BioExcel Workflows and Pipelines Interest Group http://bioexcel.eu/interest-groups/ Stian Soiland-Reyes http://orcid.org/0000-0001-9842-9718 Source: http://slides.com/soilandreyes/2016-11-21-bioexcel-workflows-ig/ Presented at 2016-10-21 BioExcel Workflow Training, BSC, Barcelona http://bioexcel.eu/events/bioexcel-workflow-training-for-computational-biomolecular-research/

1. Open PHACTS
Workflows and Pipelines
Interest Group
Stian 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.eu
EINFRA-5-2015 675728
https://slides.com/soilandreyes/2016-11-21-bioexcel-workflows-ig
1

2. This group is for users (and potential users) of
for data analysis and
pipe-lining of biomolecular simulation and
modelling tools; in particular using ,
, , and
.
Scientific Workflow systems
Galaxy Apache
Taverna KNIME COMPSs Common Workflow
Language
2 . 1

3. Covering pros and cons of these workflow
system, practical workflow design and setup,
discussion in this group also covers deployment
questions on HPC/cloud infrastructure, like the
use of for packaging command line codes.Docker
2 . 2

4. What should we
discuss?
3 . 1

5. Selecting and comparing
workflow systems
Given an idea for a particular workflow,
what wf system would be most appropriate?
3 . 2

6. Integrations and extensions
Platform integration (e.g. PRACE, EGI)
Tool integration
Workflow integration (e.g. use wf from own portal)
3 . 3

7. Workflow optimization
Improving execution speed of workflows
Debugging
Swapping tools or execution infrastructure
3 . 4

8. Develop Best Practice
Share common knowledge
"How do I combine .."
Considering alternative approaches
What is special for each wf system,
what is common for all of them?
"Which tool should I use for ...?"
3 . 5

9. Where to talk about
workflows?
4

10. Face to Face
BioExcel has funds to
support IG meetups
Venue
Lunch
Travel support
5 . 1

11. What could we do
face 2 face?
5 . 2

12. Bring Your Own
Workflow
"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

13. Tooling hackathon
If 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 or
describe it for CWL
Developer focused - what about users?
5 . 4

14. Knowledge
exchange
"Exchange notes" on technology and best practices
Science show & tell - try out your research ideas
on a small audience
"Handheld" try out new tools and techniques
5 . 5

15. "Paperthon"
Goal: Write a joint paper (draft)
Focus on science or tech?
Best Practices - e.g. "10 Simple Rules for building
biomolecular workflows"
WF/tool Review - Comparisons and experiences
5 . 6

16. Co-location?
Academic conferences (e.g. ECCB/ISMB)
events (e.g. )
ELIXIR events
Local/national research networks ( , )
.. and at your event?
Training EMBL-EBI
Bring Your Own Data
DTL Barcelona BioMed
5 . 7

17. Web forum
ask.bioexcel.eu
6 . 1

18. http://ask.bioexcel.eu/
6 . 2

19. http://ask.bioexcel.eu/
6 . 3

20. Sign up today!
6 . 4

21. Online Chat
gitter.im/bioexcel
7 . 1

22. https://gitter.im/common-workflow-language
7 . 2

23. https://gitter.im/bioexcel/workflows
7 . 3

24. Workflow sharing
myExperiment.org
8 . 1

25. http://www.myexperiment.org/groups/1311
8 . 2

26. Mailing list
9

27. 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.
10

28. BioExcel services
What services could BioExcel provide
to support workflow users?
Support, optimization, guidance, consulting, ... ?
Free tier, on-demand tier, subscription tier ?
11

29. Next Webinar:
Globus Genomics
2016-11-16 16:00 CET
Ravi Madduri, Argonne / University of Chicago
Large scale Galaxy workflows for Next-gen Sequencing
NIH Big Data for Discovery Science
http://bioexcel.eu/category/webinar/
12

30. Join the Workflow
interest group!
http://bioexcel.eu/interest-groups/
13 . 1

31. http://bioexcel.eu/interest-groups/
13 . 2