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

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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

What should wediscuss?

3 . 1

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

Where to talk aboutworkflows?

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Face to Face

BioExcel has funds tosupport IG meetups

VenueLunch

Travel support

5 . 1

What could we doface 2 face?

5 . 2

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

Web forumask.bioexcel.eu

6 . 1

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

http://ask.bioexcel.eu/

6 . 3

Sign up today!

6 . 4

Online Chatgitter.im/bioexcel

7 . 1

https://gitter.im/common-workflow-language7 . 2

https://gitter.im/bioexcel/workflows

7 . 3

Workflow sharingmyExperiment.org

8 . 1

http://www.myexperiment.org/groups/1311

8 . 2

Mailing list

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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

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