Workflows and Pipelines
Interest Group

Stian Soiland-Reyes, University of Manchester


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, EINFRA-5-2015 contract number 675728

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

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 Docker for packaging command line codes.

What should we discuss?

Selecting and comparing workflow systems

Given an idea for a particular workflow,
what wf system would be most appropriate?

Integrations and extensions

Platform integration (e.g. PRACE, EGI)

Tool integration

Workflow integration (e.g. use wf from own portal)

Workflow optimization

Improving execution speed of workflows


Swapping tools or execution infrastructure

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 ...?"

Where to talk about workflows?

Face to Face

BioExcel has funds to support IG meetups



Travel support

What could we do face 2 face?

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

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?

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



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



Academic conferences (e.g. ECCB/ISMB)

Training events (e.g. EMBL-EBI)

ELIXIR Bring Your Own Data events

Local/national research networks (DTL, Barcelona BioMed)

.. and at your event?

Web forum

Online Chat

Workflow sharing

Mailing list

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.

BioExcel services

What services could BioExcel provide
to support workflow users?


Support, optimization, guidance, consulting, ... ?


Free tier, on-demand tier, subscription tier ?

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

Join the Workflow
interest group!

2016-11-21 BioExcel Workflows IG

By Stian Soiland-Reyes

2016-11-21 BioExcel Workflows IG

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