.
type: Dataset
path: ./
name: RetroPath2.0 IBISBA workflow node
date published: 2019-02-14
contact point: contact
creator: thomas
creator: stefan
license: http://creativecommons.org/licenses/by-nc-sa/4.0/
cite-as: j.ymben.2017.12.002
distribution: master.zip
publisher: www.ibisba.eu
description: RetroPath2.0 builds a reaction network from a set of source compounds to a set of sink compounds. When applied in a retrosynthetic fashion, the source is composed of the target compounds and the sink is composed of the available reactants (for instance in the context of metabolic engineering the sink is the set of native metabolites of a chassis strain). From amongst all the chemical reactions generated using RetroPath2.0 (in the retrosynthetic way), only a subset may effectively link a source to a subset of sink compounds. This sub-network is considered as a scope and is output in dedicated files.
keywords: workflow, knime, CWL, reaction
sd publisher: researchobject.org
sd license: LICENSE-2.0
subject of: README.md
has part: workflow.knime
has part: workflow
has part: RetroPath2.cwl
has part: Dockerfile
has part: test.sh
has part: README.md

researchobject.org
name: Research Object community

thomas
type: Person
name: Thomas Duigou

stefan
type: Person
name: Stefan Helfrich
url: https://github.com/stelfrich

https://orcid.org/0000-0001-9842-9718
type: Person
name: Stian Soiland-Reyes

master.zip
type: DataDownload
encoding format: application/zip

www.ibisba.eu
type: Organization
name: IBISBA

workflow.knime
type: SoftwareSourceCode
additional type: Workflow
name: RetroPath 2.0 Knime workflow
description: KNIME implementation of RetroPath2.0 workflow
creator: thomas
programming language: knime
potential action: ActivateAction
  instrument: knime

workflow
type: Dataset
additional type: ExampleRun
description: Example of KNIME workspace after executing RetroPath2.0 workflow
example of work: workflow.knime
potential action: ViewAction
  instrument: knime

RetroPath2.cwl
type: SoftwareSourceCode
additional type: Workflow
name: RetroPath 2.0 CWL workflow
programming language: v1.0
description: CWL tool wrapper that execute KNIME workflow using its Docker image
creator: stefan
potential action: ActivateAction
  instrument: cwltool
code repository: RetroPath2-cwl
was derived from: workflow.knime

workflow.svg
type: ImageObject
additional type: Sketch
encoding format: image/svg+xml
description: Diagram of RetroPath2.0 workflow
about: workflow.knime
was derived from: workflow.knime

Dockerfile
type: SoftwareSourceCode
url: https://hub.docker.com/r/ibisba/retropath2/
description: Docker image of KNIME workflow (including KNIME runtime)
creator: stefan
imported from: workflow.knime
imported from: knime-docker

test.sh
type: SoftwareSourceCode
additional type: Script
description: Test script that validate the CWL description (should ideally execute workflow with test inputs)

knime-docker
type: SoftwareApplication
name: ibisba/knime-workflow-base:3.6.2-1
url: https://hub.docker.com/r/ibisba/knime-workflow-base/
description: KNIME workflow base Docker image
version: 3.6.2-1

knime
type: ComputerLanguage
type: SoftwareApplication
name: KNIME Analytics Platform
alternate name: KNIME
url: https://www.knime.com/knime-software/knime-analytics-platform
version: 3.6

cwltool
type: SoftwareApplication
name: cwltool
description: Common Workflow Language reference implementation
url: https://github.com/common-workflow-language/cwltool/
version: 1.0.20190618201008
cite-as: zenodo.3250191

v1.0
type: ComputerLanguage
name: Common Workflow Language
alternate name: CWL
url: https://www.commonwl.org/
version: 1.0
cite-as: m9.figshare.3115156.v2