BioExcel Workflows Interest Group newsletter #2

This is the second newsletter of the BioExcel Workflows interest group. As you probably know, BioExcel supports multiple workflow systems for computational biomolecular research, and we are keen to hear from you, either on our forum, or in our Gitter chat room. Feel free to get in touch with your questions about workflows, and we'll do our best to put you in contact with the experts!



BioExcel and OpenPHACTS: Building pharmacological workflow blocks for virtual screening

Date: Monday 17th July 2017 (2017-07-17)
Time: 15:00 BST / 16:00 CEST / 14:00 UTC

Next week (2017-07-17) BioExcel's webinar series continue with Nick Lynch, who will introduce Open PHACTS, an integrated pharmacological data platform and BioExcel strategic partner.

The Open PHACTS Discovery Platform brings together vast amounts of linked data in a single integrated, open infrastructure providing a platform for researchers to access and query publicly-available pharmacological data.

The platform integrates major open data sources (e.g. ChEMBL, UniProt, WikiPathways, SureChEMBL, DrugBank, Disgenet and their associated Chemistry) on compounds, patents, diseases, targets and pathways; linked by identifiers, semantic and structural chemistry information, re-exposed as a collection of unified web APIs, workflow components plus tool integrations. 

In this webinar, Nick Lynch (Open PHACTS Foundation), Stian Soiland-Reyes and Adam Hospital will present the Open PHACTS Platform and how BioExcel is building a Virtual Screening workflow to combine Open PHACTS with the BioExcel-supported tools for bimolecular simulation and modelling.

Please register at

You will then receive an email with details of how you can connect to the webinar.

For more on this webinar, see


Common Workflow Language

..did you miss Michael Crusoe's webinar Introduction to the Common Workflow Language (CWL) project last month? The YouTube recording is now available (

Short on time? How about a 64 seconds CWL summary? (

In this extended version, BioExcel provide an overview of CWL Viewer:


BioExcel at ISMB/ECCB 2017

The international joint conference Intelligent Systems for Molecular Biology / European Conference on Computational Biology, ISMB/ECCB 2017, takes place in Prague this July (2017-07-21 / 2017-07-25).

BioExcel will be present at ISMB/ECCB, look out for the BioExcel booth for some goodies! Too much biology? The BOSC schedule  (Bioinformatics Open Source Conference) should have plenty to keep you updated on workflows and bioinformatics tool development.

Why not come to Prague two days early, and join for free (whether you attend ISMB or not) the Codefest 2017? In this informal hackathon you will find many of the developers of workflow systems like CWL, Galaxy, Nextflow, bcbio, Arvados, Apache Taverna, as well as advanced users; come along to exchange experiences or code something new!

More on BioExcel at ISMB:


BioExcel Community Forum

The BioExcel Community Forum takes place 22nd-23rd November, 2017 in Amsterdam and is free to attend (arrange your own travel and accommodation).

This is an opportunity for members of BioExcel’s interest groups and other members of the BioExcel community to come together for discussions and to work on issues of interest to the group.

This will be an “unconference”, so it won’t just be a set of (short!) presentations; this will be a chance for you to have your voice heard and to influence the future direction of the Centre of Excellence, and will also provide you with a chance to work together with other interest group  members on topics that are of interest to you.

For the Workflows Interest Group we are in particular planning to have a Bring Your Own Workflow session - come along with your existing pipeline you would like to have advice on (e.g. performance, compatibility, sharing), or just a conceptual drawing of how your scripts and manual steps combine, and we can work together to formalize it as a workflow in one of BioExcel's supported scientific workflow systems. We'll combine this with lightning talks,  you are welcome to give a very brief intro about what you are up to, and form new collaboration with other interest group members.

Plenty of break-out space is available, as well as sessions to learn more about high performance computing (HPC). This is also your chance to hang out with lead developers of Gromacs, Haddock and the new QM/MM interface in CPMD and influence the future direction of BioExcel.

To sign up for the BioExcel Community Forum, see