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 June 19 2018

Application deadline: 

Friday August 17 2018

Participation: 

First come, first served

Contact: 

Charlotte Pearton

Registration fee: 

£0

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