MuG API Course

Date:

  Thursday 13 September 2018

Venue: 

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

Application opens: 

Tuesday 19 June 2018

Application deadline: 

Friday 17 August 2018

Participation: 

First come, first served

Contact: 

Charlotte Pearton

Registration fee: 

£0

Registration closed

Overview

The Multiscale complex Genomics (MuG) Virtual Research Environment (VRE) is a workspace designed for researchers to analyse their 3D/4D genomic data. Many tools have already been integrated including TADbit/TADkit, nucleaR and pyDock, but there are always new tools being developed. The aim of the course is to provide developers within the life sciences training to be able to wrap their own analysis tools so that it can be easily integrated into the VRE.

Audience

This course is aimed at researchers and software developers that would like to integrate a new data generation or analysis tools within the VRE. The course will require knowledge of the Python programming language. Experience with high performance computing clusters is not essential, but knowing about their benefits would be advantageous.

Syllabus, tools and resources

During this workshop you will learn about:

  • The Multi-scale complex Genomics project (MuG)
  • The MuG Virtual Research Environment (VRE)
  • Programming with (Py)COMPSs
  • MuG Tool API for wrapping tools
  • Testing your code
  • Coding standards, documentation and licenses

Outcomes

During the course you will learn:

  • How to wrap and run a tool within the COMPSs HPC environment
  • How to prepare the code repository so that it can be easily integrated within the VRE

Programme

The programme will run from 9:00 - 5:00 pm and will include the following sessions:

  • Introduction to the VRE
  • How to wrap a tool using the MuG Tools API
  • Running the tool in a COMPSs environment
  • VRE integration
  • Coding standards and documentation
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

In association with

How to apply

In order to be considered for a place on this course applicants must do the following:

  1. Complete the online application form. 
  2. Submit a WORD document to cpearton@ebi.ac.uk containing the following:
  • 100 word description of the tool you have developed / are developing that you would like to integrate with the VRE
  • Please tell us how many potential users your tool has and how it might interact with tools already in the VRE.

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.

Application deadline

17 August 2018

Number of places

15 places

Registration closed

Organisers

Sarah Morgan - EMBL-EBI, UK

Mark McDowall

Trainers

Mark McDowall - EMBL-EBI, UK

Athina Meletiou - University of Nottingham

Javier Álvarez - Barcelona Supercomputing Center

Javier Conejero - Barcelona Supercomputing Center

Laia Codó - Barcelona Supercomputing Center