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Open PHACTSWorkflows and Pipelines
Interest GroupStian Soiland-Reyes, University of Manchester
http://orcid.org/0000-0001-9842-9718@soilandreyes
This work is licensed under a .Creative Commons Attribution 4.0 International License
BioExcel Workflow Training, Barcelona, 2016-11-21
This work has been done as part of the BioExcel CoE ( ),a project funded by the EC H2020 program, contract number
www.bioexcel.euEINFRA-5-2015 675728
https://slides.com/soilandreyes/2016-11-21-bioexcel-workflows-ig
1
This group is for users (and potential users) of for data analysis and
pipe-lining of biomolecular simulation andmodelling tools; in particular using ,
, , and .
Scientific Workflow systems
Galaxy ApacheTaverna KNIME COMPSs Common Workflow
Language
2 . 1
Covering pros and cons of these workflowsystem, practical workflow design and setup,
discussion in this group also covers deploymentquestions on HPC/cloud infrastructure, like the
use of for packaging command line codes.Docker
2 . 2
Selecting and comparingworkflow systems
Given an idea for a particular workflow,what wf system would be most appropriate?
3 . 2
Integrations and extensionsPlatform integration (e.g. PRACE, EGI)
Tool integrationWorkflow integration (e.g. use wf from own portal)
3 . 3
Workflow optimizationImproving execution speed of workflows
DebuggingSwapping tools or execution infrastructure
3 . 4
Develop Best PracticeShare common knowledge
"How do I combine .."Considering alternative approachesWhat is special for each wf system,
what is common for all of them?"Which tool should I use for ...?"
3 . 5
Bring Your OwnWorkflow
"I wish I had a better workflow for X"Collaborative wf design
Build same wf in multiple wf managers?Interesting? Need common problem space
First try: Today at 14:00
5 . 3
Tooling hackathonIf the tools don't work well with your workflow,
let's fix the tool integration
Bring in BioExcel developers (GROMACS, HADDOCK,CPMD, Taverna, COMPSs)
and external devs (e.g. CWL, Galaxy, BCBio)
Learning: How to wrap a tool for the Galaxy shed ordescribe it for CWL
Developer focused - what about users?
5 . 4
Knowledgeexchange
"Exchange notes" on technology and best practicesScience show & tell - try out your research ideas
on a small audience"Handheld" try out new tools and techniques
5 . 5
"Paperthon"
Goal: Write a joint paper (draft)Focus on science or tech?
Best Practices - e.g. "10 Simple Rules for buildingbiomolecular workflows"
WF/tool Review - Comparisons and experiences
5 . 6
Co-location?
Academic conferences (e.g. ECCB/ISMB) events (e.g. )
ELIXIR eventsLocal/national research networks ( , )
.. and at your event?
Training EMBL-EBIBring Your Own Data
DTL Barcelona BioMed
5 . 7
https://gitter.im/common-workflow-language7 . 2
You decide!These were just some proposals!
Interest Group shaped by its members
IG decide itself on what is most useful,when/how to meet, technologies, etc.
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BioExcel servicesWhat services could BioExcel provide
to support workflow users?
Support, optimization, guidance, consulting, ... ?
Free tier, on-demand tier, subscription tier ?
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Next Webinar:Globus Genomics
2016-11-16 16:00 CETRavi Madduri, Argonne / University of Chicago
Large scale Galaxy workflows for Next-gen SequencingNIH Big Data for Discovery Science
http://bioexcel.eu/category/webinar/
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Join the Workflowinterest group!
http://bioexcel.eu/interest-groups/
13 . 1