Date: Monday 10 – Tuesday 11 April 2017
Venue: European Bioinformatics Institute (EMBL-EBI) – Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
Application opens: Wednesday February 08 2017
Application deadline: Sunday March 19 2017
Participation: First come, first served
Contact: Frank O’Donnell
Registration fee: £80
Overview
This workshop will introduce delegates to a Virtual Research Environment (VRE), created by the Multi-scale complex Genomics project (MuG), to facilitate the analysis and interpretation of the genome. This environment integrates a range of data from genome annotation to 3D folding and DNA flexibility. Recent studies have shown the role that genome organisation can play in gene expression and the VRE has been designed to provide a way of analysing such data. This course will explore how to use the MuG VRE through two case studies; cohesin’s role in genome organisation in yeast and the proto-oncogene DNA-binding transcription factor Ets1. Both will show how to analyse chromatin structure, model DNA flexibility and protein-DNA interactions.
Audience
The workshop is aimed at both experimental (bench-based) researchers and bioinformaticians; additionally it may be of interest to tool developers who wish to integrate their tools into the VRE.
Participants should have an undergraduate understanding of biology AND have knowledge of genome organisation and the role it can play within the nucleus.
Syllabus, tools and resources
During this workshop you will learn about:
- The Multi-scale complex Genomics project (MuG)
- The MuG Virtual Research Environment (VRE)
- Nucleosome dynamics
- Hi-C, interaction matrices and TADs (topologically associating domains)
- Protein-DNA interactions
Outcomes
After this workshop you will be able to:
Navigate the MuG VRE
- Model and analyse a protein-DNA complex at the atomistic scale
- Process Hi-C data sets to produce interaction matrices and TADs
- Apply the MuG VRE to your own data sets
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 – 10th April 2017 | ||
| 09:30 | Registration and tea/coffee | |
| 09:50 – 10:00 | Welcome to EMBL-EBI | Andy Yates |
| 10:00 – 10:30 | MuG and participants Introduction | Modesto Orozco |
| 10:30 – 11:30 |
Presentation of Nucleosome Dynamics |
Ricard Illa /Federica Battistini |
| 11:30 – 12:00 | Tea/coffee break | |
| 12:00 – 13:00 | User case : Nucleosome dynamics at cohesin binding sites throughout the cell cycle in yeast | Ricard Illa /Federica Battistini |
| 13:00 – 14:00 | Lunch | |
| 14:00 – 15:30 |
Coarse grained model of DNA; Build and analyze a sequence of interest. |
Jürgen Walther |
| 15:30 – 16:00 | Tea/coffee break | |
| 16:00 – 17:00 | Coarse grained model of Chromatin; Generation and analysis of chromatin fiber structures | Jürgen Walther |
| 17:15 | Bus back to Cambridge Train Station | |
| Day 2 – 11th April 2017 | ||
| 09:00 – 10:30 | Presentation of Protein-DNA and protein-protein docking tools. | Brian Jiménez |
| 10:30 – 11:00 | Tea/coffee break | |
| 11:00 – 12:30 | Protein-DNA interactions, DNA flexibility and binding specificity. | Marco Pasi / Federica Battistini |
| 12:30 – 13:30 | Lunch | |
| 13:30 – 15:00 | Presentation of TADbit : Generation of Hi-C interaction matrices from Hi-C data | François Serra |
| 15:00 – 15:30 | Tea/coffee break | |
| 15:30 – 17:00 |
Generation of populations of structures that satisfy the Hi-C interaction matrices and Visualization of 3D models with TADkit |
François Serra |
|
17:00 – 17:30 |
Course wrap up and feedback | Andy Yates |
| 17:30 | Course end | |