BioExcel: addressing training needs for advanced simulations in biomolecular research

Date:

 Tuesday 3 - Wednesday 4 May 2016

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Wednesday 16 March 2016

Application deadline: 

Friday 22 April 2016

Participation: 

Open application with selection

Contact: 

Maria Bacadare Goitia

Registration fee: 

Accommodation B&B £67.50 per night

Registration closed

Overview

The purpose of this workshop is twofold; firstly, it will provide users of three important biomolecular modelling and simulation resources,  GROMACS,  HADDOCK and  CPMD,  to learn directly from the developers of these resources and find out about how  BioExcel - Europe’s new centre of excellence for BioMolecular Research - will enable users to harness high-performance computing (HPC) to use these tools in a user-friendly environment that does not assume any prior experience of using HPC. Secondly, it will enable users of these services to provide BioExcel with feedback on the competencies needed to fully exploit these services. ‘Surgeries’ will enable participants to have one-to-one discussions with the developers of these resources, so that together they can ease bottlenecks in their modelling and simulation workflows

Audience

This workshop is aimed at existing users – both academic and industrial – of  GROMACS, HADDOCK and CPMD. Please be aware that this workshop focuses on knowledge exchange and is not a classical training workshop. We are looking for participants who have expertise in molecular modelling in general and in at least one of the flagship software applications in BioExcel, in addition to some proficiency in Linux. Participants  will be expected to contribute to the discussion around use cases and training requirements for BioExcel.

 

Outcomes

  • Learn about what GROMACS, HADDOCK and CPMD can currently do for your research

  • Find out about what Bioexcel is planning and how will support your research in the future

  • Get to know core developers and provide input into the future development of the applications

  • Share where your bottlenecks are so that we can develop appropriate, more automated workflows for accelerating your research

  • Provide input into your future training needs in this topic, so that we can deliver relevant and high quality training to our users

Programme

Time Topic Trainer
Day 1 - Tuesday 3 May: hands on workshop
09:00 - 09:30 Arrival and registration
09:30 - 09:45 Welcome and warm up activity Cath Brooksbank and Vera Matser, EMBL-EBI 
09:45 - 10:15 What is BioExcel and what can it do for you? Rossen Apostolov, KTH Royal Institute of Technology
10:15 - 10:35 Application overview 1: Haddock Alexandre Bonvin, Utrecht University 
10:35 - 10:55 Application overview 2: GROMACS  Mark Abraham, KTH Royal Institute of Technology 
10:55 - 11:25 Break
11:25 - 11:45 Application overview 3: CPMD  Emiliano Ippoliti, Forschungszentrum Jülich 
11:45 - 12:45 Interactive exercise - defining user groups and use cases Vera Matser, EMBL-EBI and Adam Carter, EPCC
12:45 - 13:45  Lunch 
13-45 - 15:30 Hands-on tutorials and surgery sessions GROMACS, HADDOCK and CPMD developers 
15:30 - 16:00 Break
16:00 - 17:45 Hands-on tutorials and surgery sessions continue GROMACS, HADDOCK and CPMD developers 
17:45 - 18:00 Wrap up of day 1 Cath Brooksbank
18:00 Drinks and dinner at Hinxton Hall restaurant
Day 2 - Wednesday 4 May: competency requirements
09:00 - 09:30 Intro to Bioexcel’s  competency-based training concept and draft competency profile  Cath Brooksbank and Vera Matser 
09:30 - 10:30 Use cases: three talks from users, illustrating their research challenges Speakers to be selected from registrants  
10:30 - 11:00  Break
11:00 - 12:00 Breakout 1: what competences are needed; what’s not needed and what’s provided by other training programmes? ALL 
12:00 - 12:30  Reports from breakouts  Breakout rapporteurs 
12:30 - 13:30 Lunch  
13:30 - 15:30 Hackathon: compiling input from the breakouts and adding knowledge, skills and behaviours for each competency ALL 
15:30 - 16:00 Break  
16:00 - 16:20 Presentation of outcomes Cath Brooksbank and Vera Matser 
16:20 - 17:30 Final use-case surgery GROMACS, HADDOCK and CPMD developers 
17:30 Wrap up and departures
European Bioinformatics Institute (EMBL-EBI) - Training Room 2
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

Training Room 2 in EMBL-EBI's South building is custom-built for providing computer-based training to 30 people.

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In association with

How to apply

Please note this workshop has a selection process. We will notify succesful applicants on the 22nd of April

EMBL-EBI use an on-line registration system called EBMS, if you have registered in the past using this system then simply log in using your user id e-mail address and password.  Alternatively, if you are creating a new registration account please ensure you enter your full details. Registration details can be amended at any time prior to the on-line registration deadline.

Application deadline

22 April 2016

Number of places

20 places

Registration closed

Organisers

Cath Brooksbank

Vera Matser - University of Cambridge

Rossen Apostolov - KTH Royal Institute of Technology

Adam Carter - EPCC

Trainers

Cath Brooksbank - EMBL-EBI, UK

Vera Matser - EMBL-EBI, UK

Rossen Apostolov - KTH Royal Institute of Technology

Alexandre Bonvin - Utrecht University

Mark Abraham - KTH Royal Institute of Technology

Emiliano Ippoliti - Forschungszentrum Jülich

Mikael Trellet - Utrecht University

Materials & attachments

BioExcel material