BioExcel: workflow training for computational biomolecular research

Thu 20 October 2016, 09:00 to Fri 21 October 2016, 17:30
Barcelona Supercomputing Center, Computer Architecture Department at Universitat Politecnica de Catalunya, Barcelona, Spain

Room: Sala Gran room of the Torre Girona building

Application open: Tuesday 19th July 2016

Application deadline: Friday 9th September 2016

Participation: Open application with selection. We will notify successful applicants by Friday, 16th September 2016

Contact: cpearton [at] (Charlotte Pearton)

Registration fee: Registration for the course is free. Attendees need to cover their own travel and accommodation expenses.

BioExcel will be providing a limited number of fixed amount travel bursaries for this event. If you would like to be considered for a travel bursary please indicate this during the application process.


Complex scientific studies require elaborate software pipelines necessitating interconnection of different tools and sources of data. In some cases, the complexity of the pipeline forces the definition of process dependencies, especially when those processes can be launched asynchronously in High Performance Computing (HPC) systems. Workflow managers such as Galaxy, Apache Taverna, PyCOMPSs, KNIME or Copernicus can be used to tackle this particular issue.

The purpose of this workshop is to:

  • Provide an overview of the most commonly used workflow managers in the computational biomolecular field, both in a theoretical and practical way, with hands-on practice sessions.
  • Find out about how BioExcel – Europe’s new Centre of Excellence for Computational BioMolecular Research – will help you to develop and run your own pipelines using these tools and introduce you to the BioExcel Workflows Interest Group
  • Together with experts on the different workflow managers, identify the best approach for your particular workflow problem in a “Bring Your Own Workflow” session


Prior knowledge of workflow managers is not necessary but as participants you will need to have a sufficiently clear idea of the bioinformatics problem you are trying to solve to be able to express this as a simple workflow on paper.

To maximally benefit from the workshop, you are encouraged to bring your own data or problem statement to the workshop.

You will need to bring a Wi-Fi enabled, fully charged laptop with a reasonably modern browser (including travel adapter if applicable). No software installation will be necessary, a Virtual Machine (VM) will be provided on the day.


After this course you should be able to:

  • Explain what Workflow Managers are, in which way they differ from each other, and how you can use them in your research.
  • Anticipate how BioExcel might be able to support you in your future research and know what BioExcel is planning with regards to Workflow Managers.
  • Make an action plan to implement or refine your own workflow, based on one-to-one discussions with the Workflow Managers experts.

More infomation and registration:

See also: Interoperability Platform, Rare Diseases Community