BioExcel: Workflow Training for Computational Biomolecular Research
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Date:
Thursday 20 - Friday 21 October 2016Venue:
Barcelona Supercomputing Center - Computer Architechture Dept at Universitat Politecnica de Catalunya, c/Jordi Girona, 29, 08034, Barcelona, Barcelona, SpainApplication opens:
Thursday 21 July 2016Application deadline:
Friday 30 September 2016Participation:
Open application with selectionContact:
Charlotte PeartonRegistration fee:
£0Registration closed
Course Overview
The purpose of this workshop is to:
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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.
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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 yourarticular workflow problem in a "Bring Your Own Workflow" session
Audience
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.
Learning outcomes
After this course you should be able to:
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Explain what Workflow Managers are, in which way they differ from each other, and how you can use them in your research.
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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.
Programme
| Time | Topic | Trainer | |
|---|---|---|---|
| Day 1 - Thursday 20 October 2016 | |||
| 08:30 - 09:00 | Arrival and registration | ||
| 09:00 - 09:30 | Welcome and expectations post up | Vera Matser/Cath Brooksbank, 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 | Tea/coffee break | ||
| 11:00 - 12:30 | Galaxy + Hands-on | Antonio Miguel Espinosa Morales, UAB Barcelona | |
| 12:30 - 14:00 | KNIME + OpenPHACTS & Hands-on | Daniela Digles, Universität Wien | |
| 14:00 - 15:00 | Lunch | ||
| 15:00 - 15:45 | Copernicus + Hands-on | 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 | BSC | |
| 19:00 - 21:00 | Workshop Dinner | ||
| Day 2 - Friday 21 October 2016 | |||
| 09:00 - 09:45 | Common Workflow Language (CWL) | Michael Crusoe, Brussels, Belgium | |
| 09:45 - 10:30 | BioExcel Workflows Interest Group | Adam Carter / Darren White, EPCC | |
| 10:30 - 11:00 | Tea/coffee break | |
|
| 11:00- 11:30 | BcBIO | Darren White, EPCC | |
| 11:30 - 13:00 | PyCOMPSs & Hands-on | Daniele Lezzi, BSC / Pau Andrio, BSC | |
| 13:00 - 14:00 | Lunch | ||
| 14:00 - 18:00 | Bring Your Own Workflow! | All Together | |
| 18:00 | End of course | ||
Additional information:
In association with
How to apply
**The deadline for applications has been extended from 9 September to 30 September**
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 cpearton@ebi.ac.uk 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
30 September 2016
Number of places
30 places
Organisers
Rossen Apostolov - KTH Royal Institute of Technology
Cath Brooksbank
Adam Hospital - IRB Barcelona
Vera Matser
Anna Montras - IRB Barcelona
Trainers
Rossen Apostolov - KTH Royal Institute of Technology
Mark Abraham - KTH Royal Institute of Technology
Pau Andrio - BSC
Adam Carter - EPCC
Michael Crusoe - Bucharest, Romania
Daniela Digles - Universität Wien
Toni Espinosa - UAB Barcelona
Daniele Lezzi - BSC
Stian Soiland-Reyes - UNIMAN
Darren White - EPCC