BioExcel: workflow training for computational biomolecular research

Date: Thursday 20th October 2016 – Friday 21st October 2016

Venue: 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: *Extended to Friday 30th September 2016*

Participation: Open application with selection. We will review applications as they come in.

Contact: 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.


Draft Programme – subject to slight change


Start End Title (Presenter name)
Day 1 – Thursday 20 October 2016  
08:30 09:00 Arrival and registration
09:00 09:30 Welcome and expectations post-up

(Vera Matser, EMBL-EBI)

09:30 10:00 What is BioExcel and what can it do for you.

(Rossen Apostolov, KTH Royal Institute of Technology)

10:00 10:30 State of the art of Workflow management

(Stian Soiland-Reyes, UNIMAN)

10:30 11:00 Coffee Break
11:00 12:30 Galaxy + Hands-on

(Toni Espinosa, UAB Barcelona; Gonzalo Vera, CRAG Barcelona)

12:30 14:00 KNIME + OpenPHACTS & Hands-on

(Daniela Digles, Universität Wien)

14:00 15:00 Lunch
15:00 15:45 Copernicus

(Mark Abraham, KTH)

15:45 16:30 NextFlow

(Paolo Di Tommaso, Maria Chatzou, CRG)

16:30 17:30 Taverna + Hands-on

(Stian Soiland-Reyes, UNIMAN)

17:30 18:00 Marenostrum Visit

(Barcelona Supercomputing Center, BSC)

19:00 21:00 Workshop Dinner
Day 2 – Friday 21 October 2016  
09:00 09:45 Common Workflow Language (CWL)

(Michael Crusoe, Bucharest, Romania)

(CWL Project co-founder & Community Engineer)

09:45 10:30 BioExcel Workflows Interest Group

(Darren White, EPCC)

10:30 11:00 Coffee Break
11:00 11:30 BcBIO

(Darren White, EPCC)

11:30 13:00 PyCOMPSs & Hands-on

(Daniele Lezzi, BSC)

13:00 14:00 Lunch
14:00 18:00 Bring Your Own Workflow!

(All Together)


How to apply

In order to be considered for a place at this workshop, applicants must do the following:

  • Complete the online application form.
  • Submit a WORD document to containing a short biography including your work history, a description of your current research interests and a short biography. Each document should be no longer than 100 words and written in paragraph form.
  • Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this workshop.
    Further details will be provided on your confirmation email after completing the online form.

Incomplete applications will NOT be considered. Please read through the following guidance document for more information on how to complete your application.

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.

Application deadline
09 September 2016

Number of places
30 places

Apply now

This training course is part of a week-long BioExcel activity in Barcelona, the three days prior to the training course there will be a GROMACS hackathon; this event is free to attend but registration is required.


  • Rossen Apostolov
  • Cath Brooksbank
  • Adam Hospital
  • Vera Matser
  • Anna Montras


  • Rossen Apostolov – KTH Royal Institute of Technology
  • Mark Abraham – KTH Royal Institute of Technology
  • Pau Andrio – BSC Barcelona Supercomputing Center
  • Daniele Lezzi – BSC Barcelona Supercomputing Center
  • Adam Carter – EPCC  Edinburgh Parallel Computing Centre
  • Darren White – EPCC  Edinburgh Parallel Computing Centre
  • Michael Crusoe – Brussels, Belgium
  • Daniela Digles – Universität Wien
  • Toni Espinosa – UAB Barcelona
  • Gonzalo Vera – UAB Barcelona
  • Stian Soiland-Reyes – UNIMAN

20 Oct, 2016 - 21 Oct, 2016
All Day

Barcelona Supercomputing Center


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