to formulate and answer new kinds of competency questions. Our evaluation shows the high degree to which our FAIRified OpenPREDICT workflow now adheres to the FAIR principles and the practicality and usefulness of being able to answer our new competency questions.}, author = {Celebi, Remzi and Moreira, Joao Rebelo and Hassan, Ahmed A. and Ayyar, Sandeep and Ridder, Lars and Kuhn, Tobias and Dumontier, Michel}, journal = {arXiv:1911.09531 [cs]}, keywords = {FAIR other contexts}, month = {November}, shorttitle = {Towards {FAIR} protocols and workflows}, title = {Towards {FAIR} protocols and workflows: {The} {OpenPREDICT} case study}, url = {http://arxiv.org/abs/1911.09531}, urldate = {2020-10-25}, year = {2019} } @article{chassanoff_curation_2019, author = {Chassanoff, Alexandra and Altman, Micah}, doi = {10/gf5m4r}, journal = {Journal of the Association for Information Science and Technology}, keywords = {Archive}, title = {Curation as {Interoperability} {With} the {Future}: {Preserving} {Scholarly} {Research} {Software} in {Academic} {Libraries}}, year = {2019} } @article{cheng_using_2019, author = {Cheng, Zui and Richardson, Jennifer C. and Newby, Timothy J.}, doi = {10.1007/s12528-019-09240-z}, journal = {Journal of Computing in Higher Education}, month = {October}, number = {2}, pages = {406--428}, title = {Using digital badges as goal-setting facilitators: a multiple case study}, volume = {32}, year = {2019} } @article{compeau_establishing_2019, author = {Compeau, Phillip}, doi = {10.1371/journal.pcbi.1006764}, editor = {Ouellette, Francis}, issn = {1553-7358}, journal = {PLOS Computational Biology}, month = {May}, number = {5}, pages = {e1006764}, title = {Establishing a computational biology flipped classroom}, volume = {15}, year = {2019} } @inproceedings{cosmo_software_2019, author = {Cosmo, Roberto Di}, keywords = {Open Science, ⛔ No DOI found, Archive}, title = {Software {Heritage}. {A} revolutionary infrastructure for {Open} {Science}}, url = {https://annex.softwareheritage.org/public/talks/2019/2019-02-05-MaxPlankDL.pdf}, year = {2019} } @inproceedings{dahlgren_getting_2019, author = {Dahlgren, Erin}, keywords = {⛔ No DOI found, Artifact Evaluation}, title = {Getting {Research} {Software} to {Work}: {A} {Case} {Study} on {Artifact} {Evaluation} for {OOPSLA} 2019}, year = {2019} } @article{davidson_d31_2019, abstract = {As part of the EOSC project family the FAIRsFAIR - Fostering Fair Data Practices in Europe - project aims to supply practical solutions for the use of the FAIR data principles throughout the research data life cycle. The FAIRsFAIR project runs from March 2019-February 2022. Policies are a crucial component in the FAIR ecosystem. To this end, FAIRsFAIR Work Package 3 (WP3): FAIR Data Policy and Practice carried out an analysis of the current data policy landscape at various levels (national, funder, publisher, institutional) to provide a snapshot of the situation in 2019 and to identify policy elements that support or hinder FAIR data practice. To provide a comparative baseline for reviewing the data policies of various stakeholders, the priority and supporting actions presented in the Turning FAIR into Reality (TFiR) action plan were employed. To assess how well the policies of different stakeholders currently reflect TFiR's action plan, we carried out desk research to characterise policies, undertook an analysis of responses to an open consultation, and conducted a small number of interviews. This report presents the findings of these landscape assessment activities and provides an evidence base for FAIRsFAIR to build upon as work begins to define a set of practical recommendations to support policy enhancement (D3.3). Landscaping activities have been a core activity during the initial stages of the FAIRsFAIR project and there has been close cooperation with colleagues in Work Package 3 carrying out the FAIR data policy and practice analyses; Work Package 2 on assessing FAIR requirements for interoperability and persistence; Work Package 6 on providing an overview of research communities' needs for competence centres; and Work Package 7 on mapping RDM policies and support as well as FAIR education offerings in European HEIs. In particular, efforts were made to avoid duplication of effort across the three open consultation and survey instruments developed to assess the current landscape and to define a consistent approach to presenting our findings. This is the draft version of the deliverable not yet approved by the European Commission. Though we can't undertake to respond to every comment directly, we are seeking wide feedback on this deliverable which will inform discussions and further work within FAIRsFAIR as well as collaborations with other relevant projects. Comments and suggestions can be added until 17 April 2020 at: https://drive.google.com/file/d/1EaPCF\_9ir9bNg9MPBe3heT1wNuDuS8tJ/view?usp=sharing}, author = {Davidson, Joy and Engelhardt, Claudia and Proudman, Vanessa and Stoy, Lennart and Whyte, Angus}, doi = {10.5281/zenodo.3558173}, keywords = {FAIR, FAIR practice, Research Data Management, Data Management Plans, Data Sharing, Funding Bodies, higher education institutions (HEIs), Policies, Publishers}, language = {eng}, month = {December}, title = {D3.1 {FAIR} {Policy} {Landscape} {Analysis}}, url = {https://zenodo.org/record/3558173#.XrpfmhNKiL4}, urldate = {2020-05-12}, year = {2019} } @article{de_souza_what_2019, author = {de Souza, Mario Rosado and Haines, Robert and Vigo, Markel and Jay, Caroline}, journal = {CoRR}, keywords = {Sustainability, ⛔ No DOI found}, title = {What {Makes} {Research} {Software} {Sustainable}? {An} {Interview} {Study} {With} {Research} {Software} {Engineers}}, url = {http://arxiv.org/abs/1903.06039}, volume = {abs/1903.06039}, year = {2019} } @article{di_cosmo_curated_2019, author = {Di Cosmo, Roberto and Gruenpeter, Morane and Marmol, Bruno and Monteil, Alain and Romary, Laurent and Sadowska, Jozefina}, keywords = {⛔ No DOI found, Digital Archive}, title = {Curated {Archiving} of {Research} {Software} {Artifacts}: lessons learned from the {French} open archive ({HAL})}, url = {https://hal.inria.fr/hal-02475835}, year = {2019} } @article{druskat_dare_2019, abstract = {Slides for a keynote given at the FAIR Software session, National eScience Symposium 2019 on 2019-11-21 at the Johan Cruijff ArenA, Amsterdam, The Netherlands.{\textbackslash}textlessbr{\textbackslash}textgreater}, author = {Druskat, Stephan}, copyright = {Creative Commons Attribution 4.0 International}, doi = {10.6084/M9.FIGSHARE.10565717}, keywords = {FOS: Computer and information sciences, FAIR other contexts, 160511 Research, 220107 Professional Ethics (incl. police and research ethics), 80306 Open Software, 80309 Software Engineering, 80399 Computer Software not elsewhere classified, Computer Software, ethics and religion, FOS: Philosophy, FOS: Political science, Science and Technology Policy}, pages = {6137762 Bytes}, title = {Dare to be mair than just {FAIR}! - {FAIR} {PLAY} to research software, courtesy of {RSEs}}, url = {https://figshare.com/articles/Dare\%5Fto\%5Fbe\%5Fmair\%5Fthan\%5Fjust\%5FFAIR\%5F-\%5FFAIR\%5FPLAY\%5Fto\%5Fresearch\%5Fsoftware\%5Fcourtesy\%5Fof\%5FRSEs/10565717}, urldate = {2020-11-07}, year = {2019} } @article{druskat_software_2019, abstract = {Software is essential for a lot of research, but it is not featured in citation graphs which have the potential to assign credit for software contributions. This is due to a traditionalistic focus on textual research products. In this paper, I propose an updated model for citation graphs that include software. This model takes into account intrinsic properties of software, and requirements for a robust system of software citation. I also give an outlook on future work to implement transitive credit, which is at the core of a fair system of academic citation which accounts for software on par with other research products.}, author = {Druskat, Stephan}, keywords = {Citation, ⛔ No DOI found}, month = {June}, title = {Software and their {Dependencies} in {Research} {Citation} {Graphs}}, url = {http://arxiv.org/abs/1906.06141v1}, year = {2019} } @book{erdmann_top_2019, author = {Erdmann, Christopher and Simons, Natasha and Otsuji, Reid and Labou, Stephanie and Johnson, Ryan and Castelao, Guilherme and {Bia Villas Boas} and {Anna-Lena Lamprecht} and Ortiz, Carlos Martinez and Garcia, Leyla and Kuzak, Mateusz and Martinez, Paula Andrea and Stokes, Liz and Honeyman, Tom and Wise, Sharyn and Quan, Josh and Peterson, Scott and Neeser, Amy and Karvovskaya, Lena and Lange, Otto and {Iza Witkowska} and Flores, Jacques and Bradley, Fiona and Hettne, Kristina and Verhaar, Peter and Companjen, Ben and {Laurents Sesink} and Schoots, Fieke and Schulte, Erik and {Rajaram Kaliyaperumal} and {Erzsebet Toth-Czifra} and Azevedo, Ricardo De Miranda and Muurling, Sanne and Brown, John and Chan, Janice and Quigley, Niamh and Federer, Lisa and Joubert, Douglas and {Allissa Dillman} and Wilkins, Kenneth and {Ishwar Chandramouliswaran} and Navale, Vivek and Wright, Susan and Giorgio, Silvia Di and {Akinyemi Mandela Fasemore} and F\"{o}rstner, Konrad and Sauerwein, Till and Seidlmayer, Eva and Zeitlin, Ilja and Bacon, Susannah and Hannan, Katie and Ferrers, Richard and Russell, Keith and Whitmore, Deidre and Dennis, Tim}, doi = {10.5281/zenodo.2555498}, keywords = {FAIR, Research Data}, language = {en}, publisher = {Zenodo}, title = {Top 10 {FAIR} {Data} \& {Software} {Things}}, year = {2019} } @article{faber_towards_2019, author = {Faber, Claas and Scheinert, Markus and Schmidt, Barbara}, doi = {10/gf5m4s}, keywords = {Citation}, title = {Towards {Sustainable} {Software} {Engineering} and {Citable} {Software} {Publications} at {GEOMAR}}, year = {2019} } @article{fehr_sustainable_2019, abstract = {Scientific software projects evolve rapidly in their initial development phase, yet at the end of a funding period, the completion of a research project, thesis, or publication, further engagement in the project may slow down or cease completely. To retain the invested effort for the sciences, this software needs to be preserved or handed over to a succeeding developer or team, such as the next generation of (PhD) students. Comparable guides provide top-down recommendations for project leads. This paper intends to be a bottom-up approach for sustainable hand-over processes from a developer's perspective. An important characteristic in this regard is the project's size, by which this guideline is structured. Furthermore, checklists are provided, which can serve as a practical guide for implementing the proposed measures.}, author = {Fehr, J\"{o}rg and Himpe, Christian and Rave, Stephan and Saak, Jens}, keywords = {Sustainability, ⛔ No DOI found}, month = {September}, title = {Sustainable {Research} {Software} {Hand}-{Over}}, url = {http://arxiv.org/abs/1909.09469v1}, year = {2019} } @article{fernandez_open_2019, abstract = {Open science describes the movement of making any research artefact available to the public and includes, but is not limited to, open access, open data, or open source. While open science is becoming generally accepted as a norm in other scientific disciplines, in software engineering, we are still struggling in adapting open science to the particularities of our discipline, rendering progress in our scientific community cumbersome. In this chapter, we will reflect upon the essentials of open science for software engineering including what open science is, why we should engage in it, and how we should do it. We particularly draw from our experiences in chairing roles implementing open science initiatives and researchers engaging in open science to critically discuss challenges and pitfalls, and to address more advanced topics such as how and under which conditions to share preprints, what infrastructure and licence model to cover, or how do it within the limitations of different reviewing models, such as double-blind reviewing. Our hope is to help establishing a common ground and to contribute to make open science a norm also in software engineering.}, author = {Fern\'{a}ndez, Daniel M\'{e}ndez and Graziotin, Daniel and Wagner, Stefan and Seibold, Heidi}, keywords = {Open Science, ⛔ No DOI found, Software Engineering}, month = {April}, title = {Open {Science} in {Software} {Engineering}}, year = {2019} } @article{garcia-silva_enabling_2019, author = {Garcia-Silva, Andres and Gomez-Perez, Jose Manuel and Palma, Raul and Krystek, Marcin and Mantovani, Simone and Foglini, Federica and Grande, Valentina and De Leo, Francesco and Salvi, Stefano and Trasatti, Elisa and Romaniello, Vito and Albani, Mirko and Silvagni, Cristiano and Leone, Rosemarie and Marelli, Fulvio and Albani, Sergio and Lazzarini, Michele and Napier, Hazel J. and Glaves, Helen M. and Aldridge, Timothy and Meertens, Charles and Boler, Fran and Loescher, Henry W. and Laney, Christine and Genazzio, Melissa A. and Crawl, Daniel and Altintas, Ilkay}, doi = {10.1016/j.future.2019.03.046}, issn = {0167739X}, journal = {Future Generation Computer Systems}, keywords = {FAIR other contexts}, language = {en}, month = {September}, pages = {550--564}, title = {Enabling {FAIR} research in {Earth} {Science} through research objects}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0167739X18314638}, urldate = {2020-11-07}, volume = {98}, year = {2019} } @article{georgeson_bionitio_2019, author = {Georgeson, Peter and Syme, Anna and Sloggett, Clare and Chung, Jessica and Dashnow, Harriet and Milton, Michael and Lonsdale, Andrew and Powell, David and Seemann, Torsten and Pope, Bernard}, doi = {10.1093/gigascience/giz109}, journal = {GigaScience}, month = {September}, number = {9}, title = {Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software}, volume = {8}, year = {2019} } @article{gey_workshop_2019, author = {Gey, Ronny and Leinweber, Katrin and Struck, Alexander and Str\o{}tgen, Robert and Pietsch, Christian}, doi = {10.18452/21407}, issn = {1860-7950}, journal = {LIBREAS. Library Ideas}, keywords = {⛔ No DOI found, Libraries}, title = {Workshop \@ {deRSE19}: {Libraries} for {Research} {Software} \& {Engineers}}, volume = {36}, year = {2019} } @article{goble_fair_2019, abstract = {Computational workflows describe the complex multi-step methods that are used for data collection, data preparation, analytics, predictive modelling, and simulation that lead to new data products. They can inherently contribute to the FAIR data principles: by processing data according to established metadata; by creating metadata themselves during the processing of data; and by tracking and recording data provenance. These properties aid data quality assessment and contribute to secondary data usage. Moreover, workflows are digital objects in their own right. This paper argues that FAIR principles for workflows need to address their specific nature in terms of their composition of executable software steps, their provenance, and their development.}, author = {Goble, Carole and Cohen-Boulakia, Sarah and Soiland-Reyes, Stian and Garijo, Daniel and Gil, Yolanda and Crusoe, Michael R. and Peters, Kristian and Schober, Daniel}, doi = {10.1162/dint_a_00033}, journal = {Data Intelligence}, keywords = {FAIR other contexts, Recent work}, month = {November}, number = {1-2}, pages = {108--121}, title = {{FAIR} {Computational} {Workflows}}, url = {https://doi.org/10.1162/dint\%5Fa\%5F00033}, urldate = {2020-05-11}, volume = {2}, year = {2019} } @article{gomez-diaz_evaluation_2019, author = {Gomez-Diaz, Teresa and Recio, Tomas}, doi = {10/gf69tr}, journal = {F1000Research}, keywords = {Evaluation}, month = {August}, pages = {1353--1353}, title = {On the evaluation of research software: the {CDUR} procedure}, volume = {8}, year = {2019} } @article{grange_struggle_2019, abstract = {Public availability and tracability of results from publically-funded work is a topic that gets more and more attention from funding agencies and scientific policy makers. However, most policies focus on data as the output of research. In this contribution, we focus on research software and we introduce the ASTRON Open Source Policy. Apart from the license used (Apache 2.0), the policy is written as a manual that explains how to license software, when to assign a Digital Object Identifier (DOI), and defines that all code should be put in an ASTRON managed repository. The policy has been made publically available, a DOI has been assigned to it and it has been put in a repository to stimulate the ADASS community to start a conversation on how to make our code publically accessible and citable.}, author = {Grange, Y. G. and J\"{u}rges, T. and Dijkema, T. J. and Halfwerk, R. and Schoonderbeek, G. W.}, keywords = {Policy, ⛔ No DOI found, Open Source}, month = {November}, title = {(the struggle) {Towards} an open source policy}, url = {http://arxiv.org/abs/1911.00534v1}, year = {2019} } @article{gruning_software_2019, author = {Gr\"{u}ning, Bj\"{o}rn A and Lampa, Samuel and Vaudel, Marc and Blankenberg, Daniel}, doi = {10.1093/gigascience/giz054}, journal = {GigaScience}, month = {May}, number = {5}, title = {Software engineering for scientific big data analysis}, volume = {8}, year = {2019} } @article{hasselbring_fair_2019, abstract = {In computational science and in computer science, research software is a central asset for research. Computational science is the application of computer science and software engineering principles to solving scientific problems, whereas computer science is the study of computer hardware and software design. The Open Science agenda holds that science advances faster when we can build on existing results. Therefore, research software has to be reusable for advancing science. Thus, we need proper research software engineering for obtaining reusable and sustainable research software. This way, software engineering methods may improve research in other disciplines. However, research in software engineering and computer science itself will also benefit from reuse when research software is involved. For good scientific practice, the resulting research software should be open and adhere to the FAIR principles (findable, accessible, interoperable and repeatable) to allow repeatability, reproducibility, and reuse. Compared to research data, research software should be both archived for reproducibility and actively maintained for reusability. The FAIR data principles do not require openness, but research software should be open source software. Established open source software licenses provide sufficient licensing options, such that it should be the rare exception to keep research software closed. We review and analyze the current state in this area in order to give recommendations for making computer science research software FAIR and open. We observe that research software publishing practices in computer science and in computational science show significant differences.}, author = {Hasselbring, Wilhelm and Carr, Leslie and Hettrick, Simon and Packer, Heather and Tiropanis, Thanassis}, keywords = {⛔ No DOI found, FAIR}, month = {August}, title = {{FAIR} and {Open} {Computer} {Science} {Research} {Software}}, year = {2019} } @inproceedings{hasselbring_microservices_2019, author = {Hasselbring, Wilhelm}, keywords = {Micro Services}, month = {August}, title = {Microservices as {Architectural} {Style} for {Research} {Software}}, url = {http://oceanrep.geomar.de/47554/}, year = {2019} } @article{helmholtz-gemeinschaft_empfehlungen_2019, author = {Helmholtz-Gemeinschaft, Task Group Forschungssoftware Des Arbeitskreises Open Science Der}, doi = {10/ggzwsc}, keywords = {Helmholtz}, title = {Empfehlungen zur {Implementierung} von {Leit}- und {Richtlinien} zum {Umgang} mit {Forschungssoftware} an den {Helmholtz}-{Zentren}. {Positionspapier}}, year = {2019} } @article{helmholtz-gemeinschaft_muster-richtlinie_2019, author = {Helmholtz-Gemeinschaft, Task Group Forschungssoftware Des Arbeitskreises Open Science Der}, doi = {10/ggzwsd}, keywords = {Helmholtz}, title = {Muster-{Richtlinie} {Nachhaltige} {Forschungssoftware} an den {Helmholtz}-{Zentren}}, year = {2019} } @article{herterich_d61_2019, abstract = {The overall objective of FAIRsFAIR is to accelerate the realization of the goals of the EOSC by opening up and sharing all knowledge, expertise, guidelines, implementations, new trajectories, courses and education on FAIR matters. To support this, FAIRsFAIR is tasked to set up a single FAIR Data Stewardship Competence Centre which this report defines as a shared hub of expertise in implementing FAIR data stewardship principles, offering leadership, coordination and cataloging services to connect relevant people, guidance, learning resources and curricula in different thematic areas. Requirements for competence centres in general and a core competence centre for FAIR data stewardship in general were identified by interviewing other members of the FAIRsFAIR project to understand their expectations for a core competence centre as well as the resources they will contribute to the knowledge base. Furthermore, we carried out a broad characterisation of current competence centres enriched with case studies of good examples for certain aspects of a competence centre. We created user stories for how stakeholders might interact with the competence centres and refined them through an open consultation answered by 106 people, interviews with EOSC clusters, and feedback gathered in workshops at the Open Science Fair 2019. Based on the description of work and our research, we have identified the following priorities for competence centres in general and the FAIRsFAIR core Competence Centre in particular: Advisory Create a catalogue of resources to support FAIR data stewardship Provide a help desk to support FAIR data stewardship Provide a networking tool to support FAIR data stewardship Harmonisation Apply emerging standards to describe learning resources in FAIR data stewardship Encourage economy of scale through deploying the same tools and certifying services addressing FAIR data needs Dissemination Develop training and guidance materials on FAIR data stewardship topics currently not covered Develop curation policies for the content aggregated and developed by the FAIRsFAIR Data Stewardship Competence Centre Deliver training on core competencies for FAIR data stewardship}, author = {Herterich, Patricia and Davidson, Joy and Whyte, Angus and Molloy, Laura and Matthews, Brian and Kayumbi Kabeya, Gabin}, doi = {10.5281/zenodo.3549791}, keywords = {FAIR practice, Competence Centre, Data Stewardship, Landscape analysis}, month = {December}, title = {D6.1 {Overview} of needs for competence centres}, url = {https://zenodo.org/record/3549791#.XrpfwxNKiL4}, urldate = {2020-05-12}, year = {2019} } @inproceedings{heyer_generic_2019, author = {Heyer, Gerhard and Kahmann, Christian and Kantner, Cathleen}, doi = {10/ggnd4c}, editor = {Draude, Claude and Lange, Martin and Sick, Bernhard}, keywords = {Software Engineering, Digital Humanities}, pages = {175--180}, publisher = {Gesellschaft f\"{u}r Informatik e.V.}, title = {Generic tools and individual research needs in the {Digital} {Humanities} – {Can} agile development help?}, year = {2019} } @article{hickey_recognizing_2019, author = {Hickey, Daniel T. and Chartrand, Grant T.}, doi = {10.1007/s10639-019-10000-w}, journal = {Education and Information Technologies}, month = {September}, number = {2}, pages = {943--956}, title = {Recognizing competencies vs. completion vs. participation: {Ideal} roles for web-enabled digital badges}, volume = {25}, year = {2019} } @article{hong_making_2019, author = {Hong, Neil Chue}, keywords = {Sustainability, ⛔ No DOI found, Open Source}, month = {September}, title = {Making {Open} {Source} {Research} {Software} {Visible}: {A} {Path} to {Better} {Sustainability}?}, url = {https://www.software.ac.uk/blog/2019-09-12-making-open-source-research-software-visible-path-better-sustainability}, year = {2019} } @article{hornschemeyer_mochten_2019, author = {H\"{o}rnschemeyer, J\"{o}rg}, doi = {10/ggnd4d}, journal = {Quellen und Forschungen aus italienischen Archiven und Bibliotheken}, keywords = {Humanities}, month = {November}, number = {1}, pages = {491--501}, title = {,,{M\"{o}chten} {Sie} das {Programm} wirklich l\"{o}schen?}, volume = {99}, year = {2019} } @article{imran_software_2019, abstract = {Software Engineering is a constantly evolving subject area that faces new challenges every day as it tries to automate newer business processes. One of the key challenges to the success of a software solution is attaining sustainability. The inability of numerous software to sustain for the desired time-length is caused by limited consideration given towards sustainability during the stages of software development. This review aims to present a detailed and inclusive study covering both the technical and non-technical challenges and approaches of software sustainability. A systematic and comprehensive literature review was conducted based on 107 relevant studies that were selected using the Evidence-Based Software Engineering (EBSE) technique. The study showed that sustainability can be achieved by conducting specific activities at the technical and non-technical levels. The technical level consists of software design, coding, and user experience attributes. The non-technical level consists of documentation, sustainability manifestos, training of software engineers, funding software projects, and leadership skills of project managers to achieve sustainability. This paper groups the existing research efforts based on the above aspects. Next, how those aspects affect open and closed source software is tabulated. Based on the findings of this review, it is seen that both technical and non-technical sustainability aspects are equally important, taking one into contention and ignoring the other will threaten the sustenance of software products.}, author = {Imran, Asif and Kosar, Tevfik}, keywords = {Sustainability, ⛔ No DOI found}, month = {October}, title = {Software {Sustainability}: {A} {Systematic} {Literature} {Review} and {Comprehensive} {Analysis}}, url = {http://arxiv.org/abs/1910.06109v1}, year = {2019} } @article{jay_theory-software_2019, abstract = {The Theory-Software Translation Workshop, held in New Orleans in February 2019, explored in depth the process of both instantiating theory in software - for example, implementing a mathematical model in code as part of a simulation - and using the outputs of software - such as the behavior of a simulation - to advance knowledge. As computation within research is now ubiquitous, the workshop provided a timely opportunity to reflect on the particular challenges of research software engineering - the process of developing and maintaining software for scientific discovery. In addition to the general challenges common to all software development projects, research software additionally must represent, manipulate, and provide data for complex theoretical constructs. Ensuring this process is robust is essential to maintaining the integrity of the science resulting from it, and the workshop highlighted a number of areas where the current approach to research software engineering would benefit from an evidence base that could be used to inform best practice. The workshop brought together expert research software engineers and academics to discuss the challenges of Theory-Software Translation over a two-day period. This report provides an overview of the workshop activities, and a synthesises of the discussion that was recorded. The body of the report presents a thematic analysis of the challenges of Theory-Software Translation as identified by workshop participants, summarises these into a set of research areas, and provides recommendations for the future direction of this work.}, author = {Jay, Caroline and Haines, Robert and Katz, Daniel S. and Carver, Jeffrey and Phillips, James C. and Dubey, Anshu and Gesing, Sandra and Turk, Matthew and Wan, Hui and van Dam, Hubertus and Howison, James and Morozov, Vitali and Brandt, Steven R.}, keywords = {⛔ No DOI found, Education}, month = {October}, title = {Theory-{Software} {Translation}: {Research} {Challenges} and {Future} {Directions}}, url = {http://arxiv.org/abs/1910.09902v1}, year = {2019} } @article{kaden_scholarly_2019, author = {Kaden, Ben and Kleineberg, Michael}, doi = {10/gf69ts}, journal = {LIBREAS. Library Ideas}, keywords = {Libraries}, title = {Scholarly {Makerspaces} – {Ein} {Zwischenbericht} zum {DFG}-{Projekt} {FuReSH}}, year = {2019} } @article{katz_state_2019, author = {Katz, Daniel S. and Druskat, Stephan and Haines, Robert and Jay, Caroline and Struck, Alexander}, doi = {10/gf5tgr}, journal = {Journal of Open Research Software}, keywords = {Sustainability}, title = {The {State} of {Sustainable} {Research} {Software}: {Learning} from the {Workshop} on {Sustainable} {Software} for {Science}: {Practice} and {Experiences} ({WSSSPE5}.1)}, volume = {7}, year = {2019} } @article{kullaslahti_professional_2019, author = {Kullaslahti, Jaana and Ruhalahti, Sanna and Brauer, Sanna}, doi = {10.17516/1997-1370-0387}, journal = {Journal of Siberian Federal University. Humanities \& Social Sciences}, month = {February}, number = {2}, pages = {175--186}, title = {Professional {Development} of {Digital} {Competences}: {Standardised} {Frameworks} {Supporting} {Evolving} {Digital} {Badging} {Practices}}, volume = {12}, year = {2019} } @article{kunkel_towards_2019, author = {Kunkel, Julian and Himstedt, Kai and H\"{u}bbe, Nathanael and St\"{u}ben, Hinnerk and Schr\"{o}er, Sandra and Kuhn, Michael and Riebisch, Matthias and Olbrich, Stephan and Ludwig, Thomas and Filinger, Weronika and Acquaviva, Jean-Thomas and Gerbes, Anja and Lafayette, Lev}, doi = {10.22369/issn.2153-4136/10/1/14}, issn = {2153-4136}, journal = {The Journal of Computational Science Education}, month = {January}, number = {1}, pages = {88--89}, title = {Towards an {HPC} {Certification} {Program}}, volume = {10}, year = {2019} } @article{lamprecht_towards_2019, abstract = {The FAIR Guiding Principles, published in 2016, aim to improve the findability, accessibility, interoperability and reusability of digital research objects for both humans and machines. Until now the FAIR principles have been mostly applied to resear}, author = {Lamprecht, Anna-Lena and Garcia, Leyla and Kuzak, Mateusz and Martinez, Carlos and Arcila, Ricardo and Martin Del Pico, Eva and Dominguez Del Angel, Victoria and van de Sandt, Stephanie and Ison, Jon and Martinez, Paula Andrea and McQuilton, Peter and Valencia, Alfonso and Harrow, Jennifer and Psomopoulos, Fotis and Gelpi, Josep Ll and Chue Hong, Neil and Goble, Carole and Capella-Gutierrez, Salvador}, doi = {10.3233/DS-190026}, issn = {2451-8484}, journal = {Data Science}, keywords = {FAIR, Open Science}, language = {en}, month = {November}, number = {Preprint}, pages = {1--23}, title = {Towards {FAIR} principles for research software}, url = {https://content.iospress.com/articles/data-science/ds190026}, urldate = {2020-05-11}, volume = {Preprint}, year = {2019} } @article{lee_happy_2019, author = {Lee, Michael}, doi = {10.21105/jose.00053}, journal = {Journal of Open Source Education}, month = {September}, number = {19}, pages = {53}, title = {Happy {Belly} {Bioinformatics}: an open-source resource dedicated to helping biologists utilize bioinformatics}, volume = {2}, year = {2019} } @article{lehvaslaiho_d21_2019, abstract = {This document is the first iteration of three annual reports on the state of FAIR in European scientific data by the FAIRsFAIR project. The interpretation of the FAIR data principles and their implications for services are now under intense scrutiny across Europe with multiple possible outcomes. The report is based on studies of public information, especially EOSC infrastructure efforts, and on limited surveying and interviews. The focus has been on understanding the usage of persistent identifiers and semantic interoperability. This study highlights the rapidity of change in technical solutions and wide variation across scientific domains in the uptake. More efforts are needed to guide researchers in best practices. This report is the first of three of a kind to be produced by the FAIRsFAIR project. This deliverable reviews and documents commonalities and possible gaps regarding semantic interoperability, and the use of metadata and persistent identifiers across infrastructures. Since many landscaping, specification and ``FAIRification'' activities are ongoing in the EOSC projects and elsewhere, much new information will be added to the later versions. The authors hope to get feedback to enrich and adjust the observations and conclusions made in this document. FAIR Digital Objects are central to the realisation of FAIR data principles. These objects need to be accompanied by Persistent Identifiers (PIDs) and rich metadata as they sit in a wider FAIR ecosystem comprising of services and infrastructures for FAIR, including identifiers, standards and repositories. The details of the FAIR principles for data, the implementation and implications for services are neither defined nor settled yet. The first suggestions for a more specific definition of a FAIR Digital Object has only recently been presented and will be further tested within the FAIRsFAIR project. Implications of the FAIR data principles for services, repositories and software are being investigated in other FAIRsFAIR tasks. Thus, this report focuses on semantic interoperability as it is a prerequisite for linking and finding data, as well as on the identifiers, which can offer persistence but also need context sensitive solutions. We use the term semantic artefact to overcome the terminological diversity that ironically is a challenge in discussions on this important element of the architecture we need in order to enable semantic interoperability within a FAIR Ecosystem. Development and implementation of the FAIR data principles should be driven by researcher needs to achieve wide penetration and the potentially significant benefits of FAIR data. The differences within research domains are often bigger than between them. Enforcing standards comes with the risk of making gaps grow between mature and emerging research domains. Community adoption and trust are decisive factors. Enabling services for publishing crosswalks, mappings and semantic application profiles are needed. All these should be registered and published in machine readable formats. A challenge with PID and data type registries is having them to promote reuse of data rather than bulk creation of PIDs. To support interoperability, they should be considered semantic artefacts, curated and reused. The aim should be born-FAIR data, which requires integrated and user friendly solutions throughout the research process and data lifecycle. By publishing application profiles, preferably in a common registry and in a machine readable format, reuse of semantic artefacts can be promoted, thereby enabling interoperability. Also curated registries like the EOSC Hub, FAIRsharing and re3data.org are important resources for enabling implementation of the FAIR data principles. We welcome comments and feedback. It is possible to comment here: https://docs.google.com/document/d/1LPMpuDSyIhzYT6S3bG2KPecdDXn-af4bJxzX2r\_xLIs/edit?usp=sharing}, author = {Lehv\"{a}slaiho, Heikki and Parland-von Essen, Jessica and Behnke, Claudia and Laine, Heidi and Riungu-Kalliosaari, Leah and Le Franc, Yann and Staiger, Christine}, doi = {10.5281/zenodo.3557381}, keywords = {metadata, FAIR principles, research data, FAIR practice, FAIR data, research data management, digital research infrastructures, ESFRIs, ontologies, persistent identifiers, semantic artefacts, semantic interoperability}, language = {eng}, month = {November}, title = {D2.1 {Report} on {FAIR} requirements for persistence and interoperability 2019}, url = {https://zenodo.org/record/3557381#.XrpfqBNKiL4}, urldate = {2020-05-12}, year = {2019} } @article{li_challenges_2019, author = {Li, Kai and Chen, Pei-Ying and Yan, Erjia}, doi = {10/gf8qz5}, journal = {Journal of Informetrics}, keywords = {Citation}, month = {February}, number = {1}, pages = {449--461}, title = {Challenges of measuring software impact through citations: {An} examination of the lme4 {R} package}, volume = {13}, year = {2019} } @inproceedings{loewe_sulmass_2019, author = {Loewe, Axel and Seemann, Gunnar and W\"{u}lfers, Eike Moritz and Huang, Yung-Lin and S\'{a}nchez, Jorge and Bach, Felix and Ulrich, Robert and Selzer, Michael}, doi = {10/gf5tgs}, keywords = {Management}, publisher = {Heidelberg University Library}, title = {{SuLMaSS} - {Sustainable} {Lifecycle} {Management} for {Scientific} {Software}}, year = {2019} } @article{loffler_rse4nfdi_2019, author = {L\"{o}ffler, Frank and Hammitzsch, Martin and Schieferdecker, Ina and N\"{u}st, Daniel and Druskat, Stephan}, doi = {10/gf2hxr}, keywords = {Sustainability, NFDI}, title = {{RSE4NFDI} - {Safeguarding} software sustainability in the {NFDI}}, year = {2019} } @article{lubbock_accredit_2019, author = {Lubbock, Alexander L. R.}, doi = {10/ggcmcp}, journal = {Nature}, keywords = {Sustainability}, month = {August}, number = {7771}, pages = {586--586}, title = {Accredit scientific software for sustainability}, volume = {572}, year = {2019} } @article{mangul_challenges_2019, author = {Mangul, Serghei and Mosqueiro, Thiago and Abdill, Richard J. and Duong, Dat and Mitchell, Keith and Sarwal, Varuni and Hill, Brian and Brito, Jaqueline and Littman, Russell Jared and Statz, Benjamin and Lam, Angela Ka-Mei and Dayama, Gargi and Grieneisen, Laura and Martin, Lana S. and Flint, Jonathan and Eskin, Eleazar and Blekhman, Ran}, doi = {10.1371/journal.pbio.3000333}, journal = {PLOS Biology}, month = {June}, number = {6}, pages = {e3000333}, title = {Challenges and recommendations to improve the installability and archival stability of omics computational tools}, volume = {17}, year = {2019} } @article{mangul_improving_2019, author = {Mangul, Serghei and Martin, Lana S. and Eskin, Eleazar and Blekhman, Ran}, doi = {10/ggc6j6}, journal = {Genome Biology}, keywords = {Biology}, month = {February}, number = {1}, title = {Improving the usability and archival stability of bioinformatics software}, volume = {20}, year = {2019} } @article{martinez-lopez_which_2019, author = {Mart\i{}\'nez-L\'{o}pez, J. Israel and Barr\'{o}n-Gonz\'{a}lez, Samantha and L\'{o}pez, Alejandro Mart\i{}\'nez}, doi = {10/ggcmcq}, journal = {Publications}, keywords = {Peer Review}, month = {September}, number = {3}, pages = {59--59}, title = {Which {Are} the {Tools} {Available} for {Scholars}? {A} {Review} of {Assisting} {Software} for {Authors} during {Peer} {Reviewing} {Process}}, volume = {7}, year = {2019} } @article{mcgrath_trainees_2019, author = {McGrath, Annette and Champ, Katherine and Shang, Catherine A. and van Dam, Ellen and Brooksbank, Cath and Morgan, Sarah L.}, doi = {10.1371/journal.pcbi.1006923}, editor = {Ouellette, Francis}, journal = {PLOS Computational Biology}, month = {June}, number = {6}, pages = {e1006923}, title = {From trainees to trainers to instructors: {Sustainably} building a national capacity in bioinformatics training}, volume = {15}, year = {2019} } @inproceedings{meade_changing_2019, address = {Cham}, author = {Meade, Edward and O'Keeffe, Emma and Lyons, Niall and Lynch, Dean and Yilmaz, Murat and Gulec, Ulas and O'Connor, Rory V. and Clarke, Paul M.}, booktitle = {Systems, software and services process improvement}, doi = {10.1007/978-3-030-28005-5_53}, editor = {Walker, Alastair and O'Connor, Rory V. and Messnarz, Richard}, isbn = {978-3-030-28005-5}, pages = {682--694}, publisher = {Springer International Publishing}, title = {The changing role of the software engineer}, year = {2019} } @inproceedings{milewicz_position_2019, author = {Milewicz, Reed and Rodeghero, Paige}, booktitle = {Proceedings of the 2019 {IEEE}/{ACM} 14{\textbackslash}textsuperscriptth {International} {Workshop} on {Software} {Engineering} for {Science} ({SE4Science})}, doi = {10.1109/se4science.2019.00012}, isbn = {978-1-7281-2276-2}, month = {May}, publisher = {IEEE}, title = {Position {Paper}: {Towards} {Usability} as a {First}-{Class} {Quality} of {HPC} {Scientific} {Software}}, year = {2019} } @article{mons_fair_2019, author = {Mons, Barend and Schultes, Erik and Liu, Fenghong and Jacobsen, Annika}, doi = {10.1162/dint_e_00023}, journal = {Data Intelligence}, month = {November}, number = {1-2}, pages = {1--9}, shorttitle = {The {FAIR} {Principles}}, title = {The {FAIR} {Principles}: {First} {Generation} {Implementation} {Choices} and {Challenges}}, url = {https://doi.org/10.1162/dint\%5Fe\%5F00023}, urldate = {2020-05-12}, volume = {2}, year = {2019} } @inproceedings{moreno_sortinghat_2019, author = {Moreno, David and Due\~{n}as, Santiago and Cosentino, Valerio and Fernandez, Miguel Angel and Zerouali, Ahmed and Robles, Gregorio and Gonzalez-Barahona, Jesus M.}, booktitle = {Proceedings of the 2019 {IEEE}/{ACM} 41{\textbackslash}textsuperscriptst {International} {Conference} on {Software} {Engineering}: {Companion} {Proceedings} ({ICSE}-{Companion})}, doi = {10.1109/icse-companion.2019.00036}, isbn = {978-1-7281-1764-5}, month = {May}, pages = {51--54}, publisher = {IEEE}, title = {{SortingHat}: {Wizardry} on {Software} {Project} {Members}}, year = {2019} } @article{morris_comparing_2019, author = {Morris, Bradley J. and Dragovich, Colleen and Todaro, Rachael and Balci, Sebiha and Dalton, Eve}, doi = {10.1007/s12528-019-09228-9}, journal = {Journal of Computing in Higher Education}, month = {May}, number = {3}, pages = {573--603}, title = {Comparing badges and learning goals in low- and high-stakes learning contexts}, volume = {31}, year = {2019} } @article{nielsen_tracking_2019, author = {Nielsen, Lars H. and Van De Sandt, Stephanie}, doi = {10/ggcmcr}, keywords = {Citation}, title = {Tracking citations to research software via {PIDs}}, year = {2019} } @article{noauthor_giving_2019, doi = {10/gfv4pq}, journal = {Nature Methods}, month = {February}, number = {3}, pages = {207--207}, title = {Giving software its due}, volume = {16}, year = {2019} } @article{nowogrodzki_how_2019, author = {Nowogrodzki, Anna}, doi = {10.1038/d41586-019-02046-0}, journal = {Nature}, keywords = {Open Source}, month = {July}, number = {7763}, pages = {133--134}, title = {How to support open-source software and stay sane}, volume = {571}, year = {2019} } @article{okane_building_2019, author = {O'Kane, Paula and Smith, Anne and Lerman, Michael P.}, doi = {10/gf63wz}, journal = {Organizational Research Methods}, keywords = {CAQDAS}, month = {August}, pages = {109442811986501--109442811986501}, title = {Building {Transparency} and {Trustworthiness} in {Inductive} {Research} {Through} {Computer}-{Aided} {Qualitative} {Data} {Analysis} {Software}}, year = {2019} } @article{park_badge_2019, author = {Park, Sungjin and Kim, Sangkyun}, doi = {10.2196/14342}, issn = {2291-9279}, journal = {JMIR Serious Games}, month = {May}, number = {2}, pages = {e14342}, title = {A {Badge} {Design} {Framework} for a {Gamified} {Learning} {Environment}: {Cases} {Analysis} and {Literature} {Review} for {Badge} {Design}}, volume = {7}, year = {2019} } @article{pianosi_how_2019, author = {Pianosi, Francesca and Sarrazin, Fanny and Wagener, Thorsten}, doi = {10/ggc6j8}, journal = {Environmental Modelling \& Software}, keywords = {Open Source, Adoption}, month = {November}, pages = {104579--104579}, title = {How successfully is open-source research software adopted? {Results} and implications of surveying the users of a sensitivity analysis toolbox}, year = {2019} } @article{pucker_integrating_2019, author = {Pucker, Boas and Schilbert, Hanna Marie and Schumacher, Sina Franziska}, doi = {10.1515/jib-2019-0005}, journal = {Journal of Integrative Bioinformatics}, month = {May}, number = {3}, title = {Integrating {Molecular} {Biology} and {Bioinformatics} {Education}}, volume = {16}, year = {2019} } @article{robinson_science_2019, abstract = {We should be in a golden age of scientific discovery, given that we have more data and more compute power available than ever before. But paradoxically, in many data-driven fields, the eureka moments are becoming more and more rare. Scientists, and the software tools they use, are struggling to keep pace with the explosion in the volume and complexity of scientific data. We describe here, five architectural principles we believe are essential in order to create effective, robust, and flexible platforms that make us of the best of emerging technology.}, author = {Robinson, Niall H. and Hamman, Joe and Abernathey, Ryan}, keywords = {Open Science, ⛔ No DOI found}, month = {August}, title = {Science needs to rethink how it interacts with big data: {Five} principles for effective scientific big data systems}, url = {http://arxiv.org/pdf/1908.03356v1}, year = {2019} } @article{rule_ten_2019, author = {Rule, Adam and Birmingham, Amanda and Zuniga, Cristal and Altintas, Ilkay and Huang, Shih-Cheng and Knight, Rob and Moshiri, Niema and Nguyen, Mai H. and Rosenthal, Sara Brin and P\'{e}rez, Fernando and Rose, Peter W.}, doi = {10.1371/journal.pcbi.1007007}, editor = {Lewitter, Fran}, journal = {PLOS Computational Biology}, month = {July}, number = {7}, pages = {e1007007}, title = {Ten simple rules for writing and sharing computational analyses in {Jupyter} {Notebooks}}, volume = {15}, year = {2019} } @inproceedings{schlauch_analytics_2019, author = {Schlauch, Tobias and Haupt, Carina and Meinel, Michael and Schreiber, Andreas}, booktitle = {2019 {IEEE} aerospace conference}, doi = {10.1109/AERO.2019.8741902}, isbn = {978-1-5386-6854-2}, title = {Analytics and insights about cultivating a software engineering community at {DLR}}, year = {2019} } @article{sholler_ten_2019, author = {Sholler, Dan and Steinmacher, Igor and Ford, Denae and Averick, Mara and Hoye, Mike and Wilson, Greg}, doi = {10.1371/journal.pcbi.1007296}, editor = {Markel, Scott}, journal = {PLOS Computational Biology}, month = {September}, number = {9}, pages = {e1007296}, title = {Ten simple rules for helping newcomers become contributors to open projects}, volume = {15}, year = {2019} } @article{sichani_diversity_2019, author = {Sichani, Anna-Maria and Baker, James and Afanador-Llach, Maria Jos\'{e} and Walsh, Brandon}, doi = {10.1629/uksg.465}, issn = {2048-7754}, journal = {Insights: the UKSG journal}, month = {May}, number = {1}, pages = {16}, title = {Diversity and inclusion in digital scholarship and pedagogy: the case of \emph{{The} {Programming} {Historian}}}, volume = {32}, year = {2019} } @article{sills_concerns_2019, author = {Sills, Jennifer and Hagedorn, Gregor and Kalmus, Peter and Mann, Michael and Vicca, Sara and Berge, Joke Van den and Ypersele, Jean-Pascal van and Bourg, Dominique and Rotmans, Jan and Kaaronen, Roope and Rahmstorf, Stefan and Kromp-Kolb, Helga and Kirchengast, Gottfried and Knutti, Reto and Seneviratne, Sonia I. and Thalmann, Philippe and Cretney, Raven and Green, Alison and Anderson, Kevin and Hedberg, Martin and Nilsson, Douglas and Kuttner, Amita and Hayhoe, Katharine}, doi = {10.1126/science.aax3807}, journal = {Science}, number = {6436}, pages = {139--140}, title = {Concerns of young protesters are justified}, volume = {364}, year = {2019} } @article{sims_enabling_2019, author = {Sims, Benjamin Hayden}, keywords = {⛔ No DOI found, Software Engineering, Teams}, month = {November}, title = {Enabling coordinated, distributed development of scientific software: {A} research agenda for adapting a team of teams approach}, year = {2019} } @article{stagge_assessing_2019, author = {Stagge, James H. and Rosenberg, David E. and Abdallah, Adel M. and Akbar, Hadia and Attallah, Nour A. and James, Ryan}, doi = {10.1038/sdata.2019.30}, issn = {2052-4463}, journal = {Scientific Data}, month = {February}, number = {1}, pages = {190030}, title = {Assessing data availability and research reproducibility in hydrology and water resources}, volume = {6}, year = {2019} } @article{tractenberg_mastery_2019, author = {Tractenberg, Rochelle E. and Lindvall, Jessica M. and Attwood, Teresa K. and Via, Allegra}, doi = {10.1371/journal.pone.0225256}, editor = {Provart, Nicholas J.}, journal = {PLOS ONE}, month = {November}, number = {11}, pages = {e0225256}, title = {The {Mastery} {Rubric} for {Bioinformatics}: {A} tool to support design and evaluation of career-spanning education and training}, volume = {14}, year = {2019} } @article{tsiamis_thousand_2019, author = {Tsiamis, Vasileios and Ienasescu, Hans-Ioan and Gabrielaitis, Dovydas and Palmblad, Magnus and Schw\"{a}mmle, Veit and Ison, Jon}, doi = {10/gf69tt}, journal = {Journal of Proteome Research}, keywords = {Proteomics}, month = {August}, title = {A {Thousand} and {One} {Software} for {Proteomics}: {Tales} of the {Toolmakers} of {Science}}, year = {2019} } @article{van_de_sandt_practice_2019, abstract = {Data and software citations are crucial for the transparency of research results and for the transmission of credit. But they are hard to track, because of the absence of a common citation standard. As a consequence, the FORCE11 recently proposed data and software citation principles as guidance for authors. Zenodo is recognized for the implementation of DOIs for software on a large scale. The minting of complementary DOIs for the version and concept allows measuring the impact of dynamic software. This article investigates characteristics of 5,456 citations to Zenodo data and software that were captured by the Asclepias Broker in January 2019. We analyzed the current state of data and software citation practices and the quality of software citation recommendations with regard to the impact of recent standardization efforts. Our findings prove that current citation practices and recommendations do not match proposed citation standards. We consequently suggest practical first steps towards the implementation of the software citation principles.}, author = {van de Sandt, Stephanie and Nielsen, Lars Holm and Ioannidis, Alexandros and Muench, August and Henneken, Edwin and Accomazzi, Alberto and Bigarella, Chiara and Lopez, Jose Benito Gonzalez and Dallmeier-Tiessen, S\"{u}nje}, keywords = {Citation, ⛔ No DOI found}, month = {November}, title = {Practice meets {Principle}: {Tracking} {Software} and {Data} {Citations} to {Zenodo} {DOIs}}, url = {https://arxiv.org/pdf/1911.00295.pdf}, year = {2019} } @article{vogel_challenges_2019, abstract = {Many fields of science rely on software systems to answer different research questions. For valid results researchers need to trust the results scientific software produces, and consequently quality assurance is of utmost importance. In this paper we are investigating the impact of quality assurance in the domain of computational materials science (CMS). Based on our experience in this domain we formulate challenges for validation and verification of scientific software and their results. Furthermore, we describe directions for future research that can potentially help dealing with these challenges.}, author = {Vogel, Thomas and Druskat, Stephan and Scheidgen, Markus and Draxl, Claudia and Grunske, Lars}, doi = {10.1109/SE4Science.2019.00010}, journal = {2019 IEEE/ACM 14ᵗʰ International Workshop on Software Engineering for Science (SE4Science)}, keywords = {⚠️ Invalid DOI, Validation, Verification}, month = {June}, title = {Challenges for {Verifying} and {Validating} {Scientific} {Software} in {Computational} {Materials} {Science}}, year = {2019} } @article{weigel_making_2019, abstract = {Research data currently face a huge increase of data objects with an increasing variety of types (data types, formats) and variety of workflows by which objects need to be managed across their lifecycle by data infrastructures. Researchers desire to shorten the workflows from data generation to analysis and publication, and the full workflow needs to become transparent to multiple stakeholders, including research administrators and funders. This poses challenges for research infrastructures and user-oriented data services in terms of not only making data and workflows findable, accessible, interoperable and reusable, but also doing so in a way that leverages machine support for better efficiency. One primary need to be addressed is that of findability, and achieving better findability has benefits for other aspects of data and workflow management. In this article, we describe how machine capabilities can be extended to make workflows more findable, in particular by leveraging the Digital Object Architecture, common object operations and machine learning techniques.}, author = {Weigel, Tobias and Schwardmann, Ulrich and Klump, Jens and Bendoukha, Sofiane and Quick, Robert}, doi = {10.1162/dint_a_00026}, journal = {Data Intelligence}, keywords = {FAIR other contexts}, month = {November}, number = {1-2}, pages = {40--46}, title = {Making {Data} and {Workflows} {Findable} for {Machines}}, url = {https://doi.org/10.1162/dint\%5Fa\%5F00026}, urldate = {2020-05-11}, volume = {2}, year = {2019} } @article{white_future_2019, author = {White, Samantha R. and Amarante, Linda M. and Kravitz, Alexxai V. and Laubach, Mark}, doi = {10/ggcmcv}, journal = {eNeuro}, keywords = {Open Source, Neuroscience}, month = {July}, number = {4}, pages = {ENEURO.0223--19.2019}, title = {The {Future} {Is} {Open}: {Open}-{Source} {Tools} for {Behavioral} {Neuroscience} {Research}}, volume = {6}, year = {2019} } @article{whyte_d32_2019, abstract = {This document provides an analysis of practices to support FAIR data production within a broad selection of research disciplines and research data repositories. It aims to inform the priorities of stakeholders interested in embedding those practices in research communities. Those stakeholders include policy makers, data librarians and others providing data services to research communities, as well as champions of FAIR principles in those communities. It also identifies priority themes for initial work in FAIRsFAIR to support ESFRI cluster and EOSC projects in FAIR culture change. These include developing a self-assessment framework for research infrastructures and institutions on their progress to support FAIR enabling practices in the communities they serve. This will underpin further work to build capabilities, describe good practice and address the highly uneven awareness of FAIR principles and the lack of information on research community implementation. Though we can't undertake to respond to every comment directly, we are seeking wide feedback on this deliverable which will inform discussions and further work within FAIRsFAIR as well as collaborations with other relevant projects. Comments and suggestions can be added at: https://docs.google.com/document/d/1xtFL21mlrI7YqzyNUnpRWz3uRqe0-EGocTStn\_ctOGo/edit?pli=1\#}, author = {Whyte, Angus and Engelhart, Claudia and Bangert, Daniel and Kayumbi-Kabeya, Gabin and Lambert, Simon and Thorley, Mark and O'Connor, Ryan and Herterich, Patricia and Davidson, Joy}, doi = {10.5281/zenodo.3581353}, keywords = {RDM, FAIR practice, FAIR data, research data management, data practices, data stewardship}, language = {eng}, month = {December}, title = {D3.2 {FAIR} {Data} {Practice} {Analysis}}, url = {https://zenodo.org/record/3581353#.XrpftRNKiL4}, urldate = {2020-05-12}, year = {2019} } @article{wiese_naming_2019, author = {Wiese, Igor Scaliante and Polato, Ivanilton and Pinto, Gustavo}, doi = {10.1109/ms.2019.2899838}, journal = {IEEE Software}, keywords = {Software Engineering, Survey}, title = {Naming the {Pain} in {Developing} {Scientific} {Software}}, year = {2019} } @article{wilkinson_addendum_2019, author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, Ijsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Merc\`{e} and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J. G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and 't Hoen, Peter A. C. and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and van der Lei, Johan and van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend}, doi = {10.1038/s41597-019-0009-6}, issn = {2052-4463}, journal = {Scientific Data}, month = {March}, number = {1}, title = {Addendum: {The} {FAIR} {Guiding} {Principles} for scientific data management and stewardship}, volume = {6}, year = {2019} } @article{wise_implementation_2019, abstract = {Biopharmaceutical industry R\&D, and indeed other life sciences R\&D such as biomedical, environmental, agricultural and food production, is becoming increasingly data-driven and can significantly improve its efficiency and effectiveness by implementing the FAIR (findable, accessible, interoperable, reusable) guiding principles for scientific data management and stewardship. By so doing, the plethora of new and powerful analytical tools such as artificial intelligence and machine learning will be able, automatically and at scale, to access the data from which they learn, and on which they thrive. FAIR is a fundamental enabler for digital transformation.}, author = {Wise, John and de Barron, Alexandra Grebe and Splendiani, Andrea and Balali-Mood, Beeta and Vasant, Drashtti and Little, Eric and Mellino, Gaspare and Harrow, Ian and Smith, Ian and Taubert, Jan and van Bochove, Kees and Romacker, Martin and Walgemoed, Peter and Jimenez, Rafael C. and Winnenburg, Rainer and Plasterer, Tom and Gupta, Vibhor and Hedley, Victoria}, doi = {10.1016/j.drudis.2019.01.008}, issn = {1359-6446}, journal = {Drug Discovery Today}, keywords = {FAIR practice}, language = {en}, month = {April}, number = {4}, pages = {933--938}, title = {Implementation and relevance of {FAIR} data principles in biopharmaceutical {R}\&{D}}, url = {http://www.sciencedirect.com/science/article/pii/S1359644618303039}, urldate = {2020-05-12}, volume = {24}, year = {2019} } @article{ye_open_2019, abstract = {The Sustainability and Industry Partnership Work Group (SIP-WG) is a part of the National Cancer Institute Informatics Technology for Cancer Research (ITCR) program. The charter of the SIP-WG is to investigate options of long-term sustainability of open source software (OSS) developed by the ITCR, in part by developing a collection of business model archetypes that can serve as sustainability plans for ITCR OSS development initiatives. The workgroup assembled models from the ITCR program, from other studies, and via engagement of its extensive network of relationships with other organizations (e.g., Chan Zuckerberg Initiative, Open Source Initiative and Software Sustainability Institute). This article reviews existing sustainability models and describes ten OSS use cases disseminated by the SIP-WG and others, and highlights five essential attributes (alignment with unmet scientific needs, dedicated development team, vibrant user community, feasible licensing model, and sustainable financial model) to assist academic software developers in achieving best practice in software sustainability.}, author = {Ye, Y. and Boyce, R. D. and Davis, M. K. and Elliston, K. and Davatzikos, C. and Fedorov, A. and Fillion-Robin, J. C. and Foster, I. and Gilbertson, J. and Heiskanen, M. and Klemm, J. and Lasso, A. and Miller, J. V. and Morgan, M. and Pieper, S. and Raumann, B. and Sarachan, B. and Savova, G. and Silverstein, J. C. and Taylor, D. and Zelnis, J. and Zhang, G. Q. and Becich, M. J.}, keywords = {Sustainability, ⛔ No DOI found, Open Source}, month = {December}, title = {Open {Source} {Software} {Sustainability} {Models}: {Initial} {White} {Paper} from the {Informatics} {Technology} for {Cancer} {Research} {Sustainability} and {Industry} {Partnership} {Work} {Group}}, year = {2019} } @article{abramatic_building_2018, author = {Abramatic, Jean-Fran\c{c}ois and Cosmo, Roberto Di and Zacchiroli, Stefano}, doi = {10/gfvpqx}, editor = {{ACM}}, issn = {0001-0782}, journal = {Communications of the ACM}, keywords = {Digital Archive}, month = {October}, number = {10}, pages = {29--31}, title = {Building the {Universal} {Archive} of {Source} {Code}}, url = {https://cacm.acm.org/magazines/2018/10/231366-building-the-universal-archive-of-source-code/fulltext}, volume = {61}, year = {2018} } @article{alterovitz_enabling_2018, author = {Alterovitz, Gil and Dean, Dennis and Goble, Carole and Crusoe, Michael R. and Soiland-Reyes, Stian and Bell, Amanda and Hayes, Anais and Suresh, Anita and Purkayastha, Anjan and King, Charles H. and Taylor, Dan and Johanson, Elaine and Thompson, Elaine E. and Donaldson, Eric and Morizono, Hiroki and Tsang, Hsinyi and Vora, Jeet K. and Goecks, Jeremy and Yao, Jianchao and Almeida, Jonas S. and Keeney, Jonathon and Addepalli, KanakaDurga and Krampis, Konstantinos and Smith, Krista M. and Guo, Lydia and Walderhaug, Mark and Schito, Marco and Ezewudo, Matthew and Guimera, Nuria and Walsh, Paul and Kahsay, Robel and Gottipati, Srikanth and Rodwell, Timothy C. and Bloom, Toby and Lai, Yuching and Simonyan, Vahan and Mazumder, Raja}, doi = {10.1371/journal.pbio.3000099}, issn = {1545-7885}, journal = {PLOS Biology}, keywords = {FAIR other contexts}, language = {en}, month = {December}, number = {12}, pages = {e3000099}, title = {Enabling precision medicine via standard communication of {HTS} provenance, analysis, and results}, url = {https://dx.plos.org/10.1371/journal.pbio.3000099}, urldate = {2020-10-25}, volume = {16}, year = {2018} } @article{batut_community-driven_2018, author = {Batut, B\'{e}r\'{e}nice and Hiltemann, Saskia and Bagnacani, Andrea and Baker, Dannon and Bhardwaj, Vivek and Blank, Clemens and Bretaudeau, Anthony and Brillet-Gu\'{e}guen, Loraine and \v{C}ech, Martin and Chilton, John and Clements, Dave and Doppelt-Azeroual, Olivia and Erxleben, Anika and Freeberg, Mallory Ann and Gladman, Simon and Hoogstrate, Youri and Hotz, Hans-Rudolf and Houwaart, Torsten and Jagtap, Pratik and Larivi\`{e}re, Delphine and Le Corguill\'{e}, Gildas and Manke, Thomas and Mareuil, Fabien and Ram\'{\i}rez, Fidel and Ryan, Devon and Sigloch, Florian Christoph and Soranzo, Nicola and Wolff, Joachim and Videm, Pavankumar and Wolfien, Markus and Wubuli, Aisanjiang and Yusuf, Dilmurat and Taylor, James and Backofen, Rolf and Nekrutenko, Anton and Gr\"{u}ning, Bj\"{o}rn}, doi = {10.1016/j.cels.2018.05.012}, issn = {2405-4712}, journal = {Cell Systems}, month = {June}, number = {6}, pages = {752--758.e1}, title = {Community-{Driven} {Data} {Analysis} {Training} for {Biology}}, volume = {6}, year = {2018} } @article{boeckhout_fair_2018, abstract = {The FAIR guiding principles for research data stewardship (findability, accessibility, interoperability, and reusability) look set to become a cornerstone of research in the life sciences. A critical appraisal of these principles in light of ongoing discussions and developments about data sharing is in order. The FAIR principles point the way forward for facilitating data sharing more systematically--provided that a number of ethical, methodological, and organisational challenges are addressed as well.}, author = {Boeckhout, Martin and Zielhuis, Gerhard A. and Bredenoord, Annelien L.}, copyright = {2018 European Society of Human Genetics}, doi = {10.1038/s41431-018-0160-0}, issn = {1476-5438}, journal = {European Journal of Human Genetics}, keywords = {FAIR other contexts}, language = {en}, month = {July}, number = {7}, pages = {931--936}, shorttitle = {The {FAIR} guiding principles for data stewardship}, title = {The {FAIR} guiding principles for data stewardship: fair enough?}, url = {https://www.nature.com/articles/s41431-018-0160-0}, urldate = {2020-10-25}, volume = {26}, year = {2018} } @article{bolyen_introduction_2018, author = {Bolyen, Evan and Rideout, Jai Ram and Chase, John and Pitman, T. Anders and Shiffer, Arron and Mercurio, Willow and Dillon, Matthew R. and Caporaso, J. Gregory}, doi = {10.21105/jose.00027}, journal = {Journal of Open Source Education}, month = {October}, number = {5}, pages = {27}, title = {An {Introduction} to {Applied} {Bioinformatics}: a free, open, and interactive text.}, volume = {1}, year = {2018} } @inproceedings{borras-gene_use_2018, author = {Borr\'{a}s-Gen\'{e}, Oriol}, booktitle = {2018 {International} {Symposium} on {Computers} in {Education} ({SIIE})}, doi = {10.1109/siie.2018.8586734}, isbn = {978-1-5386-6505-3}, month = {September}, publisher = {IEEE}, title = {Use of digital badges for training in digital skills within higher education}, year = {2018} } @article{bryan_excuse_2018, author = {Bryan, Jennifer}, doi = {10.1080/00031305.2017.1399928}, journal = {The American Statistician}, month = {January}, number = {1}, pages = {20--27}, title = {Excuse {Me}, {Do} {You} {Have} a {Moment} to {Talk} {About} {Version} {Control}?}, volume = {72}, year = {2018} } @article{carey_ten_2018, author = {Carey, Maureen A. and Papin, Jason A.}, doi = {10.1371/journal.pcbi.1005871}, editor = {Markel, Scott}, journal = {PLOS Computational Biology}, month = {January}, number = {1}, pages = {e1005871}, title = {Ten simple rules for biologists learning to program}, volume = {14}, year = {2018} } @article{cetinkaya-rundel_infrastructure_2018, author = {\c{C}etinkaya-Rundel, Mine and Rundel, Colin}, doi = {10.1080/00031305.2017.1397549}, journal = {The American Statistician}, month = {January}, number = {1}, pages = {58--65}, title = {Infrastructure and {Tools} for {Teaching} {Computing} {Throughout} the {Statistical} {Curriculum}}, volume = {72}, year = {2018} } @article{cicirello_software_2018, author = {Cicirello, Vincent}, doi = {10.4108/eai.28-1-2021.168507}, journal = {EAI Endorsed Transactions on Cognitive Communications}, keywords = {research software, publication}, month = {July}, pages = {168507--168507}, title = {Software {Articles} and {Open} {Source} {Research} {Software}: {The} {Why}, the {What}, and the {How}}, year = {2018} } @inproceedings{cohen_building_2018, author = {Cohen, Jeremy and Katz, Daniel S. and Barker, Michelle and Haines, Robert and Hong, Neil Chue}, booktitle = {2018 {IEEE} 14{\textbackslash}textbackslashtextsuperscriptth {International} {Conference} on e-{Science} (e-{Science})}, doi = {10/gfvpq4}, keywords = {Policy, Sustainability, Software Engineering, Training}, publisher = {IEEE}, title = {Building a {Sustainable} {Structure} for {Research} {Software} {Engineering} {Activities}}, year = {2018} } @article{cope_library_2018, author = {Cope, Jez and Baker, James}, doi = {10.2218/ijdc.v12i2.576}, issn = {1746-8256}, journal = {International Journal of Digital Curation}, month = {May}, number = {2}, pages = {266--273}, title = {Library {Carpentry}: {Software} {Skills} {Training} for {Library} {Professionals}}, volume = {12}, year = {2018} } @inproceedings{cosmo_identifiers_2018, author = {Cosmo, Roberto Di and Gruenpeter, Morane and Zacchiroli, Stefano}, booktitle = {{iPRES} 2018 - 15{\textbackslash}textbackslashtextsuperscriptth {International} {Conference} on {Digital} {Preservation}}, keywords = {Digital Archive, Preservation, Identifiers}, month = {September}, title = {Identifiers for {Digital} {Objects}: the {Case} of {Software} {Source} {Code} {Preservation}}, url = {https://hal.archives-ouvertes.fr/hal-01865790 https://hal.archives-ouvertes.fr/hal-01865790/file/main.pdf}, year = {2018} } @article{deelman_future_2018, abstract = {Today's computational, experimental, and observational sciences rely on computations that involve many related tasks. The success of a scientific mission often hinges on the computer automation of these workflows. In April 2015, the US Department of Energy DOE invited a diverse group of domain and computer scientists from national laboratories supported by the Office of Science, the National Nuclear Security Administration, from industry, and from academia to review the workflow requirements of DOE's science and national security missions, to assess the current state of the art in science workflows, to understand the impact of emerging extreme-scale computing systems on those workflows, and to develop requirements for automated workflow management in future and existing environments. This article is a summary of the opinions of over 50 leading researchers attending this workshop. We highlight use cases, computing systems, workflow needs and conclude by summarizing the remaining challenges this community sees that inhibit large-scale scientific workflows from becoming a mainstream tool for extreme-scale science.}, author = {Deelman, Ewa and Peterka, Tom and Altintas, Ilkay and Carothers, Christopher D and van Dam, Kerstin Kleese and Moreland, Kenneth and Parashar, Manish and Ramakrishnan, Lavanya and Taufer, Michela and Vetter, Jeffrey}, issn = {1094-3420}, journal = {International Journal of High Performance Computing Applications}, keywords = {FAIR other contexts}, month = {January}, number = {1}, pages = {159--175}, title = {The future of scientific workflows}, volume = {32}, year = {2018} } @incollection{donnelly_irelands_2018, author = {Donnelly, Roisin and Maguire, Terry}, booktitle = {Transforming our {World} {Through} {Design}, {Diversity} and {Education}}, doi = {10.3233/978-1-61499-923-2-655}, editor = {Craddock, Gerald and Doran, Cormac and McNutt, Larry and Rice, D\'{o}nal}, isbn = {978-1-61499-923-2}, pages = {655--666}, publisher = {IOS Press}, series = {Studies in {Health} {Technology} and {Informatics}}, title = {Ireland's {Higher} {Education} {Teachers} {Have} a {National} {Professional} {Development} {Framework}, {Now} {What}?}, volume = {256}, year = {2018} } @article{european_commission_commission_2018, author = {{European Commission}}, issn = {1977-0677}, journal = {Official Journal of the European Union}, month = {May}, number = {134}, pages = {12--18}, title = {Commission {Recommendation} ({EU}) 2018/790 of 25 {April} 2018 on access to and preservation of scientific information}, url = {http://data.europa.eu/eli/reco/2018/790/oj}, volume = {61}, year = {2018} } @inproceedings{facey-shaw_digital_2018, author = {Facey-Shaw, Lisa and Specht, Marcus and Bartley-Bryan, Jeanette}, booktitle = {2018 {IEEE} {Frontiers} in {Education} {Conference} ({FIE})}, doi = {10.1109/fie.2018.8659227}, isbn = {978-1-5386-1174-6}, month = {October}, publisher = {IEEE}, title = {Digital {Badges} for {Motivating} {Introductory} {Programmers}: {Qualitative} {Findings} from {Focus} {Groups}}, year = {2018} } @article{garnett_use_2018, author = {Garnett, Timna and Button, Didy}, doi = {10.1016/j.nepr.2018.06.013}, journal = {Nurse Education in Practice}, month = {September}, pages = {1--8}, title = {The use of digital badges by undergraduate nursing students: {A} three-year study}, volume = {32}, year = {2018} } @article{gruning_practical_2018, author = {Gr\"{u}ning, Bj\"{o}rn and Chilton, John and K\"{o}ster, Johannes and Dale, Ryan and Soranzo, Nicola and van den Beek, Marius and Goecks, Jeremy and Backofen, Rolf and Nekrutenko, Anton and Taylor, James}, doi = {10.1016/j.cels.2018.03.014}, journal = {Cell Systems}, keywords = {reproducibility, life sciences}, month = {June}, number = {6}, pages = {631--635--631--635}, title = {Practical {Computational} {Reproducibility} in the {Life} {Sciences}}, volume = {6}, year = {2018} } @inproceedings{haupt_software_2018, address = {New York, New York, USA}, author = {Haupt, Carina and Schlauch, Tobias and Meinel, Michael}, booktitle = {Proceedings of the {SE4Science} '18: 2018 {IEEE}/{ACM} 13{\textbackslash}textsuperscriptth {International} {Workshop} on {Software} {Engineering} for {Science}}, doi = {10.1145/3194747.3194749}, editor = {Bilof, Randall}, isbn = {978-1-4503-5748-7}, month = {June}, pages = {16--19}, publisher = {ACM}, title = {The software engineering initiative of {DLR}}, year = {2018} } @inproceedings{haupt_software_2018-1, author = {Haupt, Carina and Meinel, Michael and Schlauch, Tobias}, doi = {10/gf3twn}, keywords = {DLR}, pages = {16--19}, title = {The software engineering initiative of {DLR}: overcome the obstacles and develop sustainable software}, year = {2018} } @article{holub_enhancing_2018, abstract = {The known challenge of underutilization of data and biological material from biorepositories as potential resources for medical research has been the focus of discussion for over a decade. Recently developed guidelines for improved data availability and reusability--entitled FAIR Principles (Findability, Accessibility, Interoperability, and Reusability)--are likely to address only parts of the problem. In this article, we argue that biological material and data should be viewed as a unified resource. This approach would facilitate access to complete provenance information, which is a prerequisite for reproducibility and meaningful integration of the data. A unified view also allows for optimization of long-term storage strategies, as demonstrated in the case of biobanks. We propose an extension of the FAIR Principles to include the following additional components: (1) quality aspects related to research reproducibility and meaningful reuse of the data, (2) incentives to stimulate effective enrichment of data sets and biological material collections and its reuse on all levels, and (3) privacy-respecting approaches for working with the human material and data. These FAIR-Health principles should then be applied to both the biological material and data. We also propose the development of common guidelines for cloud architectures, due to the unprecedented growth of volume and breadth of medical data generation, as well as the associated need to process the data efficiently.}, author = {Holub, Petr and Kohlmayer, Florian and Prasser, Fabian and Mayrhofer, Michaela Th. and Schl\"{u}nder, Irene and Martin, Gillian M. and Casati, Sara and Koumakis, Lefteris and Wutte, Andrea and Kozera, \L{}ukasz and Strapagiel, Dominik and Anton, Gabriele and Zanetti, Gianluigi and Sezerman, Osman Ugur and Mendy, Maimuna and Val\'{\i}k, Dalibor and Lavitrano, Marialuisa and Dagher, Georges and Zatloukal, Kurt and van Ommen, GertJan B. and Litton, Jan-Eric}, doi = {10.1089/bio.2017.0110}, issn = {1947-5535}, journal = {Biopreservation and Biobanking}, keywords = {FAIR practice}, month = {January}, number = {2}, pages = {97--105}, shorttitle = {Enhancing {Reuse} of {Data} and {Biological} {Material} in {Medical} {Research}}, title = {Enhancing {Reuse} of {Data} and {Biological} {Material} in {Medical} {Research}: {From} {FAIR} to {FAIR}-{Health}}, url = {https://www.liebertpub.com/doi/10.1089/bio.2017.0110}, urldate = {2020-05-12}, volume = {16}, year = {2018} } @article{institute_checklist_2018, author = {Institute, The Software Sustainability}, doi = {10/gf2hxq}, keywords = {SMP, SSI}, title = {Checklist for a {Software} {Management} {Plan}}, year = {2018} } @article{johanson_software_2018, author = {Johanson, Arne and Hasselbring, Wilhelm}, doi = {10.1109/mcse.2018.021651343}, journal = {Computing in Science \& Engineering}, keywords = {Scientific Computing, Software Engineering}, month = {March}, number = {2}, pages = {90--109}, title = {Software {Engineering} for {Computational} {Science}: {Past}, {Present}, {Future}}, volume = {20}, year = {2018} } @article{kanewala_testing_2018, abstract = {Context: Scientific software plays an important role in critical decision making, for example making weather predictions based on climate models, and computation of evidence for research publications. Recently, scientists have had to retract publications due to errors caused by software faults. Systematic testing can identify such faults in code. Objective: This study aims to identify specific challenges, proposed solutions, and unsolved problems faced when testing scientific software. Method: We conducted a systematic literature survey to identify and analyze relevant literature. We identified 62 studies that provided relevant information about testing scientific software. Results: We found that challenges faced when testing scientific software fall into two main categories: (1) testing challenges that occur due to characteristics of scientific software such as oracle problems and (2) testing challenges that occur due to cultural differences between scientists and the software engineering community such as viewing the code and the model that it implements as inseparable entities. In addition, we identified methods to potentially overcome these challenges and their limitations. Finally we describe unsolved challenges and how software engineering researchers and practitioners can help to overcome them. Conclusions: Scientific software presents special challenges for testing. Specifically, cultural differences between scientist developers and software engineers, along with the characteristics of the scientific software make testing more difficult. Existing techniques such as code clone detection can help to improve the testing process. Software engineers should consider special challenges posed by scientific software such as oracle problems when developing testing techniques.}, author = {Kanewala, Upulee and Bieman, James M.}, keywords = {⛔ No DOI found, Testing, Review}, month = {April}, title = {Testing {Scientific} {Software}: {A} {Systematic} {Literature} {Review}}, url = {http://arxiv.org/abs/1804.01954v1}, year = {2018} } @article{katz_community_2018, author = {Katz, Daniel S. and McInnes, Lois Curfman and Bernholdt, David E. and Mayes, Abigail Cabunoc and Hong, Neil P. Chue and Duckles, Jonah and Gesing, Sandra and Heroux, Michael A. and Hettrick, Simon and Jimenez, Rafael C. and Pierce, Marlon and Weaver, Belinda and Wilkins-Diehr, Nancy}, doi = {10/gfvpq3}, journal = {Computing in Science \& Engineering}, keywords = {Software Engineering, Culture, Ecosystem, Organization}, pages = {1--1}, title = {Community {Organizations}: {Changing} the {Culture} in {Which} {Research} {Software} {Is} {Developed} and {Sustained}}, year = {2018} } @article{kugler_interoperable_2018, abstract = {The first version of the Integrated Public Use Microdata Series (IPUMS) was released to users in 1993, and since that time IPUMS has come to stand for interoperable and accessible census and survey data. Initially created to harmonize U.S. census microdata over time, IPUMS now includes microdata from the U.S. and international censuses and from surveys on health, employment, and other topics. IPUMS also provides geo-spatial data, aggregate population data, and environmental data. IPUMS supports ten data products, each disseminating an integrated data collection with a set of tools that make complex data easy to find, access, and use. Key features are record-level integration to create interoperable datasets, user-friendly interfaces, and comprehensive metadata and documentation. The IPUMS philosophy aligns closely with the FAIR principles of findability, accessibility, interoperability, and re-usability. IPUMS data have catalyzed knowledge generation across a wide range of social science and other disciplines, as evidenced by the large volume of publications and other products created by the vast IPUMS user community.}, author = {Kugler, Tracy A. and Fitch, Catherine A.}, copyright = {2018 The Author(s)}, doi = {10.1038/sdata.2018.7}, issn = {2052-4463}, journal = {Scientific Data}, keywords = {FAIR practice}, language = {en}, month = {February}, number = {1}, pages = {180007}, title = {Interoperable and accessible census and survey data from {IPUMS}}, url = {https://www.nature.com/articles/sdata20187}, urldate = {2020-05-12}, volume = {5}, year = {2018} } @article{lee_ten_2018, author = {Lee, Benjamin D.}, doi = {10/gfrk2t}, journal = {PLOS Computational Biology}, keywords = {Documentation}, month = {December}, number = {12}, pages = {e1006561--e1006561}, title = {Ten simple rules for documenting scientific software}, volume = {14}, year = {2018} } @inproceedings{m_c_carvalho_semantic_2018, address = {Amsterdam}, author = {M. C. Carvalho, Lucas Augusto and Garijo, Daniel and Bauzer Medeiros, Claudia and Gil, Yolanda}, booktitle = {2018 {IEEE} 14th {International} {Conference} on e-{Science} (e-{Science})}, doi = {10.1109/eScience.2018.00132}, isbn = {978-1-5386-9156-4}, keywords = {FAIR other contexts}, month = {October}, pages = {431--441}, publisher = {IEEE}, title = {Semantic {Software} {Metadata} for {Workflow} {Exploration} and {Evolution}}, url = {https://ieeexplore.ieee.org/document/8588751/}, urldate = {2020-10-25}, year = {2018} } @article{mangul_challenges_2018, author = {Mangul, Serghei and Mosqueiro, Thiago and Abdill, Richard J. and Duong, Dat and Mitchell, Keith and Sarwal, Varuni and Hill, Brian and Brito, Jaqueline and Littman, Russell Jared and Statz, Benjamin and Lam, Angela Ka-Mei and Dayama, Gargi and Grieneisen, Laura and Martin, Lana S. and Flint, Jonathan and Eskin, Eleazar and Blekhman, Ran}, doi = {10/gfgntm}, keywords = {Reproducibility}, month = {October}, title = {Challenges and recommendations to improve installability and archival stability of omics computational tools}, year = {2018} } @article{marwick_packaging_2018, author = {Marwick, Ben and Boettiger, Carl and Mullen, Lincoln}, doi = {10.7287/peerj.preprints.3192v2}, keywords = {open science, research data, research software, R}, month = {March}, title = {Packaging data analytical work reproducibly using {R} (and friends)}, year = {2018} } @inproceedings{Mendez_2018, author = {Mendez, Christopher and Padala, Hema Susmita and Steine-Hanson, Zoe and Hilderbrand, Claudia and Horvath, Amber and Hill, Charles and Simpson, Logan and Patil, Nupoor and Sarma, Anita and Burnett, Margaret}, booktitle = {Proceedings of the 40th International Conference on Software Engineering}, collection = {ICSE '18}, doi = {10.1145/3180155.3180241}, month = {May}, pages = {1004–1015}, publisher = {ACM}, series = {ICSE '18}, title = {Open source barriers to entry, revisited: a sociotechnical perspective}, url = {http://dx.doi.org/10.1145/3180155.3180241}, year = {2018} } @article{mulder_development_2018, author = {Mulder, Nicola and Schwartz, Russell and Brazas, Michelle D. and Brooksbank, Cath and Gaeta, Bruno and Morgan, Sarah L. and Pauley, Mark A. and Rosenwald, Anne and Rustici, Gabriella and Sierk, Michael and Warnow, Tandy and Welch, Lonnie}, doi = {10.1371/journal.pcbi.1005772}, editor = {Troyanskaya, Olga G.}, journal = {PLOS Computational Biology}, month = {February}, number = {2}, pages = {e1005772}, title = {The development and application of bioinformatics core competencies to improve bioinformatics training and education}, volume = {14}, year = {2018} } @article{nust_presentations_2018, author = {N\"{u}st, Daniel and Hammitzsch, Martin and Topping, David and Drost, Niels and Fritzsch, Bernadette and Devaraju, Anusuriya}, doi = {10/gfzgkh}, keywords = {Geoscience}, title = {Presentations for {EGU} {GA} {Townhall} meeting: {Research} {Software} {Engineers} in the {Geosciences}}, year = {2018} } @article{oishi_perspectives_2018, abstract = {As the Science Mission Directorate contemplates establishing an open code policy, we consider it timely to share our experiences as the developers of the open-source partial differential equation solver Dedalus. Dedalus is a flexible framework for solving partial differential equations. Its development team primarily uses it for studying stellar and planetary astrophysics. Dedalus was developed originally for astrophysical fluid dynamics (AFD), though it has found a much broader user base, including applied mathematicians, plasma physicists, and oceanographers. Here, we will focus on issues related to open-source software from the perspective of AFD. We use the term AFD with the understanding that astrophysics simulations are inherently multi-physics: fluid dynamics coupled with some combination of gravitational dynamics, radiation transfer, relativity, and magnetic fields. In practice, a few well-known open-source simulation packages represent a large fraction of published work in the field. However, we will argue that an open-code policy should encompass not just these large simulation codes, but also the input files and analysis scripts. It is our interest that NASA adopt an open-code policy because without it, reproducibility in computational science is needlessly hampered.}, author = {Oishi, Jeffrey S. and Brown, Benjamin P. and Burns, Keaton J. and Lecoanet, Daniel and Vasil, Geoffrey M.}, doi = {10/gf2hxs}, keywords = {Sustainability, Open Source, Reproducibility}, month = {January}, title = {Perspectives on {Reproducibility} and {Sustainability} of {Open}-{Source} {Scientific} {Software} from {Seven} {Years} of the {Dedalus} {Project}}, year = {2018} } @article{parthenos_parthenos_2018, abstract = {A comprehensive set of PARTHENOS Guidelines to FAIRify data management and make data reusable is focusing on the topic of common policies. This compact guide offers twenty guidelines to align the efforts of data producers, data archivists and data users in humanities and social sciences to make research data as reusable as possible based upon the FAIR Principles. Each guideline has recommendations for both researchers and archives as it is recognised that different priorities may apply to each case. The guidelines result from the work of over fifty PARTHENOS project members. They were responsible for investigating commonalities in the implementation of policies and strategies for research data management and used results from desk research, questionnaires and interviews with selected experts to gather around one hundred current data management policies (including guides for preferred formats, data review policies and best practices, both formal as well as tacit). Translations of the Guidelines are available in: French: "PARTHENOS Recommandations pour FAIRiser vos donn\'{e}es" (https://doi.org/10.5281/zenodo.3463521) German: "PARTHENOS Leitfaden zur "FAIRifizierung" des Datenmanagements und der Erm\"{o}glichung der Nachnutzung von Daten" (https://doi.org/10.5281/zenodo.3363078) Greek: "PARTHENOS Ο\ensuremath{\delta}\ensuremath{\eta}\ensuremath{\gamma}\acute{\iota}\ensuremath{\epsilon}\ensuremath{\varsigma} \ensuremath{\gamma}\ensuremath{\iota}\ensuremath{\alpha} \ensuremath{\tau}\ensuremath{\eta}\ensuremath{\nu} \ensuremath{\epsilon}\ensuremath{\varphi}\ensuremath{\alpha}\ensuremath{\rho}\ensuremath{\mu}ο\ensuremath{\gamma}\acute{\eta} \ensuremath{\tau}\ensuremath{\omega}\ensuremath{\nu} \ensuremath{\alpha}\ensuremath{\rho}\ensuremath{\chi}\acute{\omega}\ensuremath{\nu} FAIR \ensuremath{\sigma}\ensuremath{\tau}\ensuremath{\eta} \ensuremath{\delta}\ensuremath{\iota}\ensuremath{\alpha}\ensuremath{\chi}\ensuremath{\epsilon}\acute{\iota}\ensuremath{\rho}\ensuremath{\iota}\ensuremath{\sigma}\ensuremath{\eta} \ensuremath{\kappa}\ensuremath{\alpha}\ensuremath{\iota} \ensuremath{\epsilon}\ensuremath{\pi}\ensuremath{\alpha}\ensuremath{\nu}\'{$\alpha$}\ensuremath{\chi}\ensuremath{\rho}\ensuremath{\eta}\ensuremath{\sigma}\ensuremath{\eta} \ensuremath{\delta}\ensuremath{\epsilon}\ensuremath{\delta}ο\ensuremath{\mu}\acute{\epsilon}\ensuremath{\nu}\ensuremath{\omega}\ensuremath{\nu}" (https://doi.org/10.5281/zenodo.3363386) Hungarian: "PARTHENOS A tudom\'{a}nyos adatok \'{u}jrafelhaszn\'{a}lhat\'{o}s\'{a}g\'{a}nak \'{e}s FAIR kezel\'{e}s\'{e}nek ir\'{a}nyelveii" (https://doi.org/10.5281/zenodo.3363355) Italian: "PARTHENOS Linee guida per l'applicazione dei principi FAIR alla gestione e al riuso dei dati" (https://doi.org/10.5281/zenodo.3363243)}, author = {{PARTHENOS} and Hollander, Hella and Morselli, Francesca and Uiterwaal, Frank and Admiraal, Femmy and Trippel, Thorsten and Di Giorgio, Sara}, doi = {10.5281/zenodo.2668479}, keywords = {Guidelines, Data Management, FAIR practice, Data Reuse, FAIR Principles, FAIRify}, language = {eng}, month = {December}, title = {{PARTHENOS} {Guidelines} to {FAIRify} data management and make data reusable}, url = {https://zenodo.org/record/2668479#.XrpjgBNKiL6}, urldate = {2020-05-12}, year = {2018} } @article{perkel_toolkit_2018, author = {Perkel, Jeffrey M.}, doi = {10/gd2xs9}, journal = {Nature}, keywords = {Open Science, Transparency}, month = {August}, number = {7719}, pages = {513--515}, title = {A toolkit for data transparency takes shape}, volume = {560}, year = {2018} } @article{rapp_sara-dienst_2018, author = {Rapp, Franziska and Kombrink, Stefan and Kushnarenko, Volodymyr and Fratz, Matthias and Scharon, Daniel}, doi = {10/gfvpqt}, journal = {o-bib. Das offene Bibliotheksjournal / herausgegeben vom VDB}, keywords = {Digital Archive, Repository}, language = {de}, pages = {Nr. 2 (2018)--}, title = {{SARA}-{Dienst}: {Software} langfristig verf\"{u}gbar machen}, volume = {Bd. 5}, year = {2018} } @article{rowenstrunk_langzeitverfugbarkeit_2018, author = {R\"{o}wenstrunk, Daniel}, doi = {10/ggcmcs}, journal = {Bibliothek Forschung und Praxis}, keywords = {Digitale Archive, Musikwissenschaft}, month = {June}, number = {2}, pages = {302--308}, title = {Langzeitverf\"{u}gbarkeit von wissenschaftlicher {Software} im {Bereich} historisch-kritischer {Musikedition}}, volume = {42}, year = {2018} } @article{roy_digital_2018, author = {Roy, Sherre and Clark, Damien}, doi = {10.1111/bjet.12709}, issn = {1467-8535}, journal = {British Journal of Educational Technology}, month = {September}, number = {5}, pages = {2619--2636}, title = {Digital badges, do they live up to the hype?}, volume = {50}, year = {2018} } @article{russell_large-scale_2018, author = {Russell, Pamela H. and Johnson, Rachel L. and Ananthan, Shreyas and Harnke, Benjamin and Carlson, Nichole E.}, doi = {10.1371/journal.pone.0205898}, editor = {Qin, Zhaohui}, journal = {PLOS ONE}, month = {October}, number = {10}, pages = {e0205898}, title = {A large-scale analysis of bioinformatics code on {GitHub}}, volume = {13}, year = {2018} } @inproceedings{samuel_provbook_2018, abstract = {With the rapid growth of data science and machine learning, interactive notebooks have gained widespread adoption among scientists across all disciplines to publish their computational experiments containing code, text, and results. As it is easy to modify and re-run the computations in a notebook, it is important to know how the provenance of results changed in different executions over the course of time, thus enabling trust and reproducibility. In this paper, we present ProvBook, an extension of Jupyter Notebook to capture and view the provenance over the course of time. It also allows the user to share a notebook along with its provenance in RDF and also convert it back to a notebook. We use the REPRODUCE-ME ontology extended from PROV-O and P-Plan to describe the provenance of a notebook. This helps the scientists to compare their previous results with the current ones, check whether the experiments produce the results as expected and query the sequence of executions using SPARQL. The notebook data in RDF can be used in combination with the experiments that used them and help to get a track of the complete path of the scientific experiments.}, author = {Samuel, Sheeba and K\"{o}nig-Ries, Birgitta}, keywords = {FAIR other contexts}, month = {October}, shorttitle = {{ProvBook}}, title = {{ProvBook}: {Provenance}-based {Semantic} {Enrichment} of {Interactive} {Notebooks} for {Reproducibility}}, year = {2018} } @article{schlauch_software-engineering-empfehlungen_2018, author = {Schlauch, Tobias and Meinel, Michael and Haupt, Carina}, doi = {10/gf3twm}, keywords = {Guidelines, DLR}, title = {Software-{Engineering}-{Empfehlungen} des {DLR}}, year = {2018} } @article{schopfel_research_2018, abstract = {Purpose The purpose of this paper is to present empirical evidence on the opinion and behaviour of French scientists (senior management level) regarding research data management (RDM). Design/methodology/approach The results are part of a nationwide survey on scientific information and documentation with 432 directors of French public research laboratories conducted by the French Research Center CNRS in 2014. Findings The paper presents empirical results about data production (types), management (human resources, IT, funding, and standards), data sharing and related needs, and highlights significant disciplinary differences. Also, it appears that RDM and data sharing is not directly correlated with the commitment to open access. Regarding the FAIR data principles, the paper reveals that 68 per cent of all laboratory directors affirm that their data production and management is compliant with at least one of the FAIR principles. But only 26 per cent are compliant with at least three principles, and less than 7 per cent are compliant with all four FAIR criteria, with laboratories in nuclear physics, SSH and earth sciences and astronomy being in advance of other disciplines, especially concerning the findability and the availability of their data output. The paper concludes with comments about research data service development and recommendations for an institutional RDM policy. Originality/value For the first time, a nationwide survey was conducted with the senior research management level from all scientific disciplines. Surveys on RDM usually assess individual data behaviours, skills and needs. This survey is different insofar as it addresses institutional and collective data practice. The respondents did not report on their own data behaviours and attitudes but were asked to provide information about their laboratory. The response rate was high ({\textbackslash}textgreater30 per cent), and the results provide good insight into the real support and uptake of RDM by senior research managers who provide both models (examples for good practice) and opinion leadership.}, author = {Sch\"{o}pfel, Joachim and Ferrant, Coline and Andr\'{e}, Francis and Fabre, Renaud}, doi = {10.1108/DTA-01-2017-0005}, issn = {2514-9288}, journal = {Data Technologies and Applications}, keywords = {FAIR principles, Open Science, FAIR practice, Data curation, Data preservation, Data sharing, Research data management}, month = {January}, number = {2}, pages = {248--265}, title = {Research data management in the {French} {National} {Research} {Center} ({CNRS})}, url = {https://doi.org/10.1108/DTA-01-2017-0005}, urldate = {2020-05-12}, volume = {52}, year = {2018} } @article{stark_before_2018, author = {Stark, Philip B.}, doi = {10/gdh9xc}, journal = {Nature}, keywords = {Reproducibility}, number = {7707}, pages = {613--613}, title = {Before reproducibility must come preproducibility}, volume = {557}, year = {2018} } @article{stevens_building_2018, author = {Stevens, Sarah L. R. and Kuzak, Mateusz and Martinez, Carlos and Moser, Aurelia and Bleeker, Petra and Galland, Marc}, doi = {10.1371/journal.pbio.2005561}, issn = {1545-7885}, journal = {PLOS Biology}, keywords = {life sciences, community of practice}, language = {en}, month = {November}, number = {11}, pages = {e2005561}, title = {Building a local community of practice in scientific programming for life scientists}, url = {https://dx.plos.org/10.1371/journal.pbio.2005561}, urldate = {2024-11-29}, volume = {16}, year = {2018} } @article{stodden_empirical_2018, author = {Stodden, Victoria and Seiler, Jennifer and Ma, Zhaokun}, doi = {10/gc8gkw}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Reproducibility}, month = {March}, number = {11}, pages = {2584--2589}, title = {An empirical analysis of journal policy effectiveness for computational reproducibility}, volume = {115}, year = {2018} } @inproceedings{struck_research_2018, author = {Struck, Alexander}, booktitle = {{IEEE} {eScience} 2018}, doi = {10/gfvpq5}, keywords = {Discovery, Scientific Computing}, publisher = {Zenodo}, title = {Research {Software} {Discovery}: {Challenges}, {Risks} {And} {Opportunities}}, year = {2018} } @inproceedings{struck_research_2018-1, address = {Amsterdam}, author = {Struck, Alexander}, booktitle = {2018 {IEEE} 14th {International} {Conference} on e-{Science} (e-{Science})}, doi = {10.1109/eScience.2018.00016}, isbn = {978-1-5386-9156-4}, keywords = {Discovery}, month = {October}, pages = {33--37}, publisher = {IEEE}, shorttitle = {Research {Software} {Discovery}}, title = {Research {Software} {Discovery}: {An} {Overview}}, url = {https://ieeexplore.ieee.org/document/8588635/}, urldate = {2022-09-04}, year = {2018} } @inproceedings{trockman_adding_2018, address = {New York, New York, USA}, author = {Trockman, Asher and Zhou, Shurui and K\"{a}stner, Christian and Vasilescu, Bogdan}, booktitle = {Proceedings of the 40{\textbackslash}textsuperscriptth {International} {Conference} on {Software} {Engineering} ({ICSE} 2018)}, doi = {10.1145/3180155.3180209}, isbn = {978-1-4503-5638-1}, month = {May}, pages = {511--522}, publisher = {ACM}, title = {Adding sparkle to social coding: an empirical study of repository badges in the \emph{npm} ecosystem}, year = {2018} } @article{wen_empirical_2018, author = {Wen, Shao-Fang}, doi = {10/ggcmct}, journal = {Computers}, keywords = {Open Source}, month = {October}, number = {4}, pages = {49--49}, title = {An {Empirical} {Study} on {Security} {Knowledge} {Sharing} and {Learning} in {Open} {Source} {Software} {Communities}}, volume = {7}, year = {2018} } @article{zwart_computational_2018, author = {Zwart, Simon Portegies}, doi = {10/gd546p}, journal = {Science}, keywords = {Astrophysics}, month = {September}, number = {6406}, pages = {979--980}, title = {Computational astrophysics for the future}, volume = {361}, year = {2018} } @inproceedings{ackermann_sara-service_2017, abstract = {Das SARA-Projekt (Software Archiving of Research Artefacts) hat das Ziel, einen neuen wissenschaftlichen Dienst zu entwickeln, mit dem Forschungsdaten und Software langfristig verf\"{u}gbar gemacht und publiziert werden k\"{o}nnen. Die Posterpr\"{a}sentation stellt Motivation, Zielsetzung sowie wichtige Kernelemente des SARA-Service vor. Im Zentrum der Darstellung steht der SARA-Service, der auf Git und den dort bereitgestellten Mechanismus zur Softwareversionierung aufbaut. Hierbei fungiert ein durch die Universit\"{a}t Konstanz bereitgestellter und zuk\"{u}nftig als Landesdienst betriebener GitLab-Server als Langzeitarchiv. Nutzer k\"{o}nnen hier ihre jeweiligen Versionsst\"{a}nde der Software zentral speichern. Die archivierten Versionen k\"{o}nnen mit dem SARA-Service zus\"{a}tzlich in einem DSpace-Repositorium ver\"{o}ffentlicht werden. Der neue Service soll nach Ablauf der Evaluierungsphase grunds\"{a}tzlich allen Fachdisziplinen zur Verf\"{u}gung stehen.}, author = {Ackermann, Franziska and Enderle, Petra and Fratz, Matthias and Kushnarenko, Vladimir and Scharon, Daniel and Schm\"{u}cker, Pia and Waldvogel, Marcel and Wesner, Stefan}, booktitle = {E-{Science}-{Tage} 2017: {Forschungsdaten} managen}, doi = {10/gfvpq8}, keywords = {Digital Archive, Repository}, publisher = {Heidelberg University Library}, title = {{SARA}-{Service}: {Langzeitverf\"{u}gbarkeit} und {Publikation} von {Softwareartefakten}}, year = {2017} } @inproceedings{akoh_determinants_2017, address = {Cham, Switzerland}, author = {Akoh, Ben}, booktitle = {Tomorrow's {Learning}: {Involving} {Everyone}}, doi = {10.1007/978-3-319-74310-3_4}, editor = {Tatnall, Arthur and Webb, Mary}, isbn = {978-3-319-74310-3}, lccn = {2018930742}, pages = {24--34}, publisher = {Springer International Publishing}, series = {{IFIP} {Advances} in {Information} and {Communication} {Technology}}, title = {Determinants of {Mobile} {Learning} in {Indigenous}/{Cultural} {Contexts}: {The} {Phenomenon} in {Canadian} {First} {Nations}}, volume = {515}, year = {2017} } @inproceedings{alghamdi_game-play_2017, address = {Cham, Switzerland}, author = {Alghamdi, Jawaher and Holland, Charlotte}, booktitle = {Tomorrow's {Learning}: {Involving} {Everyone}}, doi = {10.1007/978-3-319-74310-3_7}, editor = {Tatnall, Arthur and Webb, Mary}, isbn = {978-3-319-74310-3}, lccn = {2018930742}, pages = {55--63}, publisher = {Springer International Publishing}, series = {{IFIP} {Advances} in {Information} and {Communication} {Technology}}, title = {Game-{Play}: {Effects} of {Online} {Gamified} and {Game}-{Based} {Learning} on {Dispositions}, {Abilities} and {Behaviours} of {Primary} {Learners}}, volume = {515}, year = {2017} } @article{allen_engineering_2017, author = {Allen, Alice and Aragon, Cecilia and Becker, Christoph and Carver, Jeffrey and Chis, Andrei and Combemale, Benoit and Croucher, Mike and Crowston, Kevin and Garijo, Daniel and Gehani, Ashish and Goble, Carole and Haines, Robert and Hirschfeld, Robert and Howison, James and Huff, Kathryn and Jay, Caroline and Katz, Daniel S. and Kirchner, Claude and Kuksenok, Katie and L\"{a}mmel, Ralf and Nierstrasz, Oscar and Turk, Matt and van Nieuwpoort, Rob and Vaughn, Matthew and Vinju, Jurgen J.}, doi = {10/b7xv}, journal = {Dagstuhl Manifestos}, keywords = {Software Engineering}, number = {1}, pages = {1--20}, title = {Engineering {Academic} {Software} ({Dagstuhl} {Perspectives} {Workshop} 16252)}, url = {http://drops.dagstuhl.de/opus/volltexte/2017/7146}, volume = {6}, year = {2017} } @article{anel_comment_2017, author = {A\~{n}el, Juan A.}, doi = {10.1002/2016WR020190}, journal = {Water Resources Research}, number = {3}, pages = {2572--2574}, title = {Comment on ``{Most} computational hydrology is not reproducible, so is it really science?'' by {Christopher} {Hutton} et al.}, volume = {53}, year = {2017} } @article{barone_unmet_2017, author = {Barone, Lindsay and Williams, Jason and Micklos, David}, doi = {10.1371/journal.pcbi.1005755}, editor = {Ouellette, Francis}, journal = {PLOS Computational Biology}, month = {October}, number = {10}, pages = {e1005755}, title = {Unmet needs for analyzing biological big data: {A} survey of 704 {NSF} principal investigators}, volume = {13}, year = {2017} } @article{brazas_global_2017, author = {Brazas, Michelle D. and Brooksbank, Cath and Jimenez, Rafael C. and Blackford, Sarah and Palagi, Patricia M. and De Las Rivas, Javier and Ouellette, B. F. Francis and Kumuthini, Judit and Korpelainen, Eija and Lewitter, Fran and van Gelder, Celia W.G. and Mulder, Nicola and Corpas, Manuel and Schneider, Maria Victoria and Tan, Tin Wee and Clements, Dave and Davies, Angela and Attwood, Teresa K.}, doi = {10.1101/098996}, journal = {bioRxiv}, month = {February}, pages = {098996}, title = {A global perspective on bioinformatics training needs}, year = {2017} } @article{brazas_plug_2017, author = {Brazas, Michelle D. and Blackford, Sarah and Attwood, Teresa K.}, doi = {10.1038/544161c}, journal = {Nature}, month = {April}, number = {7649}, pages = {161--161}, title = {Plug gap in essential bioinformatics skills}, volume = {544}, year = {2017} } @article{brett_research_2017, author = {Brett, Alys and Croucher, Michael and Haines, Robert and Hettrick, Simon and Hetherington, James and Stillwell, Mark and Wyatt, Claire}, doi = {10/gfvpqz}, keywords = {Survey}, title = {Research {Software} {Engineers}: {State} {Of} {The} {Nation} {Report} 2017}, year = {2017} } @article{buddenbohm_quality_2017, author = {Buddenbohm, Stefan and Matoni, Markus and Schmunk, Stefan and Thiel, Carsten}, doi = {10.1515/bfp-2017-0024}, journal = {Bibliothek Forschung und Praxis}, keywords = {Digital Humanities, MA}, month = {July}, number = {2}, title = {Quality {Assessment} for the {Sustainable} {Provision} of {Software} {Components} and {Digital} {Research} {Infrastructures} for the {Arts} and {Humanities}}, volume = {41}, year = {2017} } @inproceedings{cosmo_software_2017, address = {Kyoto, Japan}, author = {Cosmo, Roberto Di and Zacchiroli, Stefano}, booktitle = {{iPRES} 2017: 14{\textbackslash}textbackslashtextsuperscriptth {International} {Conference} on {Digital} {Preservation}}, keywords = {Digital Archive, Preservation}, month = {September}, title = {Software {Heritage}: {Why} and {How} to {Preserve} {Software} {Source} {Code}}, url = {https://hal.archives-ouvertes.fr/hal-01590958 https://hal.archives-ouvertes.fr/hal-01590958/file/ipres-2017-software-heritage.pdf}, year = {2017} } @article{crick_reproducibility_2017, author = {Crick, Tom and Hall, Benjamin A. and Ishtiaq, Samin}, doi = {10.5334/jors.73}, journal = {Journal of Open Research Software}, month = {November}, number = {1}, pages = {32}, title = {Reproducibility in {Research}: {Systems}, {Infrastructure}, {Culture}}, volume = {5}, year = {2017} } @article{dingsoyr_exploring_2017, author = {Dings\o{}yr, Torgeir and Moe, Nils Brede and F\ae{}gri, Tor Erlend and Seim, Eva Amdahl}, doi = {10.1007/s10664-017-9524-2}, journal = {Empirical Software Engineering}, month = {June}, number = {1}, pages = {490--520}, title = {Exploring software development at the very large-scale: a revelatory case study and research agenda for agile method adaptation}, volume = {23}, year = {2017} } @article{dryden_upon_2017, author = {Dryden, Michael D. M. and Fobel, Ryan and Fobel, Christian and Wheeler, Aaron R.}, doi = {10/gc5sjm}, journal = {Analytical Chemistry}, keywords = {Open Source, Chemistry}, month = {April}, number = {8}, pages = {4330--4338}, title = {Upon the {Shoulders} of {Giants}: {Open}-{Source} {Hardware} and {Software} in {Analytical} {Chemistry}}, volume = {89}, year = {2017} } @article{dzale_yeumo_developing_2017, abstract = {In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently facilitate the extraction of new information from existing and new datasets. During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the use of data standards, then discussed and selected a set of recommendations based on consensual criteria. The recommendations promote standards for data types identified by the wheat research community as the most important for the coming years: nucleotide sequence variants, genome annotations, phenotypes, germplasm data, gene expression experiments, and physical maps. For each of these data types, the guidelines recommend best practices in terms of use of data formats, metadata standards and ontologies. In addition to the best practices, the guidelines provide examples of tools and implementations that are likely to facilitate the adoption of the recommendations. To maximize the adoption of the recommendations, the WDI-WG used a community-driven approach that involved the wheat research community from the start, took into account their needs and practices, and provided them with a framework to keep the recommendations up to date. We also report this approach's potential to be generalizable to other (agricultural) domains.}, author = {Dzale Yeumo, Esther and Alaux, Michael and Arnaud, Elizabeth and Aubin, Sophie and Baumann, Ute and Buche, Patrice and Cooper, Laurel and \'{C}wiek-Kupczy\'{n}ska, Hanna and Davey, Robert P. and Fulss, Richard Allan and Jonquet, Clement and Laporte, Marie-Ang\'{e}lique and Larmande, Pierre and Pommier, Cyril and Protonotarios, Vassilis and Reverte, Carmen and Shrestha, Rosemary and Subirats, Imma and Venkatesan, Aravind and Whan, Alex and Quesneville, Hadi}, doi = {10.12688/f1000research.12234.1}, issn = {2046-1402}, journal = {F1000Research}, language = {en}, month = {October}, pages = {1843}, shorttitle = {Developing data interoperability using standards}, title = {Developing data interoperability using standards: {A} wheat community use case}, url = {https://f1000research.com/articles/6-1843/v1}, urldate = {2020-06-17}, volume = {6}, year = {2017} } @article{eglen_toward_2017, author = {Eglen, Stephen J. and Marwick, Ben and Halchenko, Yaroslav O. and Hanke, Michael and Sufi, Shoaib and Gleeson, Padraig and Silver, R. Angus and Davison, Andrew P. and Lanyon, Linda and Abrams, Mathew and Wachtler, Thomas and Willshaw, David J. and Pouzat, Christophe and Poline, Jean-Baptiste}, doi = {10/gbvwr3}, journal = {Nature Neuroscience}, keywords = {Neuroscience, Code Sharing}, month = {June}, number = {6}, pages = {770--773}, title = {Toward standard practices for sharing computer code and programs in neuroscience}, volume = {20}, year = {2017} } @article{essawy_evaluation_2017, author = {Essawy, Bakinam T. and Goodall, Jonathan L. and Xu, Hao and Gil, Yolanda}, doi = {10.1016/j.envsoft.2017.01.024}, issn = {13648152}, journal = {Environmental Modelling \& Software}, keywords = {FAIR other contexts}, language = {en}, month = {June}, pages = {317--329}, title = {Evaluation of the {OntoSoft} {Ontology} for describing metadata for legacy hydrologic modeling software}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1364815216309999}, urldate = {2020-10-25}, volume = {92}, year = {2017} } @article{garijo_abstract_2017, author = {Garijo, Daniel and Gil, Yolanda and Corcho, Oscar}, doi = {10.1016/j.future.2017.01.008}, issn = {0167739X}, journal = {Future Generation Computer Systems}, keywords = {FAIR other contexts}, language = {en}, month = {October}, pages = {271--283}, shorttitle = {Abstract, link, publish, exploit}, title = {Abstract, link, publish, exploit: {An} end to end framework for workflow sharing}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0167739X17300274}, urldate = {2020-10-25}, volume = {75}, year = {2017} } @inproceedings{graziotin_unhappiness_2017, author = {Graziotin, Daniel and Fagerholm, Fabian and Wang, Xiaofeng and Abrahamsson, Pekka}, booktitle = {Proceedings of the 21\textsuperscript{st} {International} {Conference} on {Evaluation} and {Assessment} in {Software} {Engineering} - {EASE}'17}, doi = {10/gfvpqv}, keywords = {Software Engineering}, publisher = {ACM Press}, title = {On the {Unhappiness} of {Software} {Developers}}, year = {2017} } @article{grimme_computational_2017, author = {Grimme, Stefan and Schreiner, Peter R.}, doi = {10.1002/anie.201709943}, journal = {Angewandte Chemie International Edition}, keywords = {Chemistry}, month = {December}, number = {16}, pages = {4170--4176--4170--4176}, title = {Computational {Chemistry}: {The} {Fate} of {Current} {Methods} and {Future} {Challenges}}, volume = {57}, year = {2017} } @article{hamari_badges_2017, author = {Hamari, Juho}, doi = {10.1016/j.chb.2015.03.036}, journal = {Computers in Human Behavior}, month = {June}, pages = {469--478}, title = {Do badges increase user activity? {A} field experiment on the effects of gamification}, volume = {71}, year = {2017} } @inproceedings{haupt_track_2017, author = {Haupt, Carina and Schlauch, Tobias}, booktitle = {Proceedings of the {Workshop} on {Sustainable} {Software} for {Science}: {Practice} and {Experiences} ({WSSSPE5}.1)}, doi = {10.6084/m9.figshare.5331703}, editor = {Chue Hong, Neil and Druskat, Stephan and Haines, Robert and Jay, Caroline and Katz, Daniel S. and Sufi, Shoaib}, month = {September}, publisher = {figshare}, title = {Track 1 {Paper}: {The} {Software} {Engineering} {Community} at {DLR} -- {How} we got where we are}, year = {2017} } @article{hennah_using_2017, author = {Hennah, Naomi and Seery, Michael K.}, doi = {10.1021/acs.jchemed.7b00175}, journal = {Journal of Chemical Education}, month = {May}, number = {7}, pages = {844--848}, title = {Using {Digital} {Badges} for {Developing} {High} {School} {Chemistry} {Laboratory} {Skills}}, volume = {94}, year = {2017} } @book{hong_software_2017, author = {Hong, Neil Chue}, doi = {10.6084/m9.figshare.4793806}, keywords = {Software Engineering, Sustainability}, publisher = {Figshare}, title = {Software – a different kind of research object?}, year = {2017} } @article{jimenez_four_2017, abstract = {Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.}, author = {Jim\'{e}nez, Rafael C. and Kuzak, Mateusz and Alhamdoosh, Monther and Barker, Michelle and Batut, B\'{e}r\'{e}nice and Borg, Mikael and Capella-Gutierrez, Salvador and Chue Hong, Neil and Cook, Martin and Corpas, Manuel and Flannery, Madison and Garcia, Leyla and Gelp\'{\i}, Josep Ll. and Gladman, Simon and Goble, Carole and Gonz\'{a}lez Ferreiro, Montserrat and Gonzalez-Beltran, Alejandra and Griffin, Philippa C. and Gr\"{u}ning, Bj\"{o}rn and Hagberg, Jonas and Holub, Petr and Hooft, Rob and Ison, Jon and Katz, Daniel S. and Lesko\v{s}ek, Brane and L\'{o}pez G\'{o}mez, Federico and Oliveira, Luis J. and Mellor, David and Mosbergen, Rowland and Mulder, Nicola and Perez-Riverol, Yasset and Pergl, Robert and Pichler, Horst and Pope, Bernard and Sanz, Ferran and Schneider, Maria V. and Stodden, Victoria and Suchecki, Rados\l{}aw and Svobodov\'{a} Va\v{r}ekov\'{a}, Radka and Talvik, Harry-Anton and Todorov, Ilian and Treloar, Andrew and Tyagi, Sonika and van Gompel, Maarten and Vaughan, Daniel and Via, Allegra and Wang, Xiaochuan and Watson-Haigh, Nathan S. and Crouch, Steve}, doi = {10.12688/f1000research.11407.1}, issn = {2046-1402}, journal = {F1000Research}, language = {en}, month = {June}, pages = {876}, title = {Four simple recommendations to encourage best practices in research software}, url = {https://f1000research.com/articles/6-876/v1}, urldate = {2021-11-20}, volume = {6}, year = {2017} } @article{jones_teachers_2017, author = {Jones, W. Monty and Hope, Samantha and Adams, Brianne}, doi = {10.1111/bjet.12557}, journal = {British Journal of Educational Technology}, month = {March}, number = {3}, pages = {427--438}, title = {Teachers' perceptions of digital badges as recognition of professional development}, volume = {49}, year = {2017} } @book{katz_software_2017, author = {Katz, Daniel S.}, doi = {10.6084/m9.figshare.5518933.v1}, keywords = {Citation}, title = {Software in {Research}: {Underappreciated} and {Underrewarded}}, url = {https://figshare.com/articles/Software\%5Fin\%5FResearch\%5FUnderappreciated\%5Fand\%5FUnderrewarded/5518933}, year = {2017} } @article{kethers_building_2017, abstract = {The Australian National Data Service (ANDS) has been funded by the Australian Government since 2009, with a goal to increase the value of data to researchers, research institutions and the nation. To achieve this goal, ANDS has funded more than 200 projects under seven programs. This paper provides an overview of one of these programs, the Applications Program, which focused on funding software infrastructure to enable data reuse to demonstrate the value of making data available to researchers. The paper also presents some representative projects, a summary of what the program has achieved, and lessons learned.}, author = {Kethers, Stefanie and Treloar, Andrew and Wu, Mingfang}, doi = {10/ggnd4f}, journal = {International Journal of Digital Curation}, keywords = {Research Data, Data Reuse}, month = {July}, number = {2}, pages = {1--12}, title = {Building {Tools} to {Facilitate} {Data} {Reuse}}, volume = {11}, year = {2017} } @article{landwehr_software_2017, author = {Landwehr, Carl and Ludewig, Jochen and Meersman, Robert and Parnas, David Lorge and Shoval, Peretz and Wand, Yair and Weiss, David and Weyuker, Elaine}, doi = {10.1016/j.jss.2016.12.016}, issn = {0164-1212}, journal = {Journal of Systems and Software}, pages = {354--364}, title = {Software {Systems} {Engineering} programmes a capability approach}, volume = {125}, year = {2017} } @article{larcombe_elixir-uk_2017, author = {Larcombe, L. and Hendricusdottir, R. and Attwood, T. K. and Bacall, F. and Beard, N. and Bellis, L. J. and Dunn, W. B. and Hancock, J. M. and Nenadic, A. and Orengo, C. and Overduin, B. and Sansone, S.-A. and Thurston, M. and Viant, M. R. and Winder, C. L. and Goble, C. A. and Ponting, C. P. and Rustici, G.}, doi = {10.12688/f1000research.11837.1}, journal = {F1000Research}, month = {June}, pages = {952}, title = {{ELIXIR}-{UK} role in bioinformatics training at the national level and across {ELIXIR} [version 1; peer review: 4 approved, 1 approved with reservations]}, volume = {6}, year = {2017} } @article{leprevost_biocontainers_2017, author = {Leprevost, Felipe da Veiga and Gr\"{u}ning, Bj\"{o}rn A and Aflitos, Saulo Alves and R\"{o}st, Hannes L. and Uszkoreit, Julian and Barsnes, Harald and Vaudel, Marc and Moreno, Pablo and Gatto, Laurent and Weber, Jonas and Bai, Mingze and Jimenez, Rafael C. and Sachsenberg, Timo and Pfeuffer, Julianus and Alvarez, Roberto Vera and Griss, Johannes and Nesvizhskii, Alexey I. and Perez-Riverol, Yasset}, doi = {10.1093/bioinformatics/btx192}, editor = {Valencia, Alfonso}, journal = {Bioinformatics}, month = {March}, number = {16}, pages = {2580--2582}, title = {{BioContainers}: an open-source and community-driven framework for software standardization}, volume = {33}, year = {2017} } @article{list_ten_2017, author = {List, Markus and Ebert, Peter and Albrecht, Felipe}, doi = {10.1371/journal.pcbi.1005265}, editor = {Markel, Scott}, journal = {PLOS Computational Biology}, month = {January}, number = {1}, pages = {e1005265}, title = {Ten {Simple} {Rules} for {Developing} {Usable} {Software} in {Computational} {Biology}}, volume = {13}, year = {2017} } @article{liyanagunawardena_open_2017, author = {Liyanagunawardena, Tharindu R. and Scalzavara, Sandra and Williams, Shirley A.}, doi = {10.1515/eurodl-2017-0013}, issn = {1027-5207}, journal = {European Journal of Open, Distance and E-Learning}, month = {December}, number = {2}, pages = {1--16}, title = {Open {Badges}: {A} {Systematic} {Review} of {Peer}-{Reviewed} {Published} {Literature} (2011-2015)}, volume = {20}, year = {2017} } @article{lowndes_our_2017, author = {Lowndes, Julia S. Stewart and Best, Benjamin D. and Scarborough, Courtney and Afflerbach, Jamie C. and Frazier, Melanie R. and O'Hara, Casey C. and Jiang, Ning and Halpern, Benjamin S.}, doi = {10.1038/s41559-017-0160}, journal = {Nature Ecology \& Evolution}, month = {May}, number = {6}, title = {Our path to better science in less time using open data science tools}, volume = {1}, year = {2017} } @inproceedings{maassen_track_2017, author = {Maassen, Jason and Drost, Niels and van Hage, Willem and van Nieuwpoort, Rob}, booktitle = {Proceedings of the {Workshop} on {Sustainable} {Software} for {Science}: {Practice} and {Experiences} ({WSSSPE5}.1)}, doi = {10.6084/m9.figshare.5327587}, editor = {Chue Hong, Neil and Druskat, Stephan and Haines, Robert and Jay, Caroline and Katz, Daniel S. and Sufi, Shoaib}, month = {September}, publisher = {figshare}, title = {Track 2 {Lightning} {Talk}: {Software} {Development} {Best} {Practices} at the {Netherlands} {eScience} {Center}}, year = {2017} } @article{maria_taxonomy_2017, abstract = {The Open Access (OA) to knowledge is a principle established by the European Commission, underlying the H2020 EU Framework Programme for Research and Innovation. OA aims at optimizing the impact of publicly funded projects, by making information openly available and reusable to everyone in Europe. The Open Data (OD) policy is part of the OA strategy and is widely acknowledged as a fundamental step to support a fast track from research to innovation. Although there is a general acknowledgment for the need of OD, a mindset similar to the "not-in-my-backyard" holds back the scientific and industrial communities to implement a joint OD policy. This is partly due to the fear that sensitive and proprietary data could be misused. To overcome this problem, the European Commission posed an important milestone by declaring that data must be at the same time ``Findable, Accessible, Interoperable and Reusable (FAIR)'' and ``as much open as possible, and as closed as necessary''. The Joint Programme on Wind Energy of the European Energy Research Alliance (EERA JPWind), represents the largest public European scientific community in the Wind Energy (WE) sector. JP WIND recognises the necessity of implementing an OD plan by setting the goal to create a data portal. The data portal will a) collect information on data from ``cloud distributed'' data centers, b) catalogue the collected information and c) provide end-users with tools to find data for their needs. In this report, we focus on the first phase that lays the basis for the implementation of a Data Web Portal i.e. the information architecture to make data Findable and Interoperable. The first phase relates to making data ``Findable'' and ``Interoperable'' helping data owners to describe the data and end-users to accurately locate and retrieve the needed data. There are two components for this task: (i) Metadata (data tagging) and (ii) taxonomy for the WE sector topics, the topic related data and descriptive types of metadata.}, author = {Maria, Sempreviva Anna and Allan, Vesth and Christian, Bak and Robert, Verelst David and Gregor, Giebel and Kjartansson, Danielsen Hilmar and Pilgaard, Mikkelsen Lars and Mattias, Andersson and Nikola, Vasiljevic and Stephan, Barth and Javier, Sanz Rodrigo and Pawel, Gancarski and Inge, Reigstad Tor and Christian, Bolstad Hans and Willem, Wagenaar Jan and W, Hermans Koen}, doi = {10.5281/zenodo.1199489}, keywords = {reproducibility, metadata, Transparency, FAIR practice, Fair data, Taxonomy, wind energy}, language = {eng}, month = {December}, title = {Taxonomy and metadata for wind energy {Research} \&{Development}}, url = {https://zenodo.org/record/1199489#.XrpibxNKiL5}, urldate = {2020-05-12}, year = {2017} } @article{markowetz_all_2017, author = {Markowetz, Florian}, doi = {10/gf3krm}, journal = {PLOS Biology}, keywords = {Biology}, month = {March}, number = {3}, pages = {e2002050--e2002050}, title = {All biology is computational biology}, volume = {15}, year = {2017} } @inproceedings{mcinerney_computing_2017, address = {Cham, Switzerland}, author = {McInerney, Clare and Lamprecht, Anna-Lena and Margaria, Tiziana}, booktitle = {Tomorrow's {Learning}: {Involving} {Everyone}}, doi = {10.1007/978-3-319-74310-3_50}, editor = {Tatnall, Arthur and Webb, Mary}, isbn = {978-3-319-74310-3}, lccn = {2018930742}, pages = {494--505}, publisher = {Springer International Publishing}, series = {{IFIP} {Advances} in {Information} and {Communication} {Technology}}, title = {Computing {Camps} for {Girls} – {A} {First}-{Time} {Experience} at the {University} of {Limerick}}, volume = {515}, year = {2017} } @article{mons_cloudy_2017, abstract = {The FAIR Data Principles propose that all scholarly output should be Findable, Accessible, Interoperable, and Reusable. As a set of guiding principles, expressing only the kinds of behaviours that researchers should expect from contemporary data reso}, author = {Mons, Barend and Neylon, Cameron and Velterop, Jan and Dumontier, Michel and da Silva Santos, Luiz Olavo Bonino and Wilkinson, Mark D.}, doi = {10.3233/ISU-170824}, issn = {0167-5265}, journal = {Information Services \& Use}, language = {en}, month = {January}, number = {1}, pages = {49--56}, title = {Cloudy, increasingly {FAIR}; revisiting the {FAIR} {Data} guiding principles for the {European} {Open} {Science} {Cloud}}, url = {https://content.iospress.com/articles/information-services-and-use/isu824}, urldate = {2020-05-11}, volume = {37}, year = {2017} } @article{morgan_elixir-excelerate_2017, author = {Morgan, Sarah L. and Palagi, Patricia M. and Fernandes, Pedro L. and Koperlainen, Eija and Dimec, Jure and Marek, Diana and Larcombe, Lee and Rustici, Gabriella and Attwood, Teresa K. and Via, Allegra}, doi = {10.12688/f1000research.12332.1}, journal = {F1000Research}, month = {August}, pages = {1557}, title = {The {ELIXIR}-{EXCELERATE} {Train}-the-{Trainer} pilot programme: empower researchers to deliver high-quality training [version 1; peer review: 2 approved]}, volume = {6}, year = {2017} } @article{pinto_energy_2017, author = {Pinto, Gustavo and Castor, Fernando}, doi = {10.1145/3154384}, issn = {1557-7317}, journal = {Communications of the ACM}, month = {November}, number = {12}, pages = {68--75}, title = {Energy {Efficiency}: {A} {New} {Concern} for {Application} {Software} {Developers}}, volume = {60}, year = {2017} } @inproceedings{queiroz_track_2017, author = {Queiroz, Francisco and Silva, Raniere and Miller, Jonah and {Sandor Brockhauser} and Fangohr, Hans}, booktitle = {Proceedings of the {Workshop} on {Sustainable} {Software} for {Science}: {Practice} and {Experiences} ({WSSSPE5}.1)}, doi = {10.6084/m9.figshare.5331814}, editor = {Chue Hong, Neil and Druskat, Stephan and Haines, Robert and Jay, Caroline and Katz, Daniel S. and Sufi, Shoaib}, month = {September}, publisher = {figshare}, title = {Track 1 {Paper}: {Good} {Usability} {Practices} in {Scientific} {Software} {Development}}, year = {2017} } @inproceedings{ramakrishnan_ten_2017, author = {Ramakrishnan, Lavanya and Gunter, Daniel}, booktitle = {Proceedings of the 13{\textbackslash}textsuperscriptth {International} {Conference} on e-{Science} (e-{Science})}, doi = {10.1109/escience.2017.34}, isbn = {978-1-5386-2686-3}, month = {October}, publisher = {IEEE}, title = {Ten {Principles} for {Creating} {Usable} {Software} for {Science}}, year = {2017} } @article{richardson_research_2017, author = {Richardson, Chris}, doi = {10/gf5tgv}, keywords = {UK}, month = {March}, title = {The {Research} {Software} {Engineer}- {An} {Emerging} {New} {Role} in {Academia} in the {UK}.pdf}, url = {https://figshare.com/articles/The\%5FResearch\%5FSoftware\%5FEngineer-\%5FAn\%5FEmerging\%5FNew\%5FRole\%5Fin\%5FAcademia\%5Fin\%5Fthe\%5FUK\%5Fpdf/4712488/1}, year = {2017} } @inproceedings{sale_badges_2017, author = {Sale, Jeff}, booktitle = {Blue {Waters} {Webinars}}, month = {August}, publisher = {Blue Waters}, title = {Badges for {Visualization} {Micro}-{Certification}}, url = {https://bluewaters.ncsa.illinois.edu/liferay-content/document-library/BW%20Webinars/Slides/Badges%20for%20Visualization%20Micro-Certification%20by%20Jeff%20Sale.pdf}, year = {2017} } @book{scheliga_helmholtz_2017, author = {Scheliga, Katharina Sara and Pampel, Heinz and Bernstein, Erik and Bruch, Christoph and Zu Castell, Wolfgang and Diesmann, Markus and Fritzsch, Bernadette and Fuhrmann, J\"{u}rgen and Haas, Holger and Hammitzsch, M. and Laehnemann, David and McHardy, Alice and Konrad, Uwe and Scharnberg, Gianna and Schreiber, Andreas and Steglich, Dirk}, doi = {10.2312/lis.17.01}, keywords = {hgfos16, Sustainability, Workshop}, language = {deu}, month = {November}, publisher = {Deutsches GeoForschungsZentrum GFZ}, title = {Helmholtz {Open} {Science} {Workshop} ,,{Zugang} zu und {Nachnutzung} von wissenschaftlicher {Software}``}, year = {2017} } @article{science_zugang_2017, author = {Science, Arbeitskreis Open}, keywords = {Sustainability, ⛔ No DOI found, Workshop}, month = {March}, title = {Zugang zu und {Nachnutzung} von wissenschaftlicher {Software}.}, url = {https://os.helmholtz.de/index.php?id=2766}, year = {2017} } @inproceedings{shelton_how_2017, address = {Cham, Switzerland}, author = {Shelton, Chris}, booktitle = {Tomorrow's {Learning}: {Involving} {Everyone}}, doi = {10.1007/978-3-319-74310-3_51}, editor = {Tatnall, Arthur and Webb, Mary}, isbn = {978-3-319-74310-3}, lccn = {2018930742}, pages = {506--514}, publisher = {Springer International Publishing}, series = {{IFIP} {Advances} in {Information} and {Communication} {Technology}}, title = {How {Can} {We} {Make} {Computing} {Lessons} {More} {Inclusive}?}, volume = {515}, year = {2017} } @article{soito_citations_2017, author = {Soito, Laura and Hwang, Lorraine J.}, doi = {10/ggb7v6}, journal = {International Journal of Digital Curation}, keywords = {Citation}, month = {July}, number = {2}, pages = {48--63}, title = {Citations for {Software}: {Providing} {Identification}, {Access} and {Recognition} for {Research} {Software}}, volume = {11}, year = {2017} } @article{storer_bridging_2017, author = {Storer, Tim}, doi = {10.1145/3084225}, journal = {ACM Computing Surveys}, month = {August}, number = {4}, pages = {1--32}, title = {Bridging the {Chasm}}, volume = {50}, year = {2017} } @article{taschuk_ten_2017, author = {Taschuk, Morgan and Wilson, Greg}, doi = {10/gfvpqw}, journal = {PLOS Computational Biology}, keywords = {Software Engineering, Best Practices, Reproducibility}, month = {April}, number = {4}, pages = {e1005412}, title = {Ten simple rules for making research software more robust}, volume = {13}, year = {2017} } @article{the_emphplos_computational_biology_staff_correction_2017, author = {{The {\textbackslash}emphPLOS Computational Biology Staff}}, doi = {10.1371/journal.pcbi.1005858}, journal = {PLOS Computational Biology}, month = {November}, number = {11}, pages = {e1005858}, title = {Correction: {Unmet} needs for analyzing biological big data: {A} survey of 704 {NSF} principal investigators}, volume = {13}, year = {2017} } @inproceedings{van_horn_democratizing_2017, address = {Singapore}, author = {Van Horn, John Darrell and Fierro, Lily and Kamdar, Jeana and Gordon, Jonathan and Stewart, Crystal and Bhattrai, Avnish and Abe, Sumiko and Lei, Xiaoxiao and O'Driscoll, Caroline and Sinha, Aakanchha and Jain, Priyambada and Burns, Gully and Lerman, Kristina and Ambite, Jos\'{e} Luis}, booktitle = {Proceedings of the {Pacific} {Symposium} on {Biocomputing} 2018}, doi = {10.1142/9789813235533_0027}, editor = {Altman, Russ B. and Dunker, A. Keith and Hunter, Lawrence and Ritchie, Marylyn D. and Murray, Tiffany and Klein, Teri E.}, isbn = {978-981-323-553-3}, month = {November}, pages = {292--303}, publisher = {World Scientific}, title = {Democratizing data science through data science training}, year = {2017} } @article{wilson_good_2017, author = {Wilson, Greg and Bryan, Jennifer and Cranston, Karen and Kitzes, Justin and Nederbragt, Lex and Teal, Tracy K.}, doi = {10/gbkbwp}, editor = {Ouellette, Francis}, journal = {PLOS Computational Biology}, keywords = {Software Engineering, Best Practices, Scientific Computing, Git, Open Science Fellows}, month = {June}, number = {6}, pages = {e1005510}, title = {Good enough practices in scientific computing}, volume = {13}, year = {2017} } @article{artaza_top_2016, author = {Artaza, Haydee and Chue Hong, Neil and Corpas, Manuel and Corpuz, Angel and Hooft, Rob W. W. and Jim\'{e}nez, Rafael C. and Lesko\v{s}ek, Brane and Olivier, Brett G. and Stourac, Jan and Svobodov\'{a} Va\v{r}ekov\'{a}, Radka and Van Parys, Thomas and Vaughan, Daniel}, doi = {10.12688/f1000research.9206.1}, journal = {F1000Research}, keywords = {Best Practices, Software Engineering}, month = {August}, pages = {2000}, title = {Top 10 metrics for life science software good practices}, volume = {5}, year = {2016} } @article{baker_library_2016, author = {Baker, James and Moore, Caitlin and Priego, Ernesto and Alegre, Raquel and Cope, Jez and Price, Ludi and Stephens, Owen and van Strien, Daniel and Wilson, Greg}, doi = {10.18352/lq.10176}, issn = {2213-056X}, journal = {Liber Quarterly}, month = {November}, number = {3}, pages = {141--162}, title = {Library {Carpentry}: {Software} {Skills} {Training} for {Library} {Professionals}}, volume = {26}, year = {2016} } @article{bird_using_2016, author = {Bird, Colin and Coles, Simon and Garrelfs, Iris and Griffin, Tom and Hagdorn, Magnus and Klyne, Graham and Mineter, Mike and Willoughby, Cerys}, doi = {10.2218/ijdc.v11i1.412}, issn = {1746-8256}, journal = {International Journal of Digital Curation}, number = {1}, title = {Using {Metadata} {Actively}}, volume = {11}, year = {2016} } @article{brazas_continuing_2016, author = {Brazas, Michelle D. and Ouellette, B. F. Francis}, doi = {10.1371/journal.pcbi.1004916}, editor = {Lewitter, Fran}, journal = {PLOS Computational Biology}, month = {June}, number = {6}, pages = {e1004916}, title = {Continuing {Education} {Workshops} in {Bioinformatics} {Positively} {Impact} {Research} and {Careers}}, volume = {12}, year = {2016} } @article{collberg_repeatability_2016, author = {Collberg, Christian and Proebsting, Todd A.}, doi = {10.1145/2812803}, issn = {1557-7317}, journal = {Communications of the ACM}, keywords = {reproducability}, month = {February}, number = {3}, pages = {62--69}, title = {Repeatability in computer systems research}, volume = {59}, year = {2016} } @article{crusoe_walking_2016, author = {Crusoe, Michael R. and Brown, C. Titus}, doi = {10.5334/jors.35}, journal = {Journal of Open Research Software}, month = {November}, number = {1}, pages = {e44}, title = {Walking the {Talk}: {Adopting} and {Adapting} {Sustainable} {Scientific} {Software} {Development} processes in a {Small} {Biology} {Lab}}, volume = {4}, year = {2016} } @article{crymble_identifying_2016, author = {Crymble, Adam}, journal = {Blended Learning in Practice}, number = {Autumn}, pages = {49--60}, title = {Identifying and {Removing} {Gender} {Barriers} in {Open} {Learning} {Communities}: \emph{{The} {Programming} {Historian}}}, url = {https://uhra.herts.ac.uk/bitstream/handle/2299/17271/Blip\%5F2016\%5FAutumn\%5F2016\%5FFinal\%5FAutumn\%5F2016.pdf#page=49}, year = {2016} } @book{dallmeier-tiessen_reproduzierbarkeit_2016, author = {Dallmeier-Tiessen, S\"{u}nje}, doi = {10.5281/zenodo.168384}, keywords = {hgfos16, Reproducibility, Workshop}, publisher = {Zenodo}, title = {Reproduzierbarkeit {Und} {Open} {Science}: {Bestandteile} {Und} {Erste} {Erfahrungswerte} - {Mit} {Besonderem} {Augenmerk} {Auf} {Software}}, year = {2016} } @incollection{diamond_digital_2016, address = {Cham, Switzerland}, author = {Diamond, James and Gonzalez, Pilar Carmina}, booktitle = {Foundation of {Digital} {Badges} and {Micro}-{Credentials}}, doi = {10.1007/978-3-319-15425-1_21}, editor = {Ifenthaler, Dirk and Bellin-Mularski, Nicole and Mah, Dana-Kristin}, isbn = {978-3-319-15425-1}, month = {June}, pages = {391--409}, publisher = {Springer International Publishing}, title = {Digital {Badges} for {Professional} {Development}: {Teachers}' {Perceptions} of the {Value} of a {New} {Credentialing} {Currency}}, year = {2016} } @book{druskat_entwurf_2016, author = {Druskat, Stephan}, doi = {10.5281/zenodo.168383}, keywords = {hgfos16, Repository, Workshop}, publisher = {Zenodo}, title = {Entwurf {Eines} {Metadatenrepositoriums} {Zur} {Erfassung} {Technischer} {Nachhaltigkeit} {Von} {Forschungssoftware}}, year = {2016} } @article{eklund_cluster_2016, author = {Eklund, Anders and Nichols, Thomas E. and Knutsson, Hans}, doi = {10.1073/pnas.1602413113}, journal = {Proceedings of the National Academy of Sciences}, number = {28}, pages = {7900--7905}, title = {Cluster failure: {Why} {fMRI} inferences for spatial extent have inflated false-positive rates}, volume = {113}, year = {2016} } @incollection{grant_building_2016, address = {Cham, Switzerland}, author = {Grant, Sheryl}, booktitle = {Foundation of {Digital} {Badges} and {Micro}-{Credentials}}, doi = {10.1007/978-3-319-15425-1_6}, editor = {Ifenthaler, Dirk and Bellin-Mularski, Nicole and Mah, Dana-Kristin}, isbn = {978-3-319-15425-1}, month = {June}, pages = {97--114}, publisher = {Springer International Publishing}, title = {Building {Collective} {Belief} in {Badges}: {Designing} {Trust} {Networks}}, year = {2016} } @article{henriksen-bulmer_re-identification_2016, author = {Henriksen-Bulmer, Jane and Jeary, Sheridan}, doi = {10.1016/j.ijinfomgt.2016.08.002}, issn = {0268-4012}, journal = {International Journal of Information Management}, number = {6, Part B}, pages = {1184--1192}, title = {Re-identification attacks--{A} systematic literature review}, volume = {36}, year = {2016} } @incollection{holzmann_archiving_2016, author = {Holzmann, Helge and Sperber, Wolfram and Runnwerth, Mila}, booktitle = {Research and {Advanced} {Technology} for {Digital} {Libraries}}, doi = {10.1007/978-3-319-43997-6_17}, keywords = {Archive}, pages = {215--226}, publisher = {Springer International Publishing}, title = {Archiving {Software} {Surrogates} on the {Web} for {Future} {Reference}}, year = {2016} } @article{hucka_software_2016, abstract = {Improved software discovery is a prerequisite for greater software reuse: after all, if someone cannot find software for a particular task, they cannot reuse it. Understanding people's approaches and preferences when they look for software could help improve facilities for software discovery. We surveyed people working in several scientific and engineering fields to better understand their approaches and selection criteria. We found that even among highly-trained people, the rudimentary approaches of relying on general Web searches, the opinions of colleagues, and the literature were still the most commonly used. However, those who were involved in software development differed from nondevelopers in their use of social help sites, software project repositories, software catalogs, and organization-specific mailing lists or forums. For example, software developers in our sample were more likely to search in community sites such as Stack Overflow even when seeking ready-to-run software rather than source code, and likewise, asking colleagues was significantly more important when looking for ready-to-run software. Our survey also provides insight into the criteria that matter most to people when they are searching for ready-to-run software. Finally, our survey also identifies some factors that can prevent people from finding software.}, author = {Hucka, Michael and Graham, Matthew J.}, doi = {10/ggc6j4}, journal = {Journal of Systems and Software, 141:171-191, 2018}, keywords = {Retrieval}, title = {Software search is not a science, even among scientists: {A} survey of how scientists and engineers find software}, year = {2016} } @article{hutton_most_2016, author = {Hutton, Christopher and Wagener, Thorsten and Freer, Jim and Han, Dawei and Duffy, Chris and Arheimer, Berit}, doi = {10.1002/2016WR019285}, journal = {Water Resources Research}, number = {10}, pages = {7548--7555}, title = {Most computational hydrology is not reproducible, so is it really science?}, volume = {52}, year = {2016} } @book{ifenthaler_foundation_2016, address = {Cham, Switzerland}, doi = {10.1007/978-3-319-15425-1}, editor = {Ifenthaler, Dirk and Bellin-Mularski, Nicole and Mah, Dana-Kristin}, isbn = {978-3-319-15425-1}, month = {June}, publisher = {Springer International Publishing}, title = {Foundation of {Digital} {Badges} and {Micro}-{Credentials}: {Demonstrating} and {Recognizing} {Knowledge} and {Competencies}}, year = {2016} } @article{jay_not_2016, author = {Jay, Caroline and Sanyour, Rawan and Haines, Robert}, journal = {Journal of open research software}, keywords = {⛔ No DOI found, Git}, month = {June}, pages = {null--null}, title = {Not everyone can use {Git}: {Research} {Software} {Engineers} recommendations for scientist-centred software support (and what researchers really think of them)}, url = {https://www.research.manchester.ac.uk/portal/files/53599032/JayCaroline\%5F2.pdf; https://lens.org/139-612-968-828-896}, year = {2016} } @book{katerbow_nachhaltigkeit_2016, author = {Katerbow, Matthias}, doi = {10.5281/zenodo.168387}, keywords = {hgfos16, Sustainability, Workshop}, publisher = {Zenodo}, title = {Nachhaltigkeit {Von} {Forschungssoftware}}, year = {2016} } @article{katz_software_2016, author = {Katz, Daniel S. and Niemeyer, Kyle E. and Smith, Arfon M. and Anderson, William L. and Boettiger, Carl and Hinsen, Konrad and Hooft, Rob and Hucka, Michael and Lee, Allen and L\"{o}ffler, Frank and Pollard, Tom and Rios, Fernando}, doi = {10/gfvpq2}, keywords = {Citation, Research Data}, title = {Software vs. data in the context of citation}, year = {2016} } @book{kislinskiy_qualitatsmanagement_2016, author = {Kislinskiy, Stefan and Goch, Caspar}, doi = {10.5281/zenodo.168385}, keywords = {hgfos16, Infrastructure, Open Source, Quality Assurance, Workshop}, publisher = {Zenodo}, title = {Qualit\"{a}tsmanagement {Von} {Und} {Infrastruktur} {F\"{u}r} {Open} {Source} {Software} {In} {Der} {Wissenschaft} {Am} {Beispiel} {Des} {Medical} {Imaging} {Interaction} {Toolkits} ({Mitk})}, year = {2016} } @article{koster_wege_2016, author = {K\"{o}ster, Johannes}, doi = {10.5281/zenodo.168388}, keywords = {Reproducibility, Workshop}, title = {Wege {Aus} {Der} {In}-{Silico}-{Reproduzierbarkeitskrise}}, year = {2016} } @article{lewandowsky_research_2016, author = {Lewandowsky, Stephan and Bishop, Dorothy}, doi = {10/ggc6j5}, journal = {Nature}, keywords = {Transparency}, month = {January}, number = {7587}, pages = {459--461}, title = {Research integrity: {Dont} let transparency damage science}, volume = {529}, year = {2016} } @inproceedings{manotas_empirical_2016, address = {New York, New York, USA}, author = {Manotas, Irene and Bird, Christian and Zhang, Rui and Shepherd, David and Jaspan, Ciera and Sadowski, Caitlin and Pollock, Lori and Clause, James}, booktitle = {Proceedings of the 2016 {IEEE}/{ACM} 38{\textbackslash}textsuperscriptth {International} {Conference} on {Software} {Engineering} ({ICSE} 2016)}, doi = {10.1145/2884781.2884810}, isbn = {978-1-4503-3900-1}, month = {May}, publisher = {ACM}, title = {An empirical study of practitioners' perspectives on green software engineering}, year = {2016} } @article{mcdaniel_building_2016, author = {McDaniel, Rudy and Fanfarelli, Joseph}, doi = {10.1177/1046878115627138}, journal = {Simulation \& Gaming}, month = {February}, number = {1}, pages = {73--102}, title = {Building {Better} {Digital} {Badges}}, volume = {47}, year = {2016} } @article{miller_brain_2016, author = {Miller, Greg}, doi = {10.1126/science.353.6296.208}, journal = {Science}, number = {6296}, pages = {208--209}, title = {Brain scans are prone to false positives, study says}, volume = {353}, year = {2016} } @article{muna_astropy_2016, abstract = {The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software.}, author = {Muna, Demitri and Alexander, Michael and Allen, Alice and Ashley, Richard and Asmus, Daniel and Azzollini, Ruyman and Bannister, Michele and Beaton, Rachael and Benson, Andrew and Berriman, G. Bruce and Bilicki, Maciej and Boyce, Peter and Bridge, Joanna and Cami, Jan and Cangi, Eryn and Chen, Xian and Christiny, Nicholas and Clark, Christopher and Collins, Michelle and Comparat, Johan and Cook, Neil and Croton, Darren and Davids, Isak Delberth and Depagne, \'{E}ric and Donor, John and dos Santos, Leonardo A. and Douglas, Stephanie and Du, Alan and Durbin, Meredith and Erb, Dawn and Faes, Daniel and Fern\'{a}ndez-Trincado, J. G. and Foley, Anthony and Fotopoulou, Sotiria and Frimann, S\o{}ren and Frinchaboy, Peter and Garcia-Dias, Rafael and Gawryszczak, Artur and George, Elizabeth and Gonzalez, Sebastian and Gordon, Karl and Gorgone, Nicholas and Gosmeyer, Catherine and Grasha, Katie and Greenfield, Perry and Grellmann, Rebekka and Guillochon, James and Gurwell, Mark and Haas, Marcel and Hagen, Alex and Haggard, Daryl and Haines, Tim and Hall, Patrick and Hellwing, Wojciech and Herenz, Edmund Christian and Hinton, Samuel and Hlozek, Renee and Hoffman, John and Holman, Derek and Holwerda, Benne Willem and Horton, Anthony and Hummels, Cameron and Jacobs, Daniel and Jensen, Jens Juel and Jones, David and Karick, Arna and Kelley, Luke and Kenworthy, Matthew and Kitchener, Ben and Klaes, Dominik and Kohn, Saul and Konorski, Piotr and Krawczyk, Coleman and Kuehn, Kyler and Kuutma, Teet and Lam, Michael T. and Lane, Richard and Liske, Jochen and Lopez-Camara, Diego and Mack, Katherine and Mangham, Sam and Mao, Qingqing and Marsh, David J. E. and Mateu, Cecilia and Maurin, Lo\"{\i}c and McCormac, James and Momcheva, Ivelina and Monteiro, Hektor and Mueller, Michael and Munoz, Roberto and Naidu, Rohan and Nelson, Nicholas and Nitschelm, Christian and North, Chris and Nunez-Iglesias, Juan and Ogaz, Sara and Owen, Russell and Parejko, John and Patr\'{\i}cio, Vera and Pepper, Joshua and Perrin, Marshall and Pickering, Timothy and Piscionere, Jennifer and Pogge, Richard and Poleski, Radek and Pourtsidou, Alkistis and Price-Whelan, Adrian M. and Rawls, Meredith L. and Read, Shaun and Rees, Glen and Rein, Hanno and Rice, Thomas and Riemer-S\o{}rensen, Signe and Rusomarov, Naum and Sanchez, Sebastian F. and Santander-Garc\'{\i}a, Miguel and Sarid, Gal and Schoenell, William and Scholz, Aleks and Schuhmann, Robert L. and Schuster, William and Scicluna, Peter and Seidel, Marja and Shao, Lijing and Sharma, Pranav and Shulevski, Aleksandar and Shupe, David and Sif\'{o}n, Crist\'{o}bal and Simmons, Brooke and Sinha, Manodeep and Skillen, Ian and Soergel, Bjoern and Spriggs, Thomas and Srinivasan, Sundar and Stevens, Abigail and Streicher, Ole and Suchyta, Eric and Tan, Joshua and Telford, O. Grace and Thomas, Romain and Tonini, Chiara and Tremblay, Grant and Tuttle, Sarah and Urrutia, Tanya and Vaughan, Sam and Verdugo, Miguel and Wagner, Alexander and Walawender, Josh and Wetzel, Andrew and Willett, Kyle and Williams, Peter K. G. and Yang, Guang and Zhu, Guangtun and Zonca, Andrea}, keywords = {⛔ No DOI found, Astrophysics}, month = {October}, title = {The {Astropy} {Problem}}, url = {http://arxiv.org/abs/1610.03159v1}, year = {2016} } @article{niemeyer_challenge_2016, author = {Niemeyer, Kyle E. and Smith, Arfon M. and Katz, Daniel S.}, doi = {10/gc5sjd}, journal = {Journal of Data and Information Quality}, keywords = {Citation, Discovery}, number = {4}, pages = {1--5}, title = {The {Challenge} and {Promise} of {Software} {Citation} for {Credit}, {Identification}, {Discovery}, and {Reuse}}, volume = {7}, year = {2016} } @article{pan_disciplinary_2016, abstract = {Software plays an important role in the advancement of science. Software developers, users, and funding agencies have deep interests in the impact of software on science. This study investigates the use and impact of software by examining how software is mentioned and cited among 9548 articles published in PLOS ONE in 12 defined disciplines. Our results demonstrate that software is widely used in scientific research and a substantial uncitedness of software exists across different disciplines. Findings also show that the practice of software citations varies noticeably at the discipline level and software that is free for academic use is more likely to receive citations than commercial software.}, author = {Pan, Xuelian and Yan, Erjia and Hua, Weina}, doi = {10/f9fp4p}, issn = {1588-2861}, journal = {Scientometrics}, keywords = {Bibliometrics}, number = {3}, pages = {1593--1610}, title = {Disciplinary differences of software use and impact in scientific literature}, url = {https://doi.org/10.1007/s11192-016-2138-4}, volume = {109}, year = {2016} } @article{raish_employer_2016, author = {Raish, Victoria and Rimland, Emily}, doi = {10.5860/crl.77.1.87}, journal = {College \& Research Libraries}, month = {January}, number = {1}, pages = {87--113}, title = {Employer {Perceptions} of {Critical} {Information} {Literacy} {Skills} and {Digital} {Badges}}, volume = {77}, year = {2016} } @article{revote_development_2016, author = {Revote, Jerico and Watson-Haigh, Nathan S. and Quenette, Steve and Bethwaite, Blair and McGrath, Annette and Shang, Catherine A.}, doi = {10.1093/bib/bbw032}, journal = {Briefings in Bioinformatics}, month = {April}, pages = {bbw032}, title = {Development of a cloud-based {Bioinformatics} {Training} {Platform}}, year = {2016} } @article{rios_pathways_2016, author = {Rios, Fernando}, doi = {10/gfvpq9}, journal = {D-Lib Magazine}, keywords = {Preservation}, month = {July}, number = {7/8}, title = {The {Pathways} of {Research} {Software} {Preservation}: {An} {Educational} and {Planning} {Resource} for {Service} {Development}}, volume = {22}, year = {2016} } @article{shields_digital_2016, author = {Shields, Rebecca and Chugh, Ritesh}, doi = {10.1007/s10639-016-9521-x}, journal = {Education and Information Technologies}, month = {July}, number = {4}, pages = {1817--1824}, title = {Digital badges – rewards for learning?}, volume = {22}, year = {2016} } @article{smith_software_2016, abstract = {Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.}, author = {Smith, Arfon M. and Katz, Daniel S. and Niemeyer, Kyle E.}, doi = {10.7717/peerj-cs.86}, issn = {2376-5992}, journal = {PeerJ Computer Science}, keywords = {Citation}, language = {en}, month = {September}, pages = {e86}, title = {Software citation principles}, url = {https://peerj.com/articles/cs-86}, urldate = {2020-05-11}, volume = {2}, year = {2016} } @article{the_european_parliament_and_the_council_of_the_european_union_regulation_2016, author = {{The European Parliament and the Council of the European Union}}, issn = {1977-0677}, journal = {Official Journal of the European Union}, month = {May}, number = {L 119}, title = {Regulation ({EU}) 2016/679 of the {European} {Parliament} and of the {Council} of 27 {April} 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing {Directive} 95/46/{EC} ({General} {Data} {Protection} {Regulation})}, url = {https://eur-lex.europa.eu/eli/reg/2016/679/2016-05-04}, volume = {59}, year = {2016} } @article{waltemath_how_2016, author = {Waltemath, Dagmar and Wolkenhauer, Olaf}, doi = {10/f86fsm}, journal = {IEEE Transactions on Biomedical Engineering}, keywords = {Reproducibility, Standards}, number = {10}, pages = {1999--2006}, title = {How {Modeling} {Standards}, {Software}, and {Initiatives} {Support} {Reproducibility} in {Systems} {Biology} and {Systems} {Medicine}}, volume = {63}, year = {2016} } @article{wilkinson_fair_2016, abstract = {There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders--representing academia, industry, funding agencies, and scholarly publishers--have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.}, author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Merc\`{e} and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J. G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and 't Hoen, Peter A. C. and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and van der Lei, Johan and van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend}, copyright = {2016 The Author(s)}, doi = {10.1038/sdata.2016.18}, issn = {2052-4463}, journal = {Scientific Data}, language = {en}, month = {March}, number = {1}, pages = {1--9}, title = {The {FAIR} {Guiding} {Principles} for scientific data management and stewardship}, url = {https://www.nature.com/articles/sdata201618}, urldate = {2020-05-11}, volume = {3}, year = {2016} } @book{zeller_wissenschaftliche_2016, author = {Zeller, Andreas}, doi = {10.5281/zenodo.168389}, keywords = {hgfos16, Workshop}, publisher = {Zenodo}, title = {Wissenschaftliche {Software} {Pflegen} – {Aber} {Wie}?}, year = {2016} } @article{attwood_correction_2015, author = {Attwood, Teresa K. and Bongcam-Rudloff, Erik and Brazas, Michelle E. and Corpas, Manuel and Gaudet, Pascale and Lewitter, Fran and Mulder, Nicola and Palagi, Patricia M. and Schneider, Maria Victoria and van Gelder, Celia W. G. and {GOBLET Consortium}}, doi = {10.1371/journal.pcbi.1004281}, journal = {PLOS Computational Biology}, month = {May}, number = {5}, pages = {e1004281}, title = {Correction: {GOBLET}: {The} {Global} {Organisation} for {Bioinformatics} {Learning}, {Education} and {Training}}, volume = {11}, year = {2015} } @article{atwood_goblet_2015, author = {Atwood, Teresa K. and Bongcam-Rudloff, Erik and Brazas, Michelle E. and Corpas, Manuel and Gaudet, Pascale and Lewitter, Fran and Mulder, Nicola and Palagi, Patricia M. and Schneider, Maria Victoria and van Gelder, Celia W. G. and {GOBLET Consortium}}, doi = {10.1371/journal.pcbi.1004143}, editor = {Welch, Lonnie}, journal = {PLOS Computational Biology}, month = {April}, number = {4}, pages = {e1004143}, title = {{GOBLET}: {The} {Global} {Organisation} for {Bioinformatics} {Learning}, {Education} and {Training}}, volume = {11}, year = {2015} } @article{barr_oracle_2015, author = {Barr, Earl T. and Harman, Mark and McMinn, Phil and Shahbaz, Muzammil and Yoo, Shin}, doi = {10.1109/tse.2014.2372785}, issn = {1939-3520}, journal = {IEEE Transactions on Software Engineering}, month = {May}, number = {5}, pages = {507--525}, title = {The {Oracle} {Problem} in {Software} {Testing}: {A} {Survey}}, volume = {41}, year = {2015} } @article{belhajjame_using_2015, author = {Belhajjame, Khalid and Zhao, Jun and Garijo, Daniel and Gamble, Matthew and Hettne, Kristina and Palma, Raul and Mina, Eleni and Corcho, Oscar and G\'{o}mez-P\'{e}rez, Jos\'{e} Manuel and Bechhofer, Sean and Klyne, Graham and Goble, Carole}, doi = {10.1016/j.websem.2015.01.003}, issn = {15708268}, journal = {Journal of Web Semantics}, keywords = {FAIR other contexts}, language = {en}, month = {May}, pages = {16--42}, title = {Using a suite of ontologies for preserving workflow-centric research objects}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1570826815000049}, urldate = {2020-10-25}, volume = {32}, year = {2015} } @article{brand_beyond_2015, author = {Brand, Amy and Allen, Liz and Altman, Micah and Hlava, Marjorie and Scott, Jo}, doi = {10.1087/20150211}, journal = {Learned Publishing}, number = {2}, pages = {151--155}, title = {Beyond authorship: attribution, contribution, collaboration, and credit}, volume = {28}, year = {2015} } @article{compeau_life_2015, author = {Compeau, Phillip and Pevzner, Pavel A.}, doi = {10.1145/2686871}, issn = {1557-7317}, journal = {Communications of the ACM}, month = {September}, number = {10}, pages = {41--44}, title = {Life after {MOOCs}}, volume = {58}, year = {2015} } @article{crick_reproducibility_2015, abstract = {The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around the ability to implement (and exploit) novel algorithms and models. Taking a new approach from the literature and applying it to a new codebase frequently requires local knowledge missing from the published manuscripts and transient project websites. Alongside this issue, benchmarking, and the lack of open, transparent and fair benchmark sets present another barrier to the verification and validation of claimed results. In this paper, we outline several recommendations to address these issues, driven by specific examples from a range of scientific domains. Based on these recommendations, we propose a high-level prototype open automated platform for scientific software development which effectively abstracts specific dependencies from the individual researcher and their workstation, allowing easy sharing and reproduction of results. This new e-infrastructure for reproducible computational science offers the potential to incentivise a culture change and drive the adoption of new techniques to improve the quality and efficiency – and thus reproducibility – of scientific exploration.}, author = {Crick, Tom and Hall, Benjamin A. and Ishtiaq, Samin}, keywords = {Reproducibility}, month = {March}, title = {Reproducibility in {Research}: {Systems}, {Infrastructure}, {Culture}}, year = {2015} } @article{davis_git_2015, author = {Davis, Robin Camille}, doi = {10/gf5tgq}, journal = {Behavioral \& Social Sciences Librarian}, keywords = {Git}, month = {July}, number = {3}, pages = {158--164}, title = {Git and {GitHub} for {Librarians}}, volume = {34}, year = {2015} } @article{dinsdale_niblse_2015, author = {Dinsdale, Elizabeth and Elgin, Sarah C. R. and Grandgenett, Neal and Morgan, William and Rosenwald, Anne and Tapprich, William and Triplett, Eric W. and Pauley, Mark A.}, doi = {10.1187/cbe.15-06-0123}, issn = {1931-7913}, journal = {CBE--Life Sciences Education}, month = {December}, number = {4}, pages = {le3}, title = {{NIBLSE}: {A} {Network} for {Integrating} {Bioinformatics} into {Life} {Sciences} {Education}}, volume = {14}, year = {2015} } @article{fanfarelli_understanding_2015, author = {Fanfarelli, Joseph and Vie, Stephanie and McDaniel, Rudy}, doi = {10.1145/2792989.2792998}, journal = {Communication Design Quarterly}, month = {June}, number = {3}, pages = {56--60}, title = {Understanding digital badges through feedback, reward, and narrative}, volume = {3}, year = {2015} } @article{hansch_fostering_2015, author = {Hansch, Anna and Newman, Christopher and Schildhauer, Thomas}, doi = {10.2139/ssrn.2694736}, journal = {SSRN Electronic Journal}, month = {November}, title = {Fostering {Engagement} with {Gamification}: {Review} of {Current} {Practices} on {Online} {Learning} {Platforms}}, year = {2015} } @article{hayden_rule_2015, author = {Hayden, Erika Check}, doi = {10/3n4}, journal = {Nature}, keywords = {Open Science, Reproducibility}, month = {April}, number = {7547}, pages = {276--277}, title = {Rule rewrite aims to clean up scientific software}, volume = {520}, year = {2015} } @article{heaton_claims_2015, author = {Heaton, Dustin and Carver, Jeffrey C.}, doi = {10/f7tmz6}, journal = {Information and Software Technology}, keywords = {Software Engineering, Literature Review}, month = {November}, pages = {207--219--207--219}, title = {Claims about the use of software engineering practices in science: {A} systematic literature review}, volume = {67}, year = {2015} } @article{howison_software_2015, author = {Howison, James and Bullard, Julia}, doi = {10/f87339}, journal = {Journal of the Association for Information Science and Technology}, keywords = {Discovery}, number = {9}, pages = {2137--2155}, title = {Software in the scientific literature: {Problems} with seeing, finding, and using software mentioned in the biology literature}, volume = {67}, year = {2015} } @article{howison_understanding_2015, author = {Howison, James and Deelman, Ewa and McLennan, Michael J. and da Silva, Rafael Ferreira and Herbsleb, James D.}, doi = {10/f72tnc}, journal = {Research Evaluation}, keywords = {Ecosystem}, month = {July}, number = {4}, pages = {454--470}, title = {Understanding the scientific software ecosystem and its impact: {Current} and future measures}, volume = {24}, year = {2015} } @article{hurst_digital_2015, author = {Hurst, Emily Josephine}, doi = {10.1080/15424065.2015.1065661}, journal = {Journal of Electronic Resources in Medical Libraries}, month = {July}, number = {3}, pages = {182--189}, title = {Digital {Badges}: {Beyond} {Learning} {Incentives}}, volume = {12}, year = {2015} } @inproceedings{jay_developing_2015, author = {Jay, Caroline and Haines, Robert}, keywords = {⛔ No DOI found, Reproducibility}, title = {Developing reproducible and reusable methods through research software engineering}, url = {https://www.research.manchester.ac.uk/portal/en/publications/developing-reproducible-and-reusable-methods-through-research-software-engineering(ea424bf9-1256-4738-bc62-cd3e985e001a).html}, year = {2015} } @inproceedings{kappes_using_2015, address = {New York, New York, USA}, author = {Kappes, Sandra and Betro, Vincent C.}, booktitle = {Proceedings of the 2015 {XSEDE} {Conference} on {Scientific} {Advancements} {Enabled} by {Enhanced} {Cyberinfrastructure} - {XSEDE} '15}, doi = {10.1145/2792745.2792759}, isbn = {978-1-4503-3720-5}, month = {July}, publisher = {ACM Press}, title = {Using {Mozilla} badges to certify {XSEDE} users and promote training}, year = {2015} } @article{Kelly_2015, author = {Kelly, Diane}, doi = {10.1016/j.jss.2015.07.027}, issn = {0164-1212}, journal = {Journal of Systems and Software}, month = {November}, pages = {50–61}, publisher = {Elsevier BV}, title = {Scientific software development viewed as knowledge acquisition: Towards understanding the development of risk-averse scientific software}, url = {http://dx.doi.org/10.1016/j.jss.2015.07.027}, volume = {109}, year = {2015} } @article{leek_opinion_2015, author = {Leek, Jeffrey T. and Peng, Roger D.}, doi = {10/gc4h7f}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Reproducibility}, month = {February}, number = {6}, pages = {1645--1646}, title = {Opinion: {Reproducible} research can still be wrong: {Adopting} a prevention approach: {Fig}. 1.}, volume = {112}, year = {2015} } @article{lemoine_micro-credentials_2015, author = {Lemoine, Pamela A. and Richardson, Michael D.}, doi = {10.4018/ijtem.2015010104}, journal = {International Journal of Technology and Educational Marketing}, month = {January}, number = {1}, pages = {36--49}, title = {Micro-{Credentials}, {Nano} {Degrees}, and {Digital} {Badges}}, volume = {5}, year = {2015} } @article{murphy-hill_how_2015, abstract = {Software users rely on software tools such as browser tab controls and spell checkers to work effectively and efficiently, but it is difficult for users to be aware of all the tools that might be useful to them. While there are several potential technical solutions to this difficulty, we know little about social solutions, such as one user telling a peer about a tool. To explore these social solutions, we conducted two studies, an interview study and a diary study. The interview study describes a series of interviews with 18 programmers in industry to explore how tool discovery takes place. To broaden our findings to a wider group of software users, we then conducted a diary study of 76 software users in their workplaces. One finding was that social learning of software tools, while sometimes effective, is infrequent; software users appear to discover tools from peers only once every few months. We describe several implications of our findings, such as that discovery from peers can be enhanced by improving software users ability to communicate openly and concisely about tools.}, author = {Murphy-Hill, Emerson and Lee, Da Young and Murphy, Gail C. and McGrenere, Joanna}, doi = {10/ggnd4g}, journal = {Computer Supported Cooperative Work (CSCW)}, keywords = {Discovery}, month = {July}, number = {5}, pages = {389--422}, title = {How {Do} {Users} {Discover} {New} {Tools} in {Software} {Development} and {Beyond}?}, volume = {24}, year = {2015} } @article{noauthor_reviewing_2015, doi = {10/ggc6j2}, journal = {Nature Methods}, keywords = {Methods}, month = {December}, number = {12}, pages = {1099--1099}, title = {Reviewing computational methods}, volume = {12}, year = {2015} } @article{nosek_promoting_2015, author = {Nosek, B. A. and Alter, G. and Banks, G. C. and Borsboom, D. and Bowman, S. D. and Breckler, S. J. and Buck, S. and Chambers, C. D. and Chin, G. and Christensen, G. and Contestabile, M. and Dafoe, A. and Eich, E. and Freese, J. and Glennerster, R. and Goroff, D. and Green, D. P. and Hesse, B. and Humphreys, M. and Ishiyama, J. and Karlan, D. and Kraut, A. and Lupia, A. and Mabry, P. and Madon, T. and Malhotra, N. and Mayo-Wilson, E. and McNutt, M. and Miguel, E. and Paluck, E. L. and Simonsohn, U. and Soderberg, C. and Spellman, B. A. and Turitto, J. and VandenBos, G. and Vazire, S. and Wagenmakers, E. J. and Wilson, R. and Yarkoni, T.}, doi = {10/gcpzwn}, journal = {Science}, keywords = {Open Science}, month = {June}, number = {6242}, pages = {1422--1425}, title = {Promoting an open research culture}, volume = {348}, year = {2015} } @article{reid_digital_2015, author = {Reid, Alan J. and Paster, Denise and Abramovich, Samuel}, doi = {10.1007/s40692-015-0042-1}, journal = {Journal of Computers in Education}, month = {August}, number = {4}, pages = {377--398}, title = {Digital badges in undergraduate composition courses: effects on intrinsic motivation}, volume = {2}, year = {2015} } @article{shade_computing_2015, author = {Shade, Ashley and Teal, Tracy K.}, doi = {10.1371/journal.pbio.1002303}, issn = {1545-7885}, journal = {PLOS Biology}, keywords = {FAIR other contexts}, language = {en}, month = {November}, number = {11}, pages = {e1002303}, shorttitle = {Computing {Workflows} for {Biologists}}, title = {Computing {Workflows} for {Biologists}: {A} {Roadmap}}, url = {https://dx.plos.org/10.1371/journal.pbio.1002303}, urldate = {2020-10-25}, volume = {13}, year = {2015} } @article{steinmacher_systematic_2015, author = {Steinmacher, Igor and Silva, Marco Aurelio Graciotto and Gerosa, Marco Aurelio and Redmiles, David F.}, doi = {10/f6z643}, journal = {Information and Software Technology}, keywords = {Open Source}, month = {March}, pages = {67--85}, title = {A systematic literature review on the barriers faced by newcomers to open source software projects}, volume = {59}, year = {2015} } @article{teal_data_2015, author = {Teal, Tracy K. and Cranston, Karen A. and Lapp, Hilmar and White, Ethan and Wilson, Greg and Ram, Karthik and Pawlik, Aleksandra}, doi = {10.2218/ijdc.v10i1.351}, issn = {1746-8256}, journal = {International Journal of Digital Curation}, month = {March}, number = {1}, pages = {135--143}, title = {Data {Carpentry}: {Workshops} to {Increase} {Data} {Literacy} for {Researchers}}, volume = {10}, year = {2015} } @article{ahn_open_2014, author = {Ahn, June and Pellicone, Anthony and Butler, Brian S.}, doi = {10.3402/rlt.v22.23563}, issn = {2156-7077}, journal = {Research in Learning Technology}, month = {August}, title = {Open badges for education: what are the implications at the intersection of open systems and badging?}, volume = {22}, year = {2014} } @article{alvarez-moreno_managing_2014, author = {\'{A}lvarez-Moreno, M. and de Graaf, C. and L\'{o}pez, N. and Maseras, F. and Poblet, J. M. and Bo, C.}, doi = {10.1021/ci500593j}, journal = {Journal of Chemical Information and Modeling}, keywords = {Chemistry}, month = {December}, number = {1}, pages = {95--103--95--103}, title = {Managing the {Computational} {Chemistry} {Big} {Data} {Problem}: {The} {ioChem}-{BD} {Platform}}, volume = {55}, year = {2014} } @inproceedings{chue_hong_minimal_2014, author = {Chue Hong, Neil}, booktitle = {2{\textbackslash}textsuperscriptnd {Workshop} on {Sustainable} {Software} for {Science}: {Practice} and {Experiences} ({WSSSPE2})}, doi = {10.6084/m9.figshare.1112528}, month = {July}, publisher = {figshare}, title = {Minimal information for reusable scientific software}, year = {2014} } @inproceedings{cucchiara_supporting_2014, address = {Cham, Switzerland}, author = {Cucchiara, Stefania and Giglio, Alessandra and Persico, Donatella and Raffaghelli, Juliana E.}, booktitle = {New {Horizons} in {Web} {Based} {Learning}}, doi = {10.1007/978-3-319-13296-9_15}, editor = {Cao, Yiwei and V\"{a}ljataga, Terje and Tang, Jeff K.T. and Leung, Howard and Laanpere, Mart}, isbn = {978-3-319-13296-9}, lccn = {2014956244}, month = {August}, pages = {133--142}, publisher = {Springer International Publishing}, series = {Lecture {Notes} in {Computer} {Science}}, title = {Supporting {Self}-regulated {Learning} {Through} {Digital} {Badges}: {A} {Case} {Study}}, volume = {8699}, year = {2014} } @article{fitzjohn_reproducible_2014, author = {FitzJohn, Rich and Pennell, Matt and Zanne, Amy and Cornwell, Will}, keywords = {⛔ No DOI found, Reproducibility}, month = {June}, title = {Reproducible research is still a challenge}, url = {https://ropensci.org/blog/2014/06/09/reproducibility/}, year = {2014} } @article{goble_better_2014, author = {Goble, Carole}, doi = {10.1109/MIC.2014.88}, journal = {IEEE Internet Computing}, keywords = {Software Engineering, Sustainability}, number = {5}, pages = {4--8}, title = {Better {Software}, {Better} {Research}}, volume = {18}, year = {2014} } @article{leprevost_best_2014, author = {Leprevost, Felipe da Veiga and Barbosa, Valmir C. and Francisco, Eduardo L. and Perez-Riverol, Yasset and Carvalho, Paulo C.}, doi = {10.3389/fgene.2014.00199}, journal = {Frontiers in Genetics}, month = {July}, title = {On best practices in the development of bioinformatics software}, volume = {5}, year = {2014} } @article{magana_survey_2014, author = {Magana, Alejandra J. and Taleyarkhan, Manaz and Alvarado, Daniela Rivera and Kane, Michael and Springer, John and Clase, Kari}, doi = {10.1187/cbe.13-10-0193}, editor = {Ledbetter, Mary Lee}, issn = {1931-7913}, journal = {CBE--Life Sciences Education}, month = {December}, number = {4}, pages = {607--623}, title = {A {Survey} of {Scholarly} {Literature} {Describing} the {Field} of {Bioinformatics} {Education} and {Bioinformatics} {Educational} {Research}}, volume = {13}, year = {2014} } @article{noauthor_code_2014, doi = {10/wsm}, journal = {Nature}, keywords = {Code Sharing}, month = {October}, number = {7524}, pages = {536--536}, title = {Code share}, volume = {514}, year = {2014} } @incollection{otto_design_2014, address = {Cham, Switzerland}, author = {Otto, Nate and Hickey, Daniel T.}, booktitle = {New {Horizons} in {Web} {Based} {Learning}}, doi = {10.1007/978-3-319-13296-9_20}, editor = {Cao, Yiwei and V\"{a}ljataga, Terje and Tang, Jeff K.T. and Leung, Howard and Laanpere, Mart}, isbn = {978-3-319-13296-9}, lccn = {2014956244}, month = {August}, pages = {179--184}, publisher = {Springer International Publishing}, series = {Lecture {Notes} in {Computer} {Science}}, title = {Design {Principles} for {Digital} {Badge} {Systems}}, volume = {8699}, year = {2014} } @incollection{palma_rohub_2014, address = {Cham}, author = {Palma, Ra\'{u}l and Ho\l{}ubowicz, Piotr and Corcho, Oscar and G\'{o}mez-P\'{e}rez, Jos\'{e} Manuel and Mazurek, Cezary}, booktitle = {Semantic {Web} {Evaluation} {Challenge}}, doi = {10.1007/978-3-319-12024-9_9}, editor = {Presutti, Valentina and Stankovic, Milan and Cambria, Erik and Cantador, Iv\'{a}n and Di Iorio, Angelo and Di Noia, Tommaso and Lange, Christoph and Reforgiato Recupero, Diego and Tordai, Anna}, isbn = {978-3-319-12023-2 978-3-319-12024-9}, keywords = {FAIR other contexts}, pages = {77--82}, publisher = {Springer International Publishing}, title = {{ROHub} -- {A} {Digital} {Library} of {Research} {Objects} {Supporting} {Scientists} {Towards} {Reproducible} {Science}}, url = {http://link.springer.com/10.1007/978-3-319-12024-9\%5F9}, urldate = {2020-10-25}, volume = {475}, year = {2014} } @article{stodden_best_2014, author = {Stodden, Victoria and Miguez, Sheila}, doi = {10.5334/jors.ay}, journal = {Journal of Open Research Software}, month = {July}, number = {1}, pages = {e21}, title = {Best {Practices} for {Computational} {Science}: {Software} {Infrastructure} and {Environments} for {Reproducible} and {Extensible} {Research}}, volume = {2}, year = {2014} } @article{wilson_best_2014, author = {Wilson, Greg and Aruliah, D. A. and Brown, C. Titus and Hong, Neil P. Chue and Davis, Matt and Guy, Richard T. and Haddock, Steven H. D. and Huff, Kathryn D. and Mitchell, Ian M. and Plumbley, Mark D. and Waugh, Ben and White, Ethan P. and Wilson, Paul}, doi = {10/qtt}, editor = {Eisen, Jonathan A.}, journal = {PLoS Biology}, keywords = {Software Engineering, Best Practices}, month = {January}, number = {1}, pages = {e1001745}, title = {Best {Practices} for {Scientific} {Computing}}, volume = {12}, year = {2014} } @inproceedings{xiao_social_2014, abstract = {Security tools can help developers build more secure software systems by helping developers detect or fix security vulnera- bilities in source code. However, developers do not always use these tools. In this paper, we investigate a number of so- cial factors that impact developers adoption decisions, based on a multidisciplinary field of research called diffusion of in- novations. We conducted 42 one-on-one interviews with pro- fessional software developers, and our results suggest a num- ber of ways in which security tool adoption depends on de- velopers social environments and on the channels through which information about tools is communicated. For exam- ple, some participants trusted developers with strong reputa- tions on the Internet as much as they trust their colleagues for information about security tools.}, author = {Xiao, Shundan and Witschey, Jim and Murphy-Hill, Emerson}, doi = {10/ggnd4j}, keywords = {Social Influences, Tool Adoption}, pages = {1095--1106}, publisher = {ACM Press}, title = {Social influences on secure development tool adoption: why security tools spread}, year = {2014} } @article{bangerth_what_2013, author = {Bangerth, Wolfgang and Heister, Timo}, doi = {10/gf5hm4}, journal = {Computational Science \& Discovery}, keywords = {Open Source}, month = {November}, number = {1}, pages = {015010--015010}, title = {What makes computational open source software libraries successful?}, volume = {6}, year = {2013} } @article{brazas_navigating_2013, author = {Brazas, Michelle D. and Ouellette, B. F. Francis}, doi = {10.1093/bib/bbt016}, issn = {1477-4054}, journal = {Briefings in Bioinformatics}, month = {March}, number = {5}, pages = {556--562}, title = {Navigating the changing learning landscape: perspective from bioinformatics.ca}, volume = {14}, year = {2013} } @inproceedings{chue_hong_software_2013, author = {Chue Hong, Neil and Hole, Brian and Moore, Samuel}, booktitle = {1{\textbackslash}textsuperscriptst {Workshop} on {Sustainable} {Software} for {Science}: {Practice} and {Experiences} ({WSSSPE1})}, doi = {10.6084/m9.figshare.795303}, month = {September}, publisher = {figshare}, title = {Software {Papers}: improving the reusability and sustainability of scientific software}, year = {2013} } @article{crouch_software_2013, author = {Crouch, Stephen and Chue Hong, Neil and Hettrick, Simon and Jackson, Mike and Pawlik, Aleksandra and Sufi, Shoaib and Carr, Les and De Roure, David and Goble, Carole and Parsons, Mark}, doi = {10.1109/mcse.2013.133}, issn = {1558-366X}, journal = {Computing in Science \& Engineering}, month = {November}, number = {6}, pages = {74--80}, title = {The {Software} {Sustainability} {Institute}: {Changing} {Research} {Software} {Attitudes} and {Practices}}, volume = {15}, year = {2013} } @article{eng_comet_2013, author = {Eng, Jimmy K. and Jahan, Tahmina A. and Hoopmann, Michael R.}, doi = {10.1002/pmic.201200439}, issn = {16159853}, journal = {Proteomics}, language = {en}, month = {January}, number = {1}, pages = {22--24}, shorttitle = {Comet}, title = {Comet: {An} open-source {MS}/{MS} sequence database search tool}, url = {https://onlinelibrary.wiley.com/doi/10.1002/pmic.201200439}, urldate = {2021-12-05}, volume = {13}, year = {2013} } @article{joppa_troubling_2013, author = {Joppa, L. N. and McInerny, G. and Harper, R. and Salido, L. and Takeda, K. and OHara, K. and Gavaghan, D. and Emmott, S.}, doi = {10/mk7}, journal = {Science}, keywords = {Open Science, Reproducibility}, number = {6134}, pages = {814--815}, title = {Troubling {Trends} in {Scientific} {Software} {Use}}, volume = {340}, year = {2013} } @article{marinovici_many_2013, author = {Marinovici, Maria C. and Kirkham, Harold}, keywords = {⛔ No DOI found, Research Software Engineer}, month = {October}, title = {The {Many} {Faces} of a {Software} {Engineer} in a {Research} {Community}}, url = {http://www.uploads.pnsqc.org/2013/papers/t-033\%5FMarinovici\%5Fpaper.pdf; https://lens.org/122-334-582-872-953}, year = {2013} } @article{martinez-torres_current_2013, author = {Martinez-Torres, M. R. and Diaz-Fernandez, M. C.}, doi = {10/gc5sjj}, journal = {Technology Analysis \& Strategic Management}, keywords = {Open Source}, month = {October}, number = {1}, pages = {55--68}, title = {Current issues and research trends on open-source software communities}, volume = {26}, year = {2013} } @article{mehta_just_2013, author = {Mehta, Neil B. and Hull, Alan L. and Young, James B. and Stoller, James K.}, doi = {10.1097/acm.0b013e3182a36a07}, issn = {1040-2446}, journal = {Academic Medicine}, month = {October}, number = {10}, pages = {1418--1423}, title = {Just {Imagine}: {New} {Paradigms} for {Medical} {Education}}, volume = {88}, year = {2013} } @article{morin_collaboration_2013, author = {Morin, Andrew and Eisenbraun, Ben and Key, Jason and Sanschagrin, Paul C. and Timony, Michael A. and Ottaviano, Michelle and Sliz, Piotr}, doi = {10/ggc6j7}, journal = {eLife}, keywords = {Collaboration}, month = {September}, title = {Collaboration gets the most out of software}, volume = {2}, year = {2013} } @article{ram_git_2013, abstract = {Reproducibility is the hallmark of good science. Maintaining a high degree of transparency in scientific reporting is essential not just for gaining trust and credibility within the scientific community but also for facilitating the development of new ideas. Sharing data and computer code associated with publications is becoming increasingly common, motivated partly in response to data deposition requirements from journals and mandates from funders. Despite this increase in transparency, it is still difficult to reproduce or build upon the findings of most scientific publications without access to a more complete workflow. Version control systems (VCS), which have long been used to maintain code repositories in the software industry, are now finding new applications in science. One such open source VCS, Git, provides a lightweight yet robust framework that is ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts. For individual researchers, Git provides a powerful way to track and compare versions, retrace errors, explore new approaches in a structured manner, while maintaining a full audit trail. For larger collaborative efforts, Git and Git hosting services make it possible for everyone to work asynchronously and merge their contributions at any time, all the while maintaining a complete authorship trail. In this paper I provide an overview of Git along with use-cases that highlight how this tool can be leveraged to make science more reproducible and transparent, foster new collaborations, and support novel uses.}, author = {Ram, Karthik}, copyright = {2013 Ram; licensee BioMed Central Ltd.}, doi = {10/krv}, issn = {1751-0473}, journal = {Source Code for Biology and Medicine}, keywords = {Reproducibility}, language = {En}, month = {December}, number = {1}, pages = {7}, title = {Git can facilitate greater reproducibility and increased transparency in science}, url = {https://scfbm.biomedcentral.com/articles/10.1186/1751-0473-8-7}, urldate = {2019-02-12}, volume = {8}, year = {2013} } @article{sandve_ten_2013, author = {Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind}, doi = {10.1371/journal.pcbi.1003285}, editor = {Bourne, Philip E.}, journal = {PLOS Computational Biology}, month = {October}, number = {10}, pages = {1--4}, title = {Ten simple rules for reproducible computational research}, volume = {9}, year = {2013} } @article{sed_results_2013, author = {Sed, Sanjaabadam and Altangerel, Munkhmagnai}, issn = {1869-5213}, journal = {Embedded Selforganising Systems}, number = {Special Issue – Proceedings of the International Symposium on Computer Science and Educational Technologies 2023}, pages = {48--54}, title = {Some {Results} of the {Study} on {Determining} {Digital} {Competence} {Needs} of {Citizens}}, url = {https://www.bibliothek.tu-chemnitz.de/ojs/index.php/cs/article/view/606}, volume = {10}, year = {2013} } @article{shamir_practices_2013, author = {Shamir, Lior and Wallin, John F. and Allen, Alice and Berriman, Bruce and Teuben, Peter and Nemiroff, Robert J. and Mink, Jessica and Hanisch, Robert J. and DuPrie, Kimberly}, doi = {10/gc5sjk}, journal = {Astronomy and Computing}, keywords = {Astrophysics, Source Code}, month = {February}, pages = {54--58}, title = {Practices in source code sharing in astrophysics}, volume = {1}, year = {2013} } @inproceedings{steinmacher_why_2013, author = {Steinmacher, Igor and Wiese, Igor and Chaves, Ana Paula and Gerosa, Marco Aurelio}, booktitle = {Proceedings of the 6{\textbackslash}textsuperscriptth {International} {Workshop} on {Cooperative} and {Human} {Aspects} of {Software} {Engineering} ({CHASE})}, doi = {10.1109/chase.2013.6614728}, isbn = {978-1-4673-6290-0}, month = {May}, publisher = {IEEE}, title = {Why do newcomers abandon open source software projects?}, year = {2013} } @article{vanganjil_competency_2013, author = {Vanganjil, Lut-Ochir and Banzragch, Buyandelger and Adiyasuren, Zolzaya and Boloo, Nyamsuren}, issn = {1869-5213}, journal = {Embedded Selforganising Systems}, number = {Special Issue – Proceedings of the International Symposium on Computer Science and Educational Technologies 2023}, pages = {23--27}, title = {A {Competency} {Framework} {Implementation} for {International} {Public} in the {Information}, {Communication} and {Technology}}, url = {https://www.bibliothek.tu-chemnitz.de/ojs/index.php/cs/article/view/606}, volume = {10}, year = {2013} } @article{wilson_benefits_2013, author = {Wilson, James A. J.}, keywords = {⛔ No DOI found, Open Source}, title = {Benefits of open source code}, url = {http://oss-watch.ac.uk/resources/whoneedssource}, year = {2013} } @inproceedings{baxter_research_2012, author = {Baxter, Rob and Chue Hong, Neil and Gorissen, Dirk and Hetherington, James and Todorov, Ilian}, booktitle = {Digital {Research} 2012}, keywords = {Research Software Engineer}, month = {September}, publisher = {e-Research South}, title = {The {Research} {Software} {Engineer}}, url = {https://web.archive.org/web/20180202071627/http://digital-research-2012.oerc.ox.ac.uk/papers/the-research-software-engineer/view}, year = {2012} } @inproceedings{chue_hong_doing_2012, author = {Chue Hong, Neil}, booktitle = {Digital {Research} 2012}, month = {September}, publisher = {e-Research South}, title = {Doing science properly in the digital age}, url = {https://web.archive.org/web/20130802135655/http://digital-research-2012.oerc.ox.ac.uk/papers/doing-science-properly-in-the-digital-age/view}, year = {2012} } @article{halavais_genealogy_2012, author = {Halavais, Alexander M.C.}, doi = {10.1080/1369118x.2011.641992}, journal = {Information, Communication \& Society}, month = {April}, number = {3}, pages = {354--373}, title = {A {Genealogy} of {Badges}: {Inherited} meaning and monstrous moral hybrids}, volume = {15}, year = {2012} } @article{ince_case_2012, author = {Ince, Darrel C. and Hatton, Leslie and Graham-Cumming, John}, doi = {10/hqg}, journal = {Nature}, keywords = {Open Source}, month = {February}, number = {7386}, pages = {485--488}, title = {The case for open computer programs}, volume = {482}, year = {2012} } @article{kulikowski_amia_2012, author = {Kulikowski, Casimir A. and Shortliffe, Edward H. and Currie, Leanne M. and Elkin, Peter L. and Hunter, Lawrence E. and Johnson, Todd R. and Kalet, Ira J. and Lenert, Leslie A. and Musen, Mark A. and Ozbolt, Judy G. and Smith, Jack W. and Tarczy-Hornoch, Peter Z. and Williamson, Jeffrey J.}, doi = {10.1136/amiajnl-2012-001053}, journal = {Journal of the American Medical Informatics Association}, month = {November}, number = {6}, pages = {931--938}, title = {{AMIA} {Board} white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline}, volume = {19}, year = {2012} } @article{morin_quick_2012, author = {Morin, Andrew and Urban, Jennifer and Sliz, Piotr}, doi = {10/b5hp}, journal = {PLoS Computational Biology}, keywords = {License}, month = {July}, number = {7}, pages = {e1002598--e1002598}, title = {A {Quick} {Guide} to {Software} {Licensing} for the {Scientist}-{Programmer}}, volume = {8}, year = {2012} } @article{morin_shining_2012, author = {Morin, A. and Urban, J. and Adams, P. D. and Foster, I. and Sali, A. and Baker, D. and Sliz, P.}, doi = {10/m5t}, journal = {Science}, keywords = {Open Science}, month = {April}, number = {6078}, pages = {159--160}, title = {Shining {Light} into {Black} {Boxes}}, volume = {336}, year = {2012} } @article{pashler_is_2012, author = {Pashler, Harold and Harris, Christine R.}, doi = {10.1177/1745691612463401}, journal = {Perspectives on Psychological Science}, number = {6}, pages = {531--536}, title = {Is the replicability crisis overblown? {Three} arguments examined}, volume = {7}, year = {2012} } @article{prlic_ten_2012, author = {Prli\'{c}, Andreas and Procter, James B.}, doi = {10.1371/journal.pcbi.1002802}, journal = {PLoS Computational Biology}, month = {December}, number = {12}, pages = {e1002802}, title = {Ten {Simple} {Rules} for the {Open} {Development} of {Scientific} {Software}}, volume = {8}, year = {2012} } @incollection{boehm_future_2011, address = {Berlin, Heidelberg, Germany}, author = {Boehm, Barry}, booktitle = {The future of software engineering}, doi = {10.1007/978-3-642-15187-3_1}, editor = {Nanz, Sebastian}, isbn = {978-3-642-15187-3}, lccn = {2010937182}, pages = {1--32}, publisher = {Springer Berlin Heidelberg}, title = {Some future software engineering opportunities and challenges}, year = {2011} } @article{cohen-boulakia_search_2011, author = {Cohen-Boulakia, Sarah and Leser, Ulf}, doi = {10.1145/2034863.2034865}, issn = {0163-5808}, journal = {ACM SIGMOD Record}, keywords = {FAIR other contexts}, language = {en}, month = {September}, number = {2}, pages = {6--16}, shorttitle = {Search, adapt, and reuse}, title = {Search, adapt, and reuse: the future of scientific workflows}, url = {https://dl.acm.org/doi/10.1145/2034863.2034865}, urldate = {2020-10-25}, volume = {40}, year = {2011} } @article{form_ten_2011, author = {Form, David and Lewitter, Fran}, doi = {10.1371/journal.pcbi.1002243}, journal = {PLoS Computational Biology}, month = {October}, number = {10}, pages = {e1002243}, title = {Ten {Simple} {Rules} for {Teaching} {Bioinformatics} at the {High} {School} {Level}}, volume = {7}, year = {2011} } @article{gray_journal_2011, abstract = {One of the Birds of a Feather (BoF) discussion sessions at ADASS XX considered whether a new journal is needed to serve the astronomical computing community. In this paper we discuss the nature and requirements of that community, outline the analysis that led us to propose this as a topic for a BoF, and review the discussion from the BoF session itself. We also present the results from a survey designed to assess the suitability of astronomical computing papers of different kinds for publication in a range of existing astronomical and scientific computing journals. The discussion in the BoF session was somewhat inconclusive, and it seems likely that this topic will be debated again at a future ADASS or in a similar forum.}, author = {Gray, Norman and Mann, Robert G.}, keywords = {⛔ No DOI found, Astrophysics}, month = {March}, title = {A {Journal} for the {Astronomical} {Computing} {Community}?}, url = {http://arxiv.org/abs/1103.1982v1}, year = {2011} } @inproceedings{howison_scientific_2011, address = {New York, USA}, author = {Howison, James and Herbsleb, James D.}, booktitle = {Proceedings of the {ACM} 2011 {Conference} on {Computer} {Supported} {Cooperative} {Work} ({CSCW} '11)}, doi = {10.1145/1958824.1958904}, isbn = {978-1-4503-0556-3}, keywords = {Software Engineering}, month = {March}, pages = {513--522}, publisher = {Association for Computing Machinery}, title = {Scientific software production: incentives and collaboration}, year = {2011} } @article{peng_reproducible_2011, author = {Peng, R. D.}, doi = {10/fdv356}, journal = {Science}, keywords = {Reproducibility}, month = {December}, number = {6060}, pages = {1226--1227}, title = {Reproducible {Research} in {Computational} {Science}}, volume = {334}, year = {2011} } @article{bechhofer_research_2010, abstract = {Abstract What will researchers be publishing in the future? Whilst there is little question that the Web will be the publication platform, as scholars move away from paper towards digital content, there is a need for mechanisms that support the production of self-contained units of knowledge and facilitate the publication, sharing and reuse of such entities. In this paper we discuss the notion of research objects , semantically rich aggregations of resources, that can possess some scientific intent or support some research objective. We present a number of principles that we expect such objects and their associated services to follow.}, author = {Bechhofer, Sean and De Roure, David and Gamble, Matthew and Goble, Carole and Buchan, Iain}, doi = {10.1038/npre.2010.4626.1}, issn = {1756-0357}, journal = {Nature Precedings}, language = {en}, month = {July}, shorttitle = {Research {Objects}}, title = {Research {Objects}: {Towards} {Exchange} and {Reuse} of {Digital} {Knowledge}}, url = {http://www.nature.com/articles/npre.2010.4626.1}, urldate = {2022-09-06}, year = {2010} } @article{grosbol_making_2010, abstract = {Access to astronomical data through archives and VO is essential but does not solve all problems. Availability of appropriate software for analyzing the data is often equally important for the efficiency with which a researcher can publish results. A number of legacy systems (e.g. IRAF, MIDAS, Starlink, AIPS, Gipsy), as well as others now coming online are available but have very different user interfaces and may no longer be fully supported. Users may need multiple systems or stand-alone packages to complete the full analysis which introduces significant overhead. The OPTICON Network on `Future Astronomical Software Environments' and the USVAO have discussed these issues and have outlined a general architectural concept that solves many of the current problems in accessing software packages. It foresees a layered structure with clear separation of astronomical code and IT infrastructure. By relying on modern IT concepts for messaging and distributed execution, it provides full scalability from desktops to clusters of computers. A generic parameter passing mechanism and common interfaces will offer easy access to a wide range of astronomical software, including legacy packages, through a single scripting language such as Python. A prototype based upon a proposed standard architecture is being developed as a proof-of-concept. It will be followed by definition of standard interfaces as well as a reference implementation which can be evaluated by the user community. For the long-term success of such an environment, stable interface specifications and adoption by major astronomical institutions as well as a reasonable level of support for the infrastructure are mandatory. Development and maintenance of astronomical packages would follow an open-source, Internet concept.}, author = {Grosbol, P. and Tody, D.}, keywords = {⛔ No DOI found, Astrophysics, Access}, month = {April}, title = {Making {Access} to {Astronomical} {Software} {More} {Efficient}}, url = {http://arxiv.org/abs/1004.4430v1}, year = {2010} } @article{matthews_framework_2010, author = {Matthews, Brian and Shaon, Arif and Bicarregui, Juan and Jones, Catherine}, doi = {10/fxqrbb}, journal = {International Journal of Digital Curation}, keywords = {Archive}, month = {June}, number = {1}, pages = {91--105}, title = {A {Framework} for {Software} {Preservation}}, volume = {5}, year = {2010} } @article{merali_computational_2010, author = {Merali, Zeeya}, doi = {10/b4k9jt}, journal = {Nature}, keywords = {Open Science, Software Engineering}, month = {October}, number = {7317}, pages = {775--777}, title = {Computational science: ...{Error}}, url = {https://www.nature.com/news/2010/101013/full/467775a.html?ref=nf}, volume = {467}, year = {2010} } @inproceedings{nguyen-hoan_survey_2010, address = {New York, NY, USA}, author = {Nguyen-Hoan, Luke and Flint, Shayne and Sankaranarayana, Ramesh}, booktitle = {Proceedings of the 2010 {ACM}-{IEEE} {International} {Symposium} on {Empirical} {Software} {Engineering} and {Measurement}}, doi = {10/brfqvq}, isbn = {978-1-4503-0039-1}, keywords = {Survey, Best Practices, Scientific Computing}, pages = {12:1--12:10}, publisher = {ACM}, series = {{ESEM} '10}, title = {A {Survey} of {Scientific} {Software} {Development}}, url = {http://doi.acm.org/10.1145/1852786.1852802}, year = {2010} } @inproceedings{turhan_better_2010, author = {Turhan, Burak and Meri\c{c}li, \c{C}etin and Meri\c{c}li, Tekin}, doi = {10.1145/1868328.1868345}, publisher = {ACM Press}, title = {Better, faster, and cheaper: what is better software?}, year = {2010} } @article{vega-gorgojo_semantic_2010, author = {Vega-Gorgojo, Guillermo and Bote-Lorenzo, Miguel L. and Asensio-P\'{e}rez, Juan I. and G\'{o}mez-S\'{a}nchez, Eduardo and Dimitriadis, Yannis A. and Jorr\i{}\'n-Abell\'{a}n, Iv\'{a}n M.}, doi = {10/dkzc3p}, journal = {Computers \& Education}, keywords = {Search, Semantic Web}, number = {4}, pages = {835--848}, title = {Semantic search of tools for collaborative learning with the {Ontoolsearch} system}, volume = {54}, year = {2010} } @inproceedings{xu_managing_2010, abstract = {Managing ubiquitous scientific knowledge is a part of daily life for scholars, while it also becomes a hot topic in the Semantic Web research community. In this paper, we propose a SKO Types framework aiming to facilitate managing ubiquitous Scientific Knowledge Objects (SKO) driven by semantic authoring, modularization, annotation and search. SKO Types framework comprises SKO Metadata Schema, SKO Patterns and SKO Editor corresponding to metadata layer, ontology layer and interface layer respectively. SKO Metadata Schema specifies sets of attributes describing SKOs individually and relationally. SKO Patterns is a three-ontology based model in order to modularize scientific publications syntactically and semantically, while SKO Editor supplies a LaTex-like mark-up language and editing environment for authoring and annotating SKOs concurrently.}, address = {Berlin, Heidelberg}, author = {Xu, Hao}, booktitle = {Advances in {Computer} {Science} and {Information} {Technology}}, doi = {10.1007/978-3-642-13577-4_37}, editor = {Kim, Tai-hoon and Adeli, Hojjat}, isbn = {978-3-642-13577-4}, keywords = {FAIR other contexts, Metadata Schema, Resource Description Framework, Rhetorical Structure, Semantic Match, Semantic Search}, language = {en}, pages = {421--430}, publisher = {Springer}, series = {Lecture {Notes} in {Computer} {Science}}, title = {Managing {Ubiquitous} {Scientific} {Knowledge} on {Semantic} {Web}}, year = {2010} } @article{borne_astroinformatics_2009, abstract = {Data volumes from multiple sky surveys have grown from gigabytes into terabytes during the past decade, and will grow from terabytes into tens (or hundreds) of petabytes in the next decade. This exponential growth of new data both enables and challenges effective astronomical research, requiring new approaches. Thus far, astronomy has tended to address these challenges in an informal and ad hoc manner, with the necessary special expertise being assigned to e-Science or survey science. However, we see an even wider scope and therefore promote a broader vision of this data-driven revolution in astronomical research. For astronomy to effectively cope with and reap the maximum scientific return from existing and future large sky surveys, facilities, and data-producing projects, we need our own information science specialists. We therefore recommend the formal creation, recognition, and support of a major new discipline, which we call Astroinformatics. Astroinformatics includes a set of naturally-related specialties including data organization, data description, astronomical classification taxonomies, astronomical concept ontologies, data mining, machine learning, visualization, and astrostatistics. By virtue of its new stature, we propose that astronomy now needs to integrate Astroinformatics as a formal sub-discipline within agency funding plans, university departments, research programs, graduate training, and undergraduate education. Now is the time for the recognition of Astroinformatics as an essential methodology of astronomical research. The future of astronomy depends on it.}, author = {Borne, Kirk D.}, keywords = {⛔ No DOI found, Astrophysics}, month = {September}, title = {Astroinformatics: {A} 21ˢᵗ {Century} {Approach} to {Astronomy}}, url = {http://arxiv.org/abs/0909.3892v1}, year = {2009} } @article{de_roure_design_2009, author = {De Roure, David and Goble, Carole and Stevens, Robert}, doi = {10.1016/j.future.2008.06.010}, issn = {0167739X}, journal = {Future Generation Computer Systems}, keywords = {FAIR other contexts}, language = {en}, month = {May}, number = {5}, pages = {561--567}, title = {The design and realisation of the {Virtual} {Research} {Environment} for social sharing of workflows}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0167739X08000939}, urldate = {2020-10-25}, volume = {25}, year = {2009} } @article{detmer_defining_2009, author = {Detmer, Don E. and Lumpkin, John R. and Williamson, Jeffrey J.}, doi = {10.1197/jamia.m3094}, journal = {Journal of the American Medical Informatics Association}, month = {March}, number = {2}, pages = {167--168}, title = {Defining the {Medical} {Subspecialty} of {Clinical} {Informatics}}, volume = {16}, year = {2009} } @article{frigg_philosophy_2009, author = {Frigg, Roman and Reiss, Julian}, doi = {10.1007/s11229-008-9438-z}, issn = {1573-0964}, journal = {Synthese}, month = {August}, number = {3}, pages = {593--613}, shorttitle = {The philosophy of simulation}, title = {The philosophy of simulation: hot new issues or same old stew?}, volume = {169}, year = {2009} } @article{gardner_core_2009, author = {Gardner, Reed M. and Overhage, J. Marc and Steen, Elaine B. and Munger, Benson S. and Holmes, John H. and Williamson, Jeffrey J. and Detmer, Don E. and {AMIA Board of Directors}}, doi = {10.1197/jamia.m3045}, journal = {Journal of the American Medical Informatics Association}, month = {March}, number = {2}, pages = {153--157}, title = {Core {Content} for the {Subspecialty} of {Clinical} {Informatics}}, volume = {16}, year = {2009} } @inproceedings{hannay_how_2009, author = {Hannay, Jo Erskine and MacLeod, Carolyn and Singer, Janice and Langtangen, Hans Petter and Pfahl, Dietmar and Wilson, Greg}, booktitle = {Proceedings of the 2009 {ICSE} {Workshop} on {Software} {Engineering} for {Computational} {Science} and {Engineering}}, doi = {10.1109/secse.2009.5069155}, isbn = {978-1-4244-3737-5}, keywords = {Software Engineering, Usage}, month = {May}, publisher = {IEEE}, title = {How do scientists develop and use scientific software?}, year = {2009} } @inproceedings{matejka_communitycommands_2009, author = {Matejka, Justin and Li, Wei and Grossman, Tovi and Fitzmaurice, George}, doi = {10/fc4b26}, keywords = {Software Engineering}, pages = {193--202}, publisher = {ACM Press}, title = {{CommunityCommands}: command recommendations for software applications}, year = {2009} } @inproceedings{maxville_preparing_2009, author = {Maxville, Valerie}, booktitle = {Proceedings of the 2009 {ICSE} {Workshop} on {Software} {Engineering} for {Computational} {Science} and {Engineering}}, doi = {10.1109/secse.2009.5069166}, isbn = {978-1-4244-3737-5}, month = {May}, publisher = {IEEE}, title = {Preparing scientists for scalable software development}, year = {2009} } @article{patel_cognitive_2009, author = {Patel, Vimla L. and Yoskowitz, Nicole A. and Arocha, Jose F. and Shortliffe, Edward H.}, doi = {10.1016/j.jbi.2008.12.002}, journal = {Journal of Biomedical Informatics}, month = {February}, number = {1}, pages = {176--197}, title = {Cognitive and learning sciences in biomedical and health instructional design: {A} review with lessons for biomedical informatics education}, volume = {42}, year = {2009} } @article{pevzner_computing_2009, author = {Pevzner, Pavel and Shamir, Ron}, doi = {10.1126/science.1173876}, journal = {Science}, month = {July}, number = {5940}, pages = {541--542}, title = {Computing {Has} {Changed} {Biology}--{Biology} {Education} {Must} {Catch} {Up}}, volume = {325}, year = {2009} } @article{safran_program_2009, author = {Safran, Charles and Shabot, M. Michael and Munger, Benson S. and Holmes, John H. and Steen, Elaine B. and Lumpkin, John R. and Detmer, Don E. and {AMIA Board of Directors}}, doi = {10.1197/jamia.m3046}, journal = {Journal of the American Medical Informatics Association}, month = {March}, number = {2}, pages = {158--166}, title = {Program {Requirements} for {Fellowship} {Education} in the {Subspecialty} of {Clinical} {Informatics}}, volume = {16}, year = {2009} } @inproceedings{segal_challenges_2009, author = {Segal, Judith}, booktitle = {Proceedings of the 2009 {ICSE} {Workshop} on {Software} {Engineering} for {Computational} {Science} and {Engineering}}, doi = {10.1109/secse.2009.5069156}, isbn = {978-1-4244-3737-5}, month = {May}, publisher = {IEEE}, title = {Some challenges facing software engineers developing software for scientists}, year = {2009} } @article{segal_software_2009, author = {Segal, Judith}, doi = {10.1007/s10606-009-9096-9}, issn = {1573-7551}, journal = {Computer Supported Cooperative Work (CSCW)}, month = {September}, number = {5}, pages = {581--606}, title = {Software {Development} {Cultures} and {Cooperation} {Problems}: {A} {Field} {Study} of the {Early} {Stages} of {Development} of {Software} for a {Scientific} {Community}}, volume = {18}, year = {2009} } @article{shortridge_talking_2009, abstract = {Meetings such as ADASS demonstrate that there is an enthusiasm for communication within the astronomical software community. However, the amount of information and experience that can flow around in the course of one, relatively short, meeting is really quite limited. Ideally, these meetings should be just a part of a much greater, continuous exchange of knowledge. In practice, with some notable - but often short-lived - exceptions, we generally fall short of that ideal. Keeping track of what is being used, where, and how successfully, can be a challenge. A variety of new technologies such as those roughly classed as 'Web 2.0' are now available, and getting information to flow ought to be getting simpler, but somehow it seems harder to find the time to keep that information current. This paper looks at some of the ways we communicate, used to communicate, have failed to communicate, no longer communicate, and perhaps could communicate better. It is presented in the hope of stimulating additional discussion - and possibly even a little action - aimed at improving the current situation.}, author = {Shortridge, Keith}, keywords = {⛔ No DOI found, Astrophysics, Community}, month = {February}, title = {Talking {Amongst} {Ourselves} - {Communication} in the {Astronomical} {Software} {Community}}, url = {http://arxiv.org/abs/0902.0255v1}, year = {2009} } @article{tan_proposed_2009, author = {Tan, Tin Wee and Lim, Shen Jean and Khan, Asif M. and Ranganathan, Shoba}, doi = {10.1186/1471-2164-10-s3-s36}, journal = {BMC Genomics}, month = {December}, number = {Suppl 3}, pages = {S36}, title = {A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the ``-omics'' era}, volume = {10}, year = {2009} } @article{weiner_astronomical_2009, abstract = {Astronomical software is now a fact of daily life for all hands-on members of our community. Purpose-built software for data reduction and modeling tasks becomes ever more critical as we handle larger amounts of data and simulations. However, the writing of astronomical software is unglamorous, the rewards are not always clear, and there are structural disincentives to releasing software publicly and to embedding it in the scientific literature, which can lead to significant duplication of effort and an incomplete scientific record. We identify some of these structural disincentives and suggest a variety of approaches to address them, with the goals of raising the quality of astronomical software, improving the lot of scientist-authors, and providing benefits to the entire community, analogous to the benefits provided by open access to large survey and simulation datasets. Our aim is to open a conversation on how to move forward. We advocate that: (1) the astronomical community consider software as an integral and fundable part of facility construction and science programs; (2) that software release be considered as integral to the open and reproducible scientific process as are publication and data release; (3) that we adopt technologies and repositories for releasing and collaboration on software that have worked for open-source software; (4) that we seek structural incentives to make the release of software and related publications easier for scientist-authors; (5) that we consider new ways of funding the development of grass-roots software; (6) and that we rethink our values to acknowledge that astronomical software development is not just a technical endeavor, but a fundamental part of our scientific practice.}, author = {Weiner, Benjamin J. and Blanton, Michael R. and Coil, Alison L. and Cooper, Michael C. and Dav\'{e}, Romeel and Hogg, David W. and Holden, Bradford P. and Jonsson, Patrik and Kassin, Susan A. and Lotz, Jennifer M. and Moustakas, John and Newman, Jeffrey A. and Prochaska, J. X. and Teuben, Peter J. and Tremonti, Christy A. and Willmer, Christopher N. A.}, keywords = {⛔ No DOI found, Open Source, Astrophysics}, month = {March}, title = {Astronomical {Software} {Wants} {To} {Be} {Free}: {A} {Manifesto}}, url = {http://arxiv.org/abs/0903.3971v1}, year = {2009} } @article{consoli_intertwining_2008, author = {Consoli, Luca}, doi = {10.1179/174327908X366923}, journal = {Interdisciplinary Science Reviews}, number = {3}, pages = {234--243}, title = {The intertwining of ethics and methodology in science and engineering: a virtue-ethical approach}, volume = {33}, year = {2008} } @inproceedings{cherubini_lets_2007, address = {New York, New York, USA}, author = {Cherubini, Mauro and Venolia, Gina and DeLine, Rob and Ko, Amy J.}, booktitle = {Proceedings of the {SIGCHI} {Conference} on {Human} {Factors} in {Computing} {Systems}}, doi = {10.1145/1240624.1240714}, isbn = {978-1-59593-593-9}, month = {April}, publisher = {ACM}, title = {Let's {Go} to the {Whiteboard}: {How} and {Why} {Software} {Developers} {Use} {Drawings}}, year = {2007} } @article{herraiz-tabernero_libre_2007, author = {Herraiz-Tabernero, Israel and Amor-Iglesias, Juan-Jose and del Castillo-San Felix, Alvaro}, journal = {The European Journal for the Informatics Professional}, keywords = {⛔ No DOI found, Open Source}, month = {January}, number = {6}, title = {Libre {Software} for {Research}}, url = {http://www.herraiz.org/papers/english/upg8-6Herraiz-2.pdf; https://lens.org/058-536-397-671-136}, volume = {9}, year = {2007} } @article{piwowar_sharing_2007, author = {Piwowar, Heather A. and Day, Roger S. and Fridsma, Douglas B.}, doi = {10.1371/journal.pone.0000308}, editor = {Ioannidis, John}, issn = {1932-6203}, journal = {PLoS ONE}, keywords = {FAIR other contexts}, language = {en}, month = {March}, number = {3}, pages = {e308}, title = {Sharing {Detailed} {Research} {Data} {Is} {Associated} with {Increased} {Citation} {Rate}}, url = {https://dx.plos.org/10.1371/journal.pone.0000308}, urldate = {2020-10-25}, volume = {2}, year = {2007} } @inproceedings{segal_problems_2007, address = {Los Alamitos, California, USA}, author = {Segal, Judith}, booktitle = {{IEEE} {Symposium} on {Visual} {Languages} and {Human}-{Centric} {Computing} ({VL}/{HCC} 2007)}, doi = {10.1109/VLHCC.2007.17}, editor = {Cox, Philip and Hosking, John}, isbn = {978-0-7695-2987-5}, lccn = {2007904552}, pages = {111--118}, publisher = {IEEE Computer Society}, title = {Some problems of professional end user developers}, year = {2007} } @article{wroe_recycling_2007, author = {Wroe, Chris and Goble, Carole and Goderis, Antoon and Lord, Phillip and Miles, Simon and Papay, Juri and Alper, Pinar and Moreau, Luc}, doi = {10.1002/cpe.1050}, issn = {15320626, 15320634}, journal = {Concurrency and Computation: Practice and Experience}, keywords = {FAIR other contexts}, language = {en}, month = {February}, number = {2}, pages = {181--194}, title = {Recycling workflows and services through discovery and reuse}, url = {http://doi.wiley.com/10.1002/cpe.1050}, urldate = {2020-10-25}, volume = {19}, year = {2007} } @article{baxter_scientific_2006, author = {Baxter, Susan M. and Day, Steven W. and Fetrow, Jacquelyn S. and Reisinger, Stephanie J.}, doi = {10.1371/journal.pcbi.0020087}, editor = {McEntyre, Johanna}, journal = {PLoS Computational Biology}, number = {9}, pages = {e87}, title = {Scientific software development is not an oxymoron}, volume = {2}, year = {2006} } @article{lawrence_walking_2006, author = {Lawrence, Katherine A.}, doi = {10.1007/s10606-006-9025-0}, issn = {1573-7551}, journal = {Computer Supported Cooperative Work}, month = {August}, number = {4}, pages = {385--411}, title = {Walking the tightrope: the balancing acts of a large e-{Research} project}, volume = {15}, year = {2006} } @article{miller_scientists_2006, author = {Miller, Greg}, doi = {10.1126/science.314.5807.1856}, journal = {Science}, number = {5807}, pages = {1856--1857}, title = {A scientist's nightmare: software problem leads to five retractions}, volume = {314}, year = {2006} } @incollection{vega-gorgojo_ontoolcole_2006, author = {Vega-Gorgojo, Guillermo and Bote-Lorenzo, Miguel L. and G\'{o}mez-S\'{a}nchez, Eduardo and Asensio-P\'{e}rez, Juan I. and Dimitriadis, Yannis A. and Jorr\i{}\'n-Abell\'{a}n, Iv\'{a}n M.}, booktitle = {Groupware: {Design}, {Implementation}, and {Use}}, doi = {10.1007/11853862_25}, keywords = {Search, Semantic Web}, pages = {310--325}, publisher = {Springer Berlin Heidelberg}, title = {Ontoolcole: {An} {Ontology} for the {Semantic} {Search} of {CSCL} {Services}}, year = {2006} } @article{wilson_wheres_2006, author = {Wilson, Gregory V.}, journal = {American Scientist}, keywords = {Software Engineering}, number = {1}, pages = {5--5}, title = {Where's the real bottleneck in scientific computing?}, url = {https://www.jstor.org/stable/27858697}, volume = {94}, year = {2006} } @article{hack_bioinformatics_2005, author = {Hack, Catherine and Kendall, Gary}, doi = {10.1002/bmb.2005.494033022424}, issn = {1539-3429}, journal = {Biochemistry and Molecular Biology Education}, month = {March}, number = {2}, pages = {82--85}, title = {Bioinformatics: {Current} practice and future challenges for life science education}, volume = {33}, year = {2005} } @article{segal_when_2005, author = {Segal, Judith}, doi = {10.1007/s10664-005-3865-y}, issn = {1573-7616}, journal = {Empirical Software Engineering}, keywords = {Research Software Engineer}, month = {October}, number = {4}, pages = {517--536}, title = {When software engineers met research scientists: a case study}, volume = {10}, year = {2005} } @article{twidale_over_2005, abstract = {The paper reviews work on informal technical help giving between colleagues. It concentrates on the process of how colleagues help each other to use a computer application to achieve a specific work task, contrasting this with the focus of much prior work on sur- rounding issues like the choice of whom to ask, information re-use and the larger work context of encouragement or otherwise of such learning. By an analysis of the literature and a study of office activity, some strengths and weaknesses of the method are identified. The difficulties of talking about the process of performing graphical user interface actions are explored. Various design implications for functionalities to improve the efficiency of informal help giving are explored. A consideration of informal learning can help in designing more effective, learnable, robust and acceptable CSCW systems. It also provides a different perspective on interface design as an exploration of features to support human–human interaction, using the computer screen as a shared resource to support this. In this way CSCW research may contribute to HCI research, since during such help giving, all computer systems are at least temporarily collab- orative applications.}, author = {Twidale, Michael B.}, doi = {10/bcpdqn}, journal = {Computer supported cooperative work (CSCW)}, keywords = {Informal learning}, month = {November}, number = {6}, pages = {505--547}, title = {Over the shoulder learning: supporting brief informal learning}, volume = {14}, year = {2005} } @article{clear_software_2004, author = {Clear, Tony}, doi = {10/bcwdjp}, journal = {ACM SIGCSE Bulletin}, keywords = {Culture}, month = {June}, number = {2}, pages = {14--14}, title = {Software engineering and the academy: uncomfortable bedfellows?}, url = {http://dl.acm.org/citation.cfm?id=1024348; http://aut.researchgateway.ac.nz/handle/10292/560; https://dl.acm.org/citation.cfm?id=1024348; https://doi.acm.org/10.1145/1024338.1024348; https://openrepository.aut.ac.nz/handle/10292/560; https://core.ac.uk/download/pdf/56361332.pdf; https://lens.org/003-405-169-108-40X}, volume = {36}, year = {2004} } @book{humphreys_extending_2004, author = {Humphreys, Paul}, doi = {10.1093/0195158709.001.0001}, isbn = {978-0-19-978596-4}, month = {August}, publisher = {Oxford University Press}, shorttitle = {Extending {Ourselves}}, title = {Extending {Ourselves}: {Computational} {Science}, {Empiricism}, and {Scientific} {Method}}, year = {2004} } @inproceedings{schraefel_breaking_2004, author = {schraefel, m.c. and Hughes, Gareth V. and Mills, Hugo R. and Smith, Graham and Payne, Terry R. and Frey, Jeremy}, booktitle = {Proceedings of the {SIGCHI} {Conference} on {Human} {Factors} in {Computing} {Systems}}, doi = {10.1145/985692.985696}, isbn = {978-1-58113-702-6}, month = {April}, publisher = {ACM}, title = {Breaking the book: translating the chemistry lab book into a pervasive computing lab environment}, year = {2004} } @article{sweeney_k-anonymity_2002, author = {Sweeney, Latanya}, doi = {10.1142/S0218488502001648}, issn = {0218-4885}, journal = {International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems}, month = {October}, number = {05}, pages = {557--570}, title = {k-{Anonymity}: {A} {Model} {For} {Protecting} {Privacy}}, volume = {10}, year = {2002} } @article{gotterbarn_software_1999, author = {Gotterbarn, Don and Miller, Keith and Rogerson, Simon}, doi = {10.1145/317665.317682}, issn = {0001-0782}, journal = {Communications of the ACM}, month = {October}, number = {10}, pages = {102--107}, title = {Software {Engineering} {Code} of {Ethics} is {Approved}}, volume = {42}, year = {1999} } @article{maclean_swift_1999, author = {MacLean, Marlie and Miles, Colin}, doi = {10.1038/43269}, journal = {Nature}, month = {September}, number = {6748}, pages = {10--10}, title = {Swift action needed to close the skills gap in bioinformatics}, volume = {401}, year = {1999} } @article{eveland_role_1995, abstract = {The pattern of CSCW system users helping other users to resolve problems and make more effective use of such tools has been observed in a variety of settings, but little is known about how help patterns develop or their effects. Results from a pre-post study of the implementation of CSCW toolsamong university faculty, staff, and administra- tion indicate that the network of helping relationships is largely disaggregated and generally follows work group alignments rather than technical specialization. A rela- tively small group of "high providers" is responsible for mosthelp to users, and tends to act as a liaison between central support staff and work group members. These providers are not systematically different from other personnel except in terms of their expertise. Implications of thesefindingsfor the development and cultivation of help relationships in support of CSCW are develo}, author = {Eveland, J. D. and Blanchard, Anita and Brown, William and Mattocks, Jennifer}, doi = {10/dhfh8h}, journal = {The Information Society}, keywords = {CSCW, Network}, month = {April}, number = {2}, pages = {113--129}, title = {The role of help networks in facilitating use of {CSCW} tools}, volume = {11}, year = {1995} } @article{hatton_how_1994, author = {Hatton, L. and Roberts, A.}, doi = {10/dr5wch}, journal = {IEEE Transactions on Software Engineering}, keywords = {Open Science}, number = {10}, pages = {785--797}, title = {How accurate is scientific software?}, volume = {20}, year = {1994} } @article{marshall_statisticians_1992, author = {Marshall, Eliot}, doi = {10.1126/science.255.5041.152}, journal = {Science}, number = {5041}, pages = {152--153}, title = {Statisticians at odds over software ownership}, volume = {255}, year = {1992} } @article{robinson_personal_1984, author = {Robinson, Arthur L.}, doi = {10.1126/science.224.4644.40}, journal = {Science}, number = {4644}, pages = {40--44}, title = {Personal computers attract lab software}, volume = {224}, year = {1984} } @article{kolata_caltech_1983, author = {Kolata, Gina}, doi = {10.1126/science.220.4600.932}, journal = {Science}, number = {4600}, pages = {932--934}, title = {Caltech torn by dispute over software}, volume = {220}, year = {1983} } @inproceedings{boehm_software_1979, author = {Boehm, Barry W.}, booktitle = {Proceedings of the 4{\textbackslash}textsuperscriptth {International} {Conference} on {Software} {Engineering} ({ICSE} '79)}, month = {September}, pages = {11--21}, publisher = {IEEE Press}, title = {Software engineering – as it is}, year = {1979} } @inproceedings{randell_software_1979, author = {Randell, B.}, booktitle = {Proceedings of the 4{\textbackslash}textsuperscriptth {International} {Conference} on {Software} {Engineering} ({ICSE} '79)}, month = {September}, pages = {1--10}, publisher = {IEEE Press}, title = {Software engineering in 1968}, year = {1979} } @article{roberts_publication_1969, author = {Roberts, K. V.}, doi = {10.1016/0010-4655(69)90011-3}, journal = {Computer Physics Communications}, month = {July}, number = {1}, pages = {1--9}, title = {The publication of scientific {Fortran} programs}, volume = {1}, year = {1969} } @article{hosier_pitfalls_1961, author = {Hosier, W. A.}, doi = {10.1109/IRET-EM.1961.5007599}, journal = {IRE Transactions on Engineering Management}, number = {2}, pages = {99--115}, title = {Pitfalls and safeguards in real-time digital systems with emphasis on programming}, volume = {EM-8}, year = {1961} }