################################################################################
## Publications
####################
# 2017
@article{dakka-nips17,
author = {Jumana Dakka and Pouya Bashivan and Mina Gheiratmand and Irina Rish and Shantenu Jha, and Russell Greiner},
title = {Learning Neural Markers of Schizophrenia Disorder Using Recurrent Neural Networks},
journal = {31st Conference on Neural Information Processing Systems (NIPS 2017), Long Beach, California, US},
note = {\url{https://arxiv.org/abs/1712.00512}}
}
@article{line-sc17,
author = {Line Pouchard and Sterling Baldwin and Todd Elsethaggen and Carlos Gamboa and Shantenu Jha and Bibi Raju and Eric Stephan and Li Tang and Kerstin Kleese Van Dam},
title = {Computational reproducibility for scientific workflows in large-scale environments},
journal = {Proceedings of Computational Reproducibility at Exascale 2017 (in press)Special Issue of IJHPCA, Workshop at ACM/IEEE SC'17 (CRE2017)},
year = 2017
}
@article{turilli2017comprehensive,
author = {Matteo Turilli and Mark Santcroos and Shantenu Jha},
title = {A Comprehensive Perspective on Pilot-Jobs},
journal = {{ACM Computing Surveys} (accepted, in press), arXiv preprint {arXiv}:1508.04180v3},
year = 2017
}
@inproceedings{htchpc2017converging,
author={D. Oleynik and S. Panitkin and M. Turilli and A. Angius and S. Oral and K. De and A. Klimentov and J. C. Wells and S. Jha},
booktitle={2017 IEEE 13th International Conference on e-Science (e-Science)},
title={High-Throughput Computing on High-Performance Platforms: A Case Study},
year={2017},
volume={},
number={},
pages={295-304},
doi={10.1109/eScience.2017.43},
ISSN={},
month={Oct},
}
@inproceedings{turilli2016analysis,
author={M. Turilli and Y. N. Babuji and A. Merzky and M. T. Ha and M. Wilde and D. S. Katz and S. Jha},
booktitle={2017 IEEE 13th International Conference on e-Science (e-Science)},
title={Evaluating Distributed Execution of Workloads},
year={2017},
volume={},
number={},
pages={276-285},
doi={10.1109/eScience.2017.41},
ISSN={},
month={Oct},
OPTnote={\url{https://arxiv.org/pdf/1605.09513.pdf}}
}
@inproceedings{dakka2017htbac,
title = {High-throughput Binding Affinity Calculations at Extreme Scales},
author = {Jumana Dakka and et al},
journal = {accepted Computational Approaches for Cancer Workshop, 2017},
year = {2017},
url = {http://arxiv.org/abs/1712.09168},
note = {\url{http://www.scworkshops.net/cancer2017/}}
}
@inproceedings{mahzad2017scipy,
title = {Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library},
author = {Mahzad Khoshlessan and Ioannis Paraskevakos and Shantenu Jha and Oliver Beckstein},
journal = {Proceedings of the 15th Python in Science Conference. (SCIPY 2017)},
doi = {10.25080/shinma-7f4c6e7-00a},
year = {2017},
}
@inproceedings{line2017cre,
title = {Computational reproducibility for scientific workflows in large-scale environments},
author = {Line Pouchard and et al},
journal = {Proceedings of Computational Reproducibility at Exascale 2017 (CRE2017)},
year = {2017},
OPTnote = {\url{http://www.scworkshops.net/cancer2017/}}
}
@inproceedings{jay2017open,
title = {Toward Common Components for Open Workflow Systems},
author = {Jay Jay Billings and Shantenu Jha},
journal = {Proceedings of Open Source SuperComputing, Workshop at SC'17},
year = {2017},
note = {\url{https://arxiv.org/abs/1710.06774}}
OPTnote = {\url{http://www.scworkshops.net/cancer2017/}}
}
####################
# 2016
@article {3dpas_intro,
author = {Jha, Shantenu and Katz, Daniel S. and Luckow, Andre and Chue Hong , Neil and Rana, Omer and Simmhan, Yogesh},
title = {Introducing distributed dynamic data-intensive (D3) science: Understanding applications and infrastructure},
journal = {Concurrency and Computation: Practice and Experience},
publisher = {John Wiley & Sons, Ltd},
issn = {1532-0634},
url = {http://dx.doi.org/10.1002/cpe.4032},
doi = {10.1002/cpe.4032},
pages = {e4032--n/a},
keywords = {dynamic, distributed, data intensive, scientific applications},
year = {2017},
note = {e4032 cpe.4032},
}
@article{Zhang2016,
doi = {10.21105/joss.00017},
url = {https://doi.org/10.21105/joss.00017},
year = {2016},
month = {May},
publisher = {The Open Journal},
volume = {1},
number = {1},
author = {Zhao Zhang and Daniel S. Katz and Andre Merzky and Matteo Turilli and Shantenu Jha and Yadu Nand},
title = {Application Skeleton: Generating Synthetic Applications for Infrastructure Research},
journal = {The Journal of Open Source Software}
}
@article{ccpe-2016-error,
author = {Jason Maassen et al },
title = {On the Complexities of Utilizing Large-Scale Lightpath-Connected Distributed Cyberinfrastructure},
journal = {Concurrency and Computation: Practice and Experience},
issn = {in press},
opturl = {http://dx.doi.org/10.1002/cpe.3013},
optdoi = {10.1002/cpe.3013},
optpages = {n/a--n/a},
optkeywords = {next-generation sequencing data analytics, science gateway, BFAST, mapping, ChIP-Seq, human genome, Burkerholderia glumae, mouse genome, runtime environment, distributed computing, simple API for grid applications (SAGA), pilot-job abstraction},
year = {2016},
}
@Article{panda2016,
author="De, K.
and Jha, S.
and Klimentov, A.
and Maeno, T.
and Mashinistov, R.
and Nilsson, P.
and Novikov, A.
and Oleynik, D.
and Panitkin, S.
and Poyda, A.
and Read, K. F.
and Ryabinkin, E.
and Teslyuk, A.
and Velikhov, V.
and Wells, J. C.
and Wenaus, T.",
title="Integration of Panda Workload Management System with supercomputers",
journal="Physics of Particles and Nuclei Letters",
year="2016",
volume="13",
number="5",
pages="647--653",
issn="1531-8567",
doi="10.1134/S1547477116050150",
url="http://dx.doi.org/10.1134/S1547477116050150"
}
@inproceedings{extasy,
author={V. Balasubramanian and I. Bethune and A. Shkurti and E. Breitmoser and E. Hruska and C. Clementi and C. Laughton and S. Jha},
booktitle={2016 IEEE 12th International Conference on e-Science (e-Science)},
title={ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques},
year={2016},
volume={},
number={},
pages={361-370},
doi={10.1109/eScience.2016.7870921},
ISSN={},
month={Oct},
OPTnote = {\url{https://arxiv.org/abs/1606.00093}},
}
@inproceedings{entk,
author = {V. Balasubramanian and A. Treikalis and O. Weidner and S. Jha},
booktitle = {2016 45th International Conference on Parallel Processing (ICPP)},
title = {Ensemble Toolkit: Scalable and Flexible Execution of Ensembles of Tasks},
year = {2016},
volume = {00},
number = {},
pages = {458-463},
doi = {10.1109/ICPP.2016.59},
url = {doi.ieeecomputersociety.org/10.1109/ICPP.2016.59},
ISSN = {2332-5690},
month={Aug.},
OPTnote = {\url{http://arxiv.org/abs/1602.00678}}
}
@inproceedings{repex2016,
author={A. Treikalis and A. Merzky and H. Chen and T. S. Lee and D. M. York and S. Jha},
booktitle={2016 45th International Conference on Parallel Processing (ICPP)},
title={RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations},
year={2016},
volume={},
number={},
pages={628-637},
doi={10.1109/ICPP.2016.78},
ISSN={},
month={Aug},
OPTnote= {\url{ http://arxiv.org/abs/1601.05439}},
}
@inproceedings{cug-2016,
title={Executing dynamic heterogeneous workloads on Blue Waters with RADICAL-Pilot},
author={Santcroos, Mark and Castain, Ralph and Merzky, Andre and
Bethune, Iain and Jha, Shantenu},
booktitle={Cray User Group 2016 (London)},
note = {\url{http://www2.epcc.ed.ac.uk/~ibethune/files/RP-ORTE-CUG2016.pdf}
\url{https://www.youtube.com/watch?v=U3ZZTuGr0pE}},
year={2016}
}
@inproceedings{ipdps-2016,
author = {Matteo Turilli and Feng (Francis) Liu and Zhao Zhang and Andre
Merzky and Michael Wilde and Jon Weissman and Daniel S. Katz
and Shantenu Jha},
title = {Integrating Abstractions to Enhance the Execution of
Distributed Applications},
booktitle = {Proceedings of 30th IEEE International Parallel and Distributed Processing Symposium (IPDPS)},
location = {Chicago, USA},
note = {\url{http://arxiv.org/abs/1504.04720}},
year = {2016},
pages={953-962},
doi={10.1109/IPDPS.2016.64},
ISSN={1530-2075},
month={May},
}
@inproceedings{hadoop-on-hpc,
author = {Andre Luckow and Ioannis Paraskevakos and George Chantzialexiou and
Shantenu Jha},
title = {Hadoop on HPC: Integrating Hadoop and Pilot-Based Dynamic Resource
Management},
journal = {2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
volume = {00},
number = {undefined},
issn = {},
year = {2016},
pages = {1607-1616},
doi = {doi.ieeecomputersociety.org/10.1109/IPDPSW.2016.166},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
@inproceedings{merzky2015synapse,
author = {Andr{\'{e}} Merzky and
Shantenu Jha},
title = {Synapse: Synthetic Application Profiler and Emulator},
booktitle = {2016 {IEEE} International Parallel and Distributed Processing Symposium
Workshops, {IPDPS} Workshops 2016, Chicago, IL, USA, May 23-27, 2016},
pages = {1259--1268},
year = {2016},
OPTcrossref = {DBLP:conf/ipps/2016w},
url = {http://dx.doi.org/10.1109/IPDPSW.2016.168},
doi = {10.1109/IPDPSW.2016.168},
timestamp = {Fri, 05 Aug 2016 15:08:45 +0200},
biburl = {http://dblp.uni-trier.de/rec/bib/conf/ipps/MerzkyJ16},
bibsource = {dblp computer science bibliography, http://dblp.org}
}
@inproceedings{panda-acat16,
author = {A. Klimentov and K. De and S. Jha and T. Maeno and R. Mashinistov and P. Nilsson and A. Novikov and D. Oleynik and S. Panitkin and A.Poyda and K.F.Read and E. Ryabinkin and A. Teslyuk and J.C. Wells and T. Wenaus},
title = {Integration Of PanDA Workload Management System with Supercomputers
for ATLAS and Data-Intensive Sciences},
booktitle = {Journal of Physics: Conference Series, Volume 762 (2016), 012021, 17th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2016, Valparaiso, Chile, 20160118, 20160122)},
doi = {\url{http://dx.doi.org/10.1088/1742-6596/762/1/012021}},
year = {2016},
url = {\url{http://iopscience.iop.org/article/10.1088/1742-6596/762/1/012021/pdf}},
}
####################
# 2015
@article{skeleton-synapse15,
title = "Application skeletons: Construction and use in e{S}cience ",
journal = "Future Generation Computer Systems",
volume = "",
number = "",
OPTpages = " - ",
year = "2015",
note = "\url{http://dx.doi.org/10.1016/j.future.2015.10.001}",
issn = "0167-739X",
doi = "http://dx.doi.org/10.1016/j.future.2015.10.001",
url = "http://www.sciencedirect.com/science/article/pii/S0167739X15003143",
author = "Daniel S. Katz and Andre Merzky and Zhao Zhang and Shantenu Jha",
keywords = "Computational science",
keywords = "Data science",
keywords = "Application modeling",
keywords = "System modeling",
keywords = "Performance modeling",
keywords = "Parallel and distributed systems ",
}
@article{saga-x,
author = {Andre Merzky and Ole Weidner and Shantenu Jha},
title = {{SAGA}: A Standardized Access Layer to Heterogeneous Distributed
Computing Infrastructure},
journal = {Software-X},
year = 2015,
doi = {10.1016/j.softx.2015.03.001},
url = {http://dx.doi.org/10.1016/j.softx.2015.03.001},
note = {DOI: 10.1016/j.softx.2015.03.001},
}
@article{ct500776j,
author = {Brian K. Radak and Melissa Romanus and Tai-Sung Lee and Haoyuan Chen and Ming Huang and Antons Treikalis and Vivekanandan Balasubramanian and Shantenu Jha and Darrin M. York},
title = {Characterization of the Three-Dimensional Free Energy Manifold for the
{Uracil Ribonucleoside} from Asynchronous Replica Exchange Simulations},
journal = {Journal of Chemical Theory and Computation},
volume = {11},
number = {2},
pages = {373-377},
year = {2015},
doi = {10.1021/ct500776j},
URL = {http://dx.doi.org/10.1021/ct500776j},
eprint = {http://dx.doi.org/10.1021/ct500776j},
note = {\url{http://dx.doi.org/10.1021/ct500776j}},
}
@article{titan-panda,
author={A Klimentov and P Buncic and K De and S Jha and T Maeno and R Mount
and P Nilsson and D Oleynik and S Panitkin and A Petrosyan and
R J Porter and K F Read and A Vaniachine and J C Wells and T
Wenaus},
title={Next Generation Workload Management System For Big Data on Heterogeneous Distributed Computing},
journal={Journal of Physics: Conference Series},
volume={608},
number={1},
pages={012040},
url={http://stacks.iop.org/1742-6596/608/i=1/a=012040},
year={2015},
}
####################
# 2014
@article{drmaaocci-jogc-2014,
journal = {{Journal of Grid Computing}},
month = {{March}},
year = 2014,
volume = 12,
number = 1,
pages = {111-125},
title = {{Towards Standardized Job Submission and Control in
Infrastructure Clouds}},
author = {Peter Tröger and Andre Merzky},
note = {\url{http://link.springer.com/article/10.1007%2Fs10723-013-9275-2}}
}
@article{pilot-data-jpdc-2014,
author = {Andre Luckow and Mark Santcroos and Ashley Zebrowski and
Shantenu Jha},
title = {{Pilot-Data: An Abstraction for Distributed Data}},
journal = {Journal Parallel and Distributed Computing},
month = {October},
year = 2014,
doi = {10.1016/j.jpdc.2014.09.009},
note = {\url{http://dx.doi.org/10.1016/j.jpdc.2014.09.009}},
OPTnote = {\url{http://arxiv.org/abs/1301.6228}},
}
@article{ethread-biomed-2014,
author = {Anjani Ragothaman and Sairam Chowdary Boddu and Nayong Kim and
Wei Feinstein and Michal Brylinski and Shantenu Jha and
Joohyun Kim},
title = {{Developing eThread Pipeline Using SAGA- Pilot Abstraction for
Large-Scale Structural Bioinformatics}},
journal = {BioMed Research International},
volume = {2014},
year = 2014,
doi = {10.1155/2014/348725},
}
@article{nanopore-jcc-2014,
author = {Hugh S. C. Martin and Shantenu Jha and Peter V.Coveney},
title = {{Comparative analysis of nucleotide translocation through
protein nanopores using steered molecular dynamics and an
adaptive biasing force}},
journal = {Computational Chemistry},
volume = {35},
number = {9},
pages = {692-702},
month = {April},
year = 2014,
doi = {10.1002/jcc.23525},
note = {\url{http://onlinelibrary.wiley.com/doi/10.1002/jcc.23572/abstract}}
}
@article{bfe-jctc-2014,
author = {David W. Wright and Benjamin A. Hall
and Owain A. Kenway and Shantenu Jha
and Peter V. Coveney},
title = {{Computing Clinically Relevant Binding Free Energies
of HIV-1 Protease Inhibitors}},
journal = {Chemical Theory and Computation},
volume = {10},
number = {3},
pages = {1228-1241},
year = 2014,
doi = {10.1021/ct4007037},
}
@article{cfd-multiscale-2014,
author = {Soon-Heum Ko and Nayong Kim and Shantenu Jha
and Dimitris E. Nikitopoulos and Dorel Moldovan},
title = {{Numerical Experiments of Solving Moderate-velocity Flow
Field Using a Hybrid Computational Fluid Dynamics Molecular
Dynamics Approach}},
journal = {Mechanical Science and Technology},
volume = {1},
number = {28},
pages = {245-253},
year = 2014,
doi = {10.1007/s12206-013-0962-5},
}
@inproceedings{tale-of-two-ieee-2014,
author = {Shantenu Jha and Judy Qiu and Andre Luckow and Pradeep Mantha
and Geoffrey C.Fox},
title = {{A Tale of Two Data-Intensive Paradigms: Applications,
Abstractions, and Architectures}},
booktitle = {Big Data (BigData Congress), 2014 IEEE International Congress on},
series = {},
isbn = {978-1-4799-5056-0},
year = {2014},
location = {Anchorage, Alaska, USA},
pages = {645 - 652},
numpages = {7},
doi = {10.1109/BigData.Congress.2014.137},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6906840},
OPTnote = {\url{https://raw.github.com/saga-project/radical.wp/master/publications/pdf/tale-of-two-ieee-2014.pdf}},
}
###################
# 2013
@inproceedings{2013-xsede-cdi,
author = {Brian K. Radak and Melissa Romanus and Emilio Gallicchio
and Tai-Sung Lee and Ole Weidner and Nan-Jie Deng and
Peng He and Wei Dai and Darrin M. York and Ronald M. Levy
and Shantenu Jha},
title = {{A Framework for Flexible and Scalable Replica-Exchange on
Production Distributed CI}},
booktitle = {Proceedings of the Conference on Extreme Science and
Engineering Discovery Environment: Gateway to Discovery},
series = {XSEDE '13},
isbn = {978-1-4503-2170-9},
year = {2013},
location = {San Diego, California, USA},
pages = {26:1--26:8},
articleno = {26},
numpages = {8},
doi = {10.1145/2484762.2484830},
acmid = {2484830},
url = {https://raw.github.com/saga-project/radical.wp/master/publications/pdf/2013-cdi-xsede.pdf},
note = {\url{https://raw.github.com/saga-project/radical.wp/master/publications/pdf/2013-cdi-xsede.pdf}},
}
@inproceedings{2013-xsede-hthpc,
author = {Jack Smith and Melissa Romanus and James Solow and Pradeep
Kumar Mantha and Yaakoub El Khamra and Thomas C. Bishop and
Shantenu Jha},
title = {{Scalable Online Comparative Genomics of Mononucleosomes: A BigJob}},
isbn = {978-1-4503-2170-9},
booktitle = {Proceedings of the Conference on Extreme Science and
Engineering Discovery Environment: Gateway to Discovery},
series = {XSEDE '13},
year = {2013},
location = {San Diego, California, USA},
pages = {23:1--23:8},
articleno = {23},
numpages = {8},
doi = {10.1145/2484762.2484819},
acmid = {2484819},
note = {\url{https://github.com/saga-project/radical.wp/raw/master/publications/pdf/2013-xsede-hthpc.pdf}},
}
@inproceedings{ccgrid13-pilotdata,
author = {Mark Santcroos and Barbera DC van Schaik and Shayan
Shahand and Silvia Delgado Olabarriaga and Andre
Luckow and Shantenu Jha},
title = {{Exploring Dynamic Enactment of Scientific Workflows
using Pilot-Abstractions}},
booktitle = {13th IEEE/ACM International Conference on Cluster,
Cloud and Grid Computing},
year = {2013},
pages = {311-318},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
location = {Delft, Netherlands},
doi = {http://doi.ieeecomputersociety.org/10.1109/CCGrid.2013.17},
isbn = {978-1-4673-6465-2},
}
####################
# 2012
@article {dpa_surveypaper,
author = {Jha, Shantenu and Cole, Murray and Katz, Daniel S. and Parashar, Manish and Rana, Omer and Weissman, Jon},
title = {Distributed computing practice for large-scale science and engineering applications},
journal = {Concurrency and Computation: Practice and Experience},
note = "\url{http://dx.doi.org/10.1002/cpe.2897}",
volume = {25},
number = {11},
issn = {1532-0634},
XXurl = {http://dx.doi.org/10.1002/cpe.2897},
XXdoi = {10.1002/cpe.2897},
pages = {1559--1585},
year = {2013},
}
@article{jogc-2012-dare,
author = {Maddineni, Sharath and Kim, Joohyun and El-Khamra, Yaakoub and Jha, Shantenu},
title = {Distributed Application Runtime Environment (DARE): A Standards-based Middleware Framework for Science-Gateways},
journal = {J. Grid Comput.},
issue_date = {December 2012},
volume = {10},
number = {4},
month = dec,
year = {2012},
issn = {1570-7873},
pages = {647--664},
numpages = {18},
url = {http://dx.doi.org/10.1007/s10723-012-9244-1},
doi = {10.1007/s10723-012-9244-1},
acmid = {2424948},
publisher = {Springer-Verlag New York, Inc.},
address = {Secaucus, NJ, USA},
keywords = {Clouds, DARE, EGI, Grids, Interoperability, Middleware, Pilot Jobs, SAGA, Science gateways, Standards, XSEDE},
}
@article{ccpe-2012-ngs,
author = {Kim, Joohyun and Maddineni, Sharath and Jha, Shantenu},
title = {Advancing next-generation sequencing data analytics with scalable distributed infrastructure},
journal = {Concurrency and Computation: Practice and Experience},
issn = {, , },
url = {http://dx.doi.org/10.1002/cpe.3013},
doi = {10.1002/cpe.3013},
pages = {n/a--n/a},
keywords = {next-generation sequencing data analytics, science gateway, BFAST, mapping, ChIP-Seq, human genome, Burkerholderia glumae, mouse genome, runtime environment, distributed computing, simple API for grid applications (SAGA), pilot-job abstraction},
year = {2013},
}
@article{biochem-2012-jha,
author = {Benjamin A. Hall and David W. Wright and Shantenu Jha
and Peter V. Coveney},
title = {{Quantized Water Access to the HIV-1 Protease Active Site as a
Proposed Mechanism for Cooperative Mutations in Drug Affinity}},
journal = {Biochemistry},
volume = {51},
number = {33},
pages = {6487-6489},
year = 2012,
doi = {10.1021/bi300432u},
}
@article{jmb-2012-jha,
author = {Wei Huang and Joohyun Kim and Shantenu Jha
and Fareed Aboul-ela},
title = {{Conformational Heterogeneity of the SAM-I Riboswitch
Transcriptional ON State: A Chaperone-Like Role for
S-Adenosyl Methionine}},
journal = {{Journal of Molecular Biology}},
year = 2012,
volume = {418},
number = {5},
pages = {331 - 349},
issn = {0022-2836},
doi = {10.1016/j.jmb.2012.02.019},
note = {\url{http://www.sciencedirect.com/science/article/pii/S0022283612001763}},
keywords = {RNA},
keywords = {riboswitch},
keywords = {secondary-structure prediction},
keywords = {dimmer switch},
keywords = {conformation ensemble},
}
@article{pstar12,
author = {Andre Luckow and Mark Santcroos and Andre Merzky and Ole Weidner and Pradeep Mantha and Shantenu Jha},
title = {P*: A model of pilot-abstractions},
journal ={IEEE 8th International Conference on e-Science},
isbn = {978-1-4673-4467-8},
year = {2012},
pages = {1-10},
doi = {http://doi.ieeecomputersociety.org/10.1109/eScience.2012.6404423},
note = {\url{http://dx.doi.org/10.1109/eScience.2012.6404423}},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
@article{pstar-network12,
address = {Los Alamitos, CA, USA},
author = {Mark Santcroos and Silvia Delgado Olabarriaga and Daniel S. Katz and Shantenu Jha},
journal = {2012 IEEE 8th International Conference on E-Science},
pages = {1-2},
publisher = {IEEE Computer Society},
title = {Pilot abstractions for compute, data, and network},
volume = {0},
year = {2012},
doi = {http://doi.ieeecomputersociety.org/10.1109/eScience.2012.6404459},
isbn = {978-1-4673-4467-8},
}
@inproceedings{pilot-mapreduce2012,
author = {Pradeep Kumar Mantha and Andre Luckow and Shantenu Jha},
title = {{Pilot-MapReduce: an extensible and flexible MapReduce
implementation for distributed data}},
booktitle = {{Proceedings of third international workshop on MapReduce and
its Applications}},
series = {MapReduce '12},
location = {Delft, The Netherlands},
year = {2012},
pages = {17--24},
numpages = {8},
publisher = {ACM},
address = {New York, NY, USA},
OPTnote = {\url{http://dl.acm.org/citation.cfm?id=2287020\&dl=ACM\&coll=DL\&CFID=137661901\&CFTOKEN=34365530}},
url = {https://raw.github.com/saga-project/radical.wp/master/publications/pdf/pilot-mapreduce2012.pdf},
doi = {http://doi.acm.org/10.1145/2287016.2287020},
isbn = {978-1-4503-1343-8},
acmid = {2287020},
keywords = {bwa, distributed computing, genome sequence alignment, human genome,
mapreduce, pilot job and data, simple api for grid applications (saga)},
}
@inproceedings{pmr-ecmls12,
author = {Pradeep Mantha and Nayong Kim and Joohyun Kim
and Andre Luckow and Shantenu Jha},
title = {{Understanding MapReduce-based Next-Generation Sequencing
Alignment on Distributed Cyberinfrastructure}},
booktitle = {{3rd International Workshop on Emerging Methods in
Computational Life Sciences, Proceedings of the 21st
International Symposium on High-Performance Parallel
and Distributed Computing, HPDC'12}},
year = {2012},
publisher = {ACM},
month = {June},
note = {}},
}
@inproceedings{pilotjob-hpdc,
author = {Andre Luckow and Mark Santcroos and Ole Weidner and
Andre Merzky and Sharath Maddineni and Shantenu Jha},
title = {{Towards a common model for pilot-jobs}},
booktitle = {{Proceedings of the 21st International Symposium
on High-Performance Parallel and Distributed
Computing,HPDC'12}},
year = {2012},
publisher = {ACM},
month = {June},
note = {\url{http://dl.acm.org/citation.cfm?id=2287094}},
}
@inproceedings{xsede12_ensemble,
author = {Rajib Mukherjee and Abhinav Thota and Hideki Fujioka and
Thomas C. Bishop and Shantenu Jha},
title = {Running many Molecular Dynamics Simulations on many
Supercomputers},
booktitle = {Proceedings of the 1st Conference of the Extreme Science
and Engineering Discovery Environment: Bridging from the
eXtreme to the Campus and Beyond},
series = {XSEDE '12},
year = {2012},
pages = {2:1--2:9},
publisher = {ACM},
address = {New York, NY, USA},
isbn = {978-1-4503-1602-6},
location = {Chicago, Illinois},
articleno = {2},
numpages = {9},
doi = {http://doi.acm.org/10.1145/2335755.2335787},
acmid = {2335787},
keywords = {HPC, MD, NAMD, XSEDE resources, distributed computing,
experience, large scale, technology},
}
@inproceedings{Romanus:2012:ASE:2335755.2335843,
author = {Melissa Romanus and Pradeep Kumar Mantha and Matt McKenzie
and Thomas C. Bishop and Emilio Gallichio and Andre Merzky
and Yaakoub El Khamra and Shantenu Jha},
title = {{The Anatomy of Successful ECSS Projects: Lessons of
supporting High-Throughput High-Performance Ensembles on XSEDE}},
booktitle = {{Proceedings of the 1st Conference of the Extreme Science and
Engineering Discovery Environment: Bridging from the eXtreme
to the Campus and Beyond}},
series = {XSEDE '12},
location = {Chicago, Illinois},
year = {2012},
publisher = {ACM},
address = {New York, NY, USA},
pages = {46:1--46:9},
articleno = {46},
numpages = {9},
url = {http://dl.acm.org/ft_gateway.cfm?id=2335843&ftid=1264202&dwn=1&CFID=178712210&CFTOKEN=50835868},
OPTdoi = {10.1145/2335755.2335843},
acmid = {2335843},
isbn = {978-1-4503-1602-6},
keywords = {ECSS projects, SAGA, distributed computing, high performance, high throughput},
}
####################
# 2011
@article{async_repex11,
author = {Abhinav Thota and Andre Luckow and Shantenu Jha},
title = {{Efficient large-scale Replica-Exchange Simulations on
Production Infrastructure}},
journal = {{Philosophical Transactions of the Royal Society A:
Mathematical, Physical and Engineering Sciences}},
year = 2011,
volume = {369},
number = {1949},
pages = {3318-3335},
url = {http://rsta.royalsocietypublishing.org/content/369/1949/3318.abstract},
}
@article{csc7700-iccs,
author = {Gabrielle Allen and Werner Benger and Andrei Hutanu and
Shantenu Jha and Frank L{\"o}ffler and Erik Schnetter},
title = {{A Practical and Comprehensive Graduate Course preparing
Students for Research involving Scientific Computing}},
journal = {{Procedia Computer Science}},
year = 2011,
volume = {4},
number = {0},
pages = {1927 - 1936},
booktitle = {{Proceedings of the International Conference on Computational
Science, ICCS 2011}},
note = {\url{http://www.sciencedirect.com/science/article/pii/S1877050911002687}},
issn = {1877-0509},
doi = {10.1016/j.procs.2011.04.210},
keywords = {Education},
keywords = {Scientific computing},
keywords = {computation},
}
@article{ecmls10_ccpe10,
author = {Joohyun Kim and Wei Huang and Sharath Maddineni and
Fareed Aboul-ela and Shantenu Jha},
title = {{Energy Landscape Analysis for Regulatory RNA Finding using
Scalable Distributed Cyberinfrastructure}},
journal = {Concurrency and Computation: Practice and Experience},
publisher = {John Wiley \& Sons, Ltd},
year = 2011,
volume = {23},
number = {17},
pages = {2292--2304},
issn = {1532-0634},
doi = {10.1002/cpe.1796},
note = {\url{http://onlinelibrary.wiley.com/doi/10.1002/cpe.1796/abstract}},
keywords = {concurrent programming and distributed computing, Simple API
for Grid Applications (SAGA), Pilot-Job abstraction, RNA
folding energy landscape, ncRNA gene finding},
}
@article{fgcs-interop11,
author = {Saurabh Sehgal and Miklos Erdelyi and Andre Merzky and
Shantenu Jha},
title = {{Understanding Application-Level Interoperability:
Scaling-Out MapReduce over High-Performance Grids and
Clouds}},
journal = {{Future Generation Computer Systems}},
year = 2011,
volume = {27},
number = {5},
pages = {590--599},
url = {http://www.sciencedirect.com/science/article/B6V06-51KT861-2/2/0092927785fbf5e065a7788af8b65b72},
issn = {0167-739X},
doi = {10.1016/j.future.2010.11.001},
keywords = {Programming systems},
keywords = {Distributed systems},
keywords = {Scale-out},
keywords = {Interoperability},
keywords = {MapReduce},
keywords = {SAGA},
}
@inproceedings{tg-vph-interop,
author = {Owain Kenway and David W. Wright and Helmut Heller and
Andre Merzky and Gavin Pringle and Jules Wolfrat and Peter
Coveney and Shantenu Jha},
title = {{Towards high-throughput, high-performance computational
estimation of binding affinities for patient specific HIV-1
protease sequences}},
booktitle = {{Proceedings of the 2011 TeraGrid Conference: Extreme Digital
Discovery}},
location = {Salt Lake City, Utah},
year = 2011,
series = {TG '11},
pages = {4:1--4:8},
articleno = {4},
numpages = {8},
isbn = {978-1-4503-0888-5},
doi = {10.1145/2016741.2016746},
acmid = {2016746},
publisher = {ACM},
address = {New York, NY, USA},
note = {\url{http://dl.acm.org/citation.cfm?id=2016746\&dl=ACM\&coll=DL\&CFID=137661901\&CFTOKEN=34365530}},
keywords = {ensemble-based simulations, interoperability, personalised
medicine},
}
@inproceedings{dare-tg11,
author = {Joohyun Kim and Sharath Maddineni and Shantenu Jha},
title = {{Building Gateways for Life-Science Applications using the
Dynamic Application Runtime Environment (DARE) Framework}},
booktitle = {{Proceedings of the 2011 TeraGrid Conference: Extreme Digital
Discovery}},
location = {Salt Lake City, Utah},
series = {TG '11},
year = 2011,
pages = {38:1--38:8},
articleno = {38},
numpages = {8},
isbn = {978-1-4503-0888-5},
doi = {10.1145/2016741.2016782},
acmid = {2016782},
publisher = {ACM},
address = {New York, NY, USA},
note = {\url{http://dl.acm.org/citation.cfm?id=2016782\&dl=ACM\&coll=DL\&CFID=137661901\&CFTOKEN=34365530}},
keywords = {data-intensive computing, distributed computing, pilot-job
abstraction, runtime environment, science gateway, simple API
for grid applications (SAGA)},
}
@inproceedings{dare-ecmls11,
author = {Joohyun Kim and Sharath Maddineni and Shantenu Jha},
title = {{Characterizing deep sequencing analytics using BFAST:
towards a scalable distributed architecture for
next-generation sequencing data}},
booktitle = {{Proceedings of the second international workshop on Emerging
computational methods for the life sciences}},
series = {ECMLS '11},
year = 2011,
isbn = {978-1-4503-0702-4},
location = {San Jose, California, USA},
pages = {23--32},
numpages = {10},
doi = {10.1145/1996023.1996027},
acmid = {1996027},
publisher = {ACM},
address = {New York, NY, USA},
note = {\url{http://dl.acm.org/citation.cfm?id=1996027}},
keywords = {BFAST, burkerholderia glumae, distributed computing, genome
sequence alignment, human genome, pilot-job abstraction,
runtime environment, simple api for grid applications (SAGA)},
}
@inproceedings{saga-teach-fg10,
author = {Frank L\"{o}ffler and Gabrielle Allen and Werner Benger
and Andrei Hutanu and Shantenu Jha and Erik Schnetter},
title = {{Using the TeraGrid to teach Scientific Computing}},
booktitle = {{Proceedings of the 2011 TeraGrid Conference: Extreme Digital
Discovery}},
location = {Salt Lake City, Utah},
series = {TG '11},
year = 2011,
pages = {55:1--55:7},
articleno = {55},
numpages = {7},
url = {http://astrocompute.files.wordpress.com/2011/07/using-the-teragrid-to-teach-scientific-computing-1.pdf},
isbn = {978-1-4503-0888-5},
doi = {10.1145/2016741.2016800},
acmid = {2016800},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {computation, education, scientific computing},
}
####################
# 2010
@article{ddia_ptrsa10,
author = {Chris Miceli and Michael Miceli and Bety Rodriguez-Milla
and Shantenu Jha},
title = {{Understanding Performance of Distributed
Data-Intensive Applications}},
journal = {{Royal Society of London Philosophical Transactions
Series A}},
year = 2010,
month = {August},
volume = {368},
pages = {4089--4102},
url = {http://www.cct.lsu.edu/~sjha/select\_publications/saga_ptrsa10.pdf},
doi = {10.1098/rsta.2010.0168},
adsurl = {http://adsabs.harvard.edu/abs/2010RSPTA.368.4089M},
adsnote = {Provided by the SAO/NASA Astrophysics Data System},
}
@inproceedings{bigjob_cloudcom10,
author = {Andre Luckow and Shantenu Jha},
title = {{Abstractions for Loosely-Coupled and Ensemble-Based
Simulations on Azure}},
booktitle = {{International IEEE Conference on Cloud Computing Technology and
Science}},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
year = 2010,
pages = {550--556},
url = {http://www.cct.lsu.edu/~sjha/dpa_publications/azure-abstractions-cloudcom10.pdf},
doi = {10.1109/CloudCom.2010.85},
isbn = {978-0-7695-4302-4},
}
@inproceedings{saga_europar10,
author = {Mathijs Den Burger and Ceriel Jacobs and Thilo Kielmann and
Andre Merzky and Ole Weidner and Hartmut Kaiser},
title = {{What Is the Price of Simplicity? -- A Cross-Platform
Evaluation of the SAGA API}},
series = {EuroPar'10},
booktitle = {{Proceedings of the 16th international Euro-Par conference on
Parallel processing: Part I}},
pages = {392--404},
year = 2010,
publisher = {Springer},
isbn = {3-642-15276-7, 978-3-642-15276-4},
numpages = {13},
location = {Ischia, Italy},
address = {Berlin, Heidelberg},
url = {http://dl.acm.org/citation.cfm?id=1887695.1887739},
acmid = {1887739},
}
@inproceedings{co2-tg10,
author = {Yaakoub El-Khamra and Shantenu Jha and Christopher D. White},
title = {{Modelling data-driven CO2 sequestration using distributed HPC
cyberinfrastructure}},
booktitle = {{Proceedings of the 2010 TeraGrid Conference}},
location = {Pittsburgh, Pennsylvania},
series = {TG '10},
year = 2010,
pages = {6:1--6:8},
articleno = {6},
numpages = {8},
url = {invalid_url},
isbn = {978-1-60558-818-6},
doi = {10.1145/1838574.1838580},
acmid = {1838580},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {distributed applications, ensemble simulations, scaleout,
sequestration},
}
@inproceedings{ko-efficient,
author = {Soon-Heum Ko and Nayong Kim and Joohyun Kim and Abhinav Thota
and Shantenu Jha},
title = {{Efficient Runtime Environment for Coupled Multi-physics
Simulations: Dynamic Resource Allocation and Load-Balancing}},
booktitle = {{Proceedings of the 2010 10th IEEE/ACM International Conference
on Cluster, Cloud and Grid Computing}},
series = {CCGRID '10},
year = 2010,
pages = {349--358},
numpages = {10},
url = {http://www.cct.lsu.edu/~sjha/select\_publications/coupled_simulations_framework.pdf},
isbn = {978-0-7695-4039-9},
doi = {10.1109/CCGRID.2010.107},
acmid = {1845151},
publisher = {IEEE Computer Society},
address = {Washington, DC, USA},
keywords = {SAGA (Simple API for Grid Applications), BigJob, Hybrid CFD-MD
Approach, Runtime Environment, Load Balancing, Co-allocation},
}
@inproceedings{ecmls_ccpe10,
author = {Joohyun Kim and Wei Huang and Sharath Maddineni and
Fareed Aboul-Ela and Shantenu Jha},
title = {{Exploring the {RNA} folding energy landscape using
scalable distributed cyberinfrastructure}},
booktitle = {{Emerging Computational Methods in the Life Sciences,
Proceedings of the 19th ACM International Symposium on
High Performance Distributed Computing}},
location = {Chicago, Illinois},
publisher = {ACM},
address = {New York, NY, USA},
series = {HPDC '10},
year = 2010,
pages = {477--488},
numpages = {12},
OPTurl = {http://www.cct.lsu.edu/~sjha/select_publications/ecmls11.pdf},
isbn = {978-1-60558-942-8},
doi = {10.1145/1851476.1851546},
acmid = {1851546},
keywords = {RNA folding energy landscape, S gene of Bovine Corona Virus,
SAGA, SAM-I riboswitch, distributed computing, pilot-job
abstraction, runtime environment, simple API for grid
applications},
bibsource = {http://dblp.uni-trier.de},
}
@inproceedings{saga_bigjob_condor_cloud,
author = {Andre Luckow and Lukas Lacinski and Shantenu Jha},
title = {{SAGA BigJob: An Extensible and Interoperable Pilot-Job
Abstraction for Distributed Applications and Systems}},
booktitle = {{The 10th IEEE/ACM International Symposium on Cluster,
Cloud and Grid Computing}},
pages = {135-144},
OPTurl = {http://www.cct.lsu.edu/~sjha/select_publications/interop_pilot_job.pdf},
keywords = {grid computing, application level interoperability,
distributed applications, distributed infrastructure,
high-level programming interface},
issn = {978-0-7695-4039-9},
doi = {10.1109/CCGRID.2010.91},
year = 2010,
}
###################
# 2009
@article{katz2009louisiana,
author = {Daniel S. Katz and Gabrielle Allen and R. Cortez and C.
Cruz-Neira and R. Gottumukkala and Z. D. Greenwood and
L. Guice and Shantenu Jha and R. Kolluru and Tevfik Kosar and
others},
title = {{Louisiana: a model for advancing regional e-Research
through cyberinfrastructure}},
journal = {Philosophical Transactions of the Royal Society A:
Mathematical, Physical and Engineering Sciences},
volume = {367},
number = {1897},
pages = {2459},
year = 2009,
publisher = {The Royal Society},
url = {http://rsta.royalsocietypublishing.org/content/367/1897/2459.full.pdf},
}
@article{jha2009using,
author = {Shantenu Jha and Andre Merzky and Geoffrey Fox},
title = {{Using Clouds to Provide Grids with Higher Levels of
Abstraction and Explicit Support for Usage Modes}},
journal = {{Concurrency and Computation: Practice and Experience}},
publisher = {John Wiley and Sons Ltd.},
address = {Chichester, UK},
year = 2009,
volume = {21},
number = {8},
pages = {2087--1108},
url = {http://www.ogf.org/OGF_Special_Issue/cloud-grid-saga.pdf},
doi = {10.1002/cpe.v21:8},
issn = {1532-0626},
}
@article{repex_ptrsa,
author = {Andre Luckow and Shantenu Jha and Joohyun Kim and
Andre Merzky and Bettina Schnor},
journal = {Royal Society Philosophical Transactions A},
title = {{Adaptive Replica-Exchange Simulations}},
year = 2009,
month = {jun},
date = {28},
pages = {2595--2606},
url = {http://www.cct.lsu.edu/~sjha/select\_publications/adaptive_repex_ptrsa.pdf},
}
@inproceedings{10.1109.GPC.2009.17,
author = {Andre Merzky and Katerina Stamou and Shantenu Jha},
title = {{Application Level Interoperability between Clouds and
Grids}},
booktitle = {{Proceedings of the IEEE Grid and Pervasive Computing
Conference '09}},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
year = 2009,
pages = {143--150},
note = {\url{http://ieeexplore.ieee.org/xpl/login.jsp?tp=\&arnumber=4976556\&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D4976556}},
doi = {10.1109/GPC.2009.17},
isbn = {978-0-7695-3677-4},
}
@inproceedings{merzky-fresh,
author = {Andre Merzky and Katerina Stamou and Shantenu Jha and Daniel
S. Katz},
title = {{A Fresh Perspective on Developing and Executing DAG-Based
Distributed Applications: A Case-Study of SAGA-Based Montage}},
booktitle = {{Proceedings of the 2009 Fifth IEEE International Conference
on e-Science}},
publisher = {IEEE Computer Society},
address = {Washington, DC, USA},
series = {eScience '09},
year = 2009,
pages = {231--238},
numpages = {8},
OPTurl = {http://www.cct.lsu.edu/~sjha/select_publications/saga_montage_escience09.pdf},
doi = {10.1109/e-Science.2009.40},
acmid = {1724826},
isbn = {978-0-7695-3877-8},
}
@inproceedings{gmac09,
author = {Yaakoub El-Khamra and Shantenu Jha},
title = {{Developing Autonomic Distributed Scientific
Applications: A Case Study From History Matching Using
Ensemble Kalman-Filters}},
booktitle = {{GMAC '09: Proceedings of the 6th International
Conference Industry Session on Grids meets Autonomic
Computing}},
year = 2009,
pages = {19--28},
location = {Barcelona, Spain},
publisher = {IEEE},
address = {New York, NY, USA},
note = {\url{http://dl.acm.org/citation.cfm?id=1555304}},
isbn = {978-1-60558-578-9},
doi = {10.1145/1555301.1555304},
}
@inproceedings{luckow2009adaptive,
author = {Andre Luckow and Shantenu Jha and Joohyun Kim and Andre Merzky
and Bettina Schnor},
title = {{Adaptive Distributed Replica--Exchange Simulations}},
booktitle = {{Theme Issue of the Philosophical Transactions of the
Royal Society A: Crossing Boundaries: Computational
Science, E-Science and Global E-Infrastructure
Proceedings of the UK e-Science All Hands Meeting}},
volume = {367},
year = 2009,
url = {http://rsta.royalsocietypublishing.org/content/367/1897/2595.full.pdf},
}
@inproceedings{jha2009developing,
author = {Shantenu Jha and Yaakoub El-Khamra and Joohyun Kim},
title = {{Developing Scientific Applications with Loosely-Coupled
Sub-tasks}},
booktitle = {{Proceedings of the 9th International Conference on
Computational Science: Part I}},
series = {ICCS '09},
year = 2009,
isbn = {978-3-642-01969-2},
location = {Baton Rouge, LA},
pages = {641--650},
numpages = {10},
url = {http://www.cct.lsu.edu/~sjha/dpa_publications/saga_loosely_coupled.pdf},
doi = {10.1007/978-3-642-01970-8_63},
acmid = {1560829},
publisher = {Springer-Verlag},
address = {Berlin, Heidelberg},
}
@inproceedings{saga_data_intensive_abstractions,
author = {Chris Miceli and Michael Miceli and Shantenu Jha and Hartmut
Kaiser and Andre Merzky},
booktitle = {{Cluster Computing and the Grid, 2009. CCGRID '09. 9th
IEEE/ACM International Symposium on}},
title = {{Programming Abstractions for Data Intensive Computing
on Clouds and Grids}},
month = {May},
volume = {},
number = {},
pages = {478--483},
OPTurl = {http://www.cct.lsu.edu/~sjha/select_publications/saga_data_intensive.pdf},
keywords = {application program interfaces, grid computing,
parallel programmingMapReduce data-parallel programming
model, SAGA programming interface, cloud computing,
data intensive computing, data network transfer,
distributed application, grid computing, programming
abstraction},
doi = {10.1109/CCGRID.2009.87},
issn = {},
year = 2009,
}
@inproceedings{dpagrid2009,
author = {Shantenu Jha and Daniel S. Katz and Manish Parashar and Omer
Rana and Jon B. Weissman},
title = {{Critical Perspectives on Large-Scale Distributed Applications
and Production Grids (Best Paper Award)}},
booktitle = {{The 10th IEEE/ACM Conference on Grid Computing 2009}},
year = 2009,
pages = {1-8},
doi = {10.1109/GRID.2009.5353064},
bibsource = {http://dblp.uni-trier.de},
url = {"http://www.cct.lsu.edu/~sjha/dpa_publications/dpa_grid2009.pdf"},
}
@inproceedings{co2_escience2009,
author = {Yaakoub El-Khamra and Shantenu Jha},
booktitle = {{Microsoft Research eScience Workshop, Pittsburgh}},
location = {Pittsburgh, PA},
title = {{Modelling Data-Driven CO$_2$ Sequestration Using
Distributed HPC CyberInfrastructure}},
year = {2009},
url = {},
note = {\url{http://research.microsoft.com/en-us/UM/redmond/events/eScience2009/17863/lecture.htm}}
}
###################
# 2008
@inproceedings{saga_tg08,
author = {Shantenu Jha and Yaakoub El-Khamra and Hartmut Kaiser and
Ole Weidner and Andre Merzky},
title = {{Developing Large-Scale Adaptive Scientific Applications with
Hard to Predict Runtime Resource Requirements}},
booktitle = {{Proceedings of TeraGrid08}},
year = 2008,
OPTnote = {{Winner of the Performance Challenge Award
http://www.cct.lsu.edu/~sjha/select_publications/tg08-performance-award.pdf}},
}
@inproceedings{Luckow:2008la,
author = {Andre Luckow and Shantenu Jha and Joohyun Kim and
Andre Merzky and Bettina Schnor},
title = {{Distributed Replica-Exchange Simulations on Production
Environments Using SAGA and Migol}},
booktitle = {{Proceedings of the 2008 Fourth IEEE International Conference
on eScience}},
series = {ESCIENCE '08},
year = 2008,
pages = {253--260},
publisher = {IEEE Computer Society},
address = {Washington, DC, USA},
note = {\url{http://www.computer.org/portal/web/csdl/doi/10.1109/eScience.2008.20}},
isbn = {978-0-7695-3535-7},
doi = {10.1109/eScience.2008.20},
acmid = {1488923},
keywords = {SAGA, Migol, Fault-Tolerance, Replica-Exchange,
Grid Computing},
}
###################
# 2007
@inproceedings{escience07,
author = {Shantenu Jha and Hartmut Kaiser and Yaakoub El-Khamra
and Ole Weidner},
title = {{Design and Implementation of Network Performance
Aware Applications Using SAGA and Cactus}},
booktitle = {{E-SCIENCE '07: Proceedings of the Third IEEE
International Conference on e-Science and Grid
Computing}},
isbn = {0-7695-3064-8},
pages = {143--150},
url = {http://saga.cct.lsu.edu/publications/saga_cactus_escience.pdf},
doi = {10.1109/E-SCIENCE.2007.28},
publisher = {IEEE Computer Society},
address = {Washington, DC, USA},
year = 2007,
}
@inproceedings{saga_gin,
author = {Shantenu Jha and Hartmut Kaiser and Andre Merzky and
Ole Weidner},
title = {{Grid Interoperability at the Application Level Using
SAGA}},
booktitle = {{E-SCIENCE '07: Proceedings of the Third IEEE
International Conference on e-Science and Grid
Computing (e-Science 2007)}},
publisher = {IEEE Computer Society},
address = {Washington, DC, USA},
year = 2007,
pages = {584--591},
url = {http://www.cct.lsu.edu/~sjha/select_publications/saga_gin.pdf},
doi = {10.1109/E-SCIENCE.2007.39},
isbn = {0-7695-3064-8},
}
###################
# 2006
@article{saga_cmst,
author = {Tom Goodale and Shantenu Jha and Harmut Kaiser and
Thilo Kielmann and Pascal Kleijer and Gregor von
Laszewski and Craig Lee and Andre Merzky and Hrabri
Rajic and John Shalf},
title = {{SAGA: A Simple API for Grid applications, High-Level
Application Programming on the Grid}},
journal = {{Computational Methods in Science and Technology}},
year = 2006,
number = {1},
volume = {12},
pages = {7--20},
url = {http://www.cs.vu.nl/~kielmann/papers/saga-cmst.pdf},
}
###################
# 2005
@inproceedings{sirvent2005grid,
author = {Raoul Sirvent and Andre Merzky and Rosa M. Badia and
Thilo Kielmann},
title = {{GRID SuperScalar and SAGA: forming a high-level and
platform-independent Grid Programming Environment}},
booktitle = {{CoreGRID Integration WorkShop}},
year = 2005,
url = {http://www.cs.vu.nl/~kielmann/papers/gs-saga.pdf},
}
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# 2003
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# 2002
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# 2001
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# 2000
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# 2004
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# 2003
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# 2002
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# 2001
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# 2000
################################################################################
### Drafts / Under Review (note the 'review_' prefix). These need to be sorted
### into the list after publication (with a non-prefixed key!)
################################################################################
@misc{review_pilotstreaming,
author = {Andre Luckow and George Chantzialexiou and Shantenu Jha},
title = {Pilot-Streaming: A Stream Processing Framework for High-Performance Computing},
year = 2018,
note = {submitted to High-Performance Distributed Computing (HPDC) 2018}
}
@misc{review_ccgrid_char2018,
author = {Ioannis Paraskevakos and Andre Luckow and George Chantzialexiou and Mahzad Khoshlessan and Oliver Beckstein and Geoffrey C. Fox and Shantenu Jha},
title = {Task-parallel Analysis of Molecular Dynamics Trajectories},
year = 2018,
note = {under review, submitted at CCGrid 2018}
}
@misc{review_rp-titan,
author = {Andre Merzky and Matteo Turilli and Manuel Maldonado and Shantenu Jha},
title = {Design and Performance Characterization of RADICAL-Pilot on Titan},
journal = {in review, International Supercomputing Conference 2018, arXiv preprint {arXiv}:1801.01843},
year = 2018
}
@misc{review_synapse-jocs,
author = {Andre Merzky and Ming Tai Ha and Matteo Turilli and Shantenu Jha},
title = {Synapse: Synthetic Application Profiler and Emulator},
journal = {in review, Journal of Computational Science (JoCS)},
year = 2018
}
@misc{review_resource-selection,
author = {Ming Tai Ha and Matteo Turilli and Andre Merzky and Shantenu Jha},
title = {Towards General Distributed Resource Selection},
journal = {in review, IEEE CCGrid 2018, arXiv preprint {arXiv}:1801.02651},
note = {\url{https://arxiv.org/abs/1801.02651}},
year = 2018,
}
@misc{review_htbac-isc18,
author = {Jumana Dakka and Kristof Pallas Vivek Balasubramanian and Matteo Turilli and David W Wright and Stefan J Zasada and Shunzhou Wan and Peter V Coveney and Shantenu Jha},
title = {Rapid, concurrent and adaptive extreme scale binding free energy calculation},
journal = {in review, International Supercomputing Conference 2018, arXiv preprint {arXiv}:1801.01174},
year = 2018
}
@misc{review_bb_2016,
author = {Shantenu Jha and Matteo Turilli},
title = {A Building Blocks Approach towards Domain Specific Workflow Systems?},
note = {(under review) \url{http://arxiv.org/abs/1609.03484}},
year = 2017,
}
@misc{review_radicalpilot,
author = {Andre Merzky and Matteo Turilli and Manuel Maldonado and Mark Santcroos and Shantenu Jha},
title = {{Executing Dynamic and Heterogeneous Workloads on Super Computers}},
OPTjournal = {{Under Review}},
note = {(under review) \url{http://arxiv.org/abs/1512.08194}},
year = 2017,
}
@misc{review_2015-hpdc,
author = {Andre Luckow and Ioannis Paraskevakos and Shantenu Jha},
title = {{Pilot-Abstraction: A Valid Abstraction for Data-Intensive Application on HPC, Hadoop and Cloud Infrastructures?}},
booktitle = {The 24th International ACM Symposium on High Performance Distributed Computing},
year = {2015},
location = {Portland, Oregon, USA},
note = {\url{http://arxiv.org/pdf/1501.05041v1.pdf}},
OPTnote = {Submitted, Under Review},
}
@article{power-of-many17,
author = {Vivek Balasubramanian and Matteo Turilli and Weiming Hu and Matthieu Lefebvre and Wenjie Lei and Guido Cervone and Jeroen Tromp and Shantenu Jha},
title = {{Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications}},
booktitle = {under review},
year = {2017},
note = {\url{https://arxiv.org/abs/1710.08491}}
}
################################################################################
## Standards, White Papers, Technical Reports
################################################################################
###################
# 2015
@misc{ascr-wp-2015,
author = {Shantenu Jha and Daniel S. Katz and Matteo Turilli and Jon
Weissman},
title = {{From Abstractions to MOD- ELS: MOdels for Distributed and Extremely Large-scale Science}},
journal = {{White Paper Submitted to Advanced Scientific Computing and Research, DOE Office of Science}},
year = {2015},
month = {August},
note = {\url{https://zenodo.org/deposit/91947/}},
}
@techreport{steering-workflow-1,
author = {{Geoffrey Fox and Shantenu Jha and Lavanya Ramakrishnan}},
title = {{Scalable HPC Workflow Infrastructure for Steering Scientific Instruments and Streaming Applications}},
type = {{A White Paper submitted to DOE Workshop on Future of Scientific Workflows}},
year = {2015},
url = {https://zenodo.org/record/17909},
}
@techreport{steering-workflow-2,
author = {{Geoffrey Fox and Shantenu Jha}},
title = {{Implications of the HPC-ABDS High Performance Com-
puting Enhanced Apache Big Data Stack for Workflows}},
type = {{A White Paper submitted to DOE Workshop on Future of Scientific Workflows}},
year = {2015},
url = {http://dsc.soic.indiana.edu/publications/WorkflowsandHPC-ABDS.pdf}
}
@techreport{steeringsystems,
author = {{Geoffrey Fox and Shantenu Jha and Lavanya Ramakrishnan}},
title = {{Workshop on Streaming Systems, Draft Report v0.1 (08 Jan 2016)}},
type = {{NSF DOE Workshop}},
year = {2015},
url = {https://goo.gl/LaHWnq},
}
@techreport{nextgen-molsim,
author = {{Shantenu Jha and Peter M. Kasson}},
title = {{High-level software frameworks to surmount the challenge of 100x scaling for biomolecul\
ar simulation science}},
type = {{White Paper submitted to NIH-NSF Request for Information (2015)\\
\url{http://www.nsf.gov/pubs/2016/nsf16008/nsf16008.jsp}}},
OPTyear = {2015},
note = {\url{http://dx.doi.org/10.5281/zenodo.44377}},
}
@techreport{nsf-aci-multi-exec,
author = {{Shantenu Jha}},
title = {{Towards Scalable Execution Across Multiple XSEDE Resources}},
type = {{A White Paper submitted to NSF-ACI}},
year = {2015},
url = {https://zenodo.org/record/17909},
}
###################
# 2014
@misc{modsim2014,
author = {Shantenu Jha and Andre Merzky and Matteo Turilli},
title = {{Modeling Distributed Extreme-Scale Applications and Systems}},
journal = {{Workshop on Modeling \& Simulation of Exascale
Systems \& Applications}},
year = 2014,
month = {August},
note = {\url{http://hpc.pnl.gov/modsim/2014/}},
OPTurl = {\url{}}
}
###################
# 2013
@misc{modsim2013,
author = {Shantenu Jha and Andre Merzky and Matteo Turilli and
Daniel S. Katz and Jon Weissman},
title = {{Distributed Exascale Computing: An AIMES Perspective}},
journal = {{Workshop on Modeling \& Simulation of Exascale
Systems \& Applications}},
year = 2013,
month = {August},
note = {\url{http://hpc.pnl.gov/modsim/2013/}},
OPTurl = {\url{}}
}
###################
# 2012
@techreport{fgpc2012-project-45,
author = {{Pradeep Kumar Mantha and Sivakarthik Natesan and
Melissa Romanus and Sai Saripalli and Ashley Zebrowski}},
title = {{FutureGrid 2012 Project Challenge: Project 45: Building
Scalable, Dynamic and Distributed Applications Using SAGA}},
type = {{FutureGrid Project Challenge Award Winner}},
year = {2012},
url = {https://raw.github.com/saga-project/radical.wp/master/publications/pdf/fgpc2012-project-45.pdf},
}
@techreport{ogf-gfd-isn,
author = {Steve Fisher and Antony Wilson},
title = {{SAGA Extension: Information Service Navigator API}},
type = {{OGF Proposed Recommendation, GFD.195}},
institution = {{Open Grid Forum}},
year = 2012,
url = {http://ogf.org/documents/GFD.195.pdf},
}
###################
# 2011
@techreport{ogf-gfd-msg,
author = {Andre Merzky},
title = {{SAGA Extension: Message API}},
type = {{OGF Proposed Recommendation, GFD.178}},
institution = {{Open Grid Forum}},
year = 2011,
url = {http://ogf.org/documents/GFD.178.pdf},
}
@techreport{ogf-gfd-advert,
author = {Andre Merzky},
title = {{SAGA Extension: Advert API}},
type = {{OGF Proposed Recommendation, GFD.177}},
institution = {{Open Grid Forum}},
year = 2011,
url = {http://ogf.org/documents/GFD.177.pdf},
}
@techreport{dpa-pdci-tr,
author = {Daniel S. Katz and Shantenu Jha and Manish Parashar and
Omer F. Rana and Jon Weissman},
title = {{Survey and Analysis of Production Distributed Computing
Infrastructures (CI-TR-7-0811)}},
institution = {{Computation Institute, University of Chicago \& Argonne
National Laboratory}},
year = 2011,
url = {http://www.ci.uchicago.edu/research/papers/CI-TR-7-0811},
}
###################
# 2010
###################
# 2009
techreport{ogf-gfd-sd,
author = {Steve Fisher and Antony Wilson and Arumugam Paventhan},
title = {{SAGA Extension: Service Discovery API}},
type = {{OGF Proposed Recommendation, GFD.144}},
institution = {{Open Grid Forum}},
year = 2009,
url = {http://ogf.org/documents/GFD.144.pdf},
}
###################
# 2008
@techreport{ogf-gfd-cpr,
author = {Andre Merzky and Andre Luckow and Derek Simmel},
title = {{SAGA Extension: Checkpoint and Recovery API (CPR)}},
type = {{Draft for an OGF Proposed Recommendation Document}},
institution = {{Open Grid Forum}},
year = 2008,
url = {http://www.ogf.org/OGF27/materials/1767/saga_cpr.pdf},
}
###################
# 2007
@techreport{ogf-gfd-90,
author = {Tom Goodale and Shantenu Jha and Hartmut Kaiser and
Thilo Kielmann and Pascal Kleijer and Andre Merzky and
John Shalf and Christopher Smith},
title = {{A Simple API for Grid Applications (SAGA)}},
type = {{OGF Recommendation, GFD.90}},
institution = {{Open Grid Forum}},
year = 2007,
url = {http://ogf.org/documents/GFD.90.pdf},
}
###################
# 2006
@techreport{ogf-gfd-uca,
author = {Shantenu Jha and Andre Merzky},
title = {{A Requirements Analysis for a Simple API for Grid
Applications}},
type = {{GGF Proposed Recommendation, GFD.71}},
institution = {{Global Grid Forum}},
year = 2006,
url = {http://ogf.org/documents/GFD.71.pdf},
}
@techreport{ogf-gfd-uc,
author = {Andre Merzky and Shantenu Jha},
title = {{A Collection of Use Cases for a Simple API for Grid
Applications}},
type = {{GGF Proposed Recommendation, GFD.70}},
institution = {{Global Grid Forum}},
year = 2006,
url = {http://ogf.org/documents/GFD.70.pdf},
}
###################
# 2005
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# 2004
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# 2003
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# 2002
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# 2001
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# 2000