The Bioinformatics Workshop - University College London

Venue:

University College London, 25 Gordon Street, London, WC1H 0AY

United Kingdom

See map: Google Maps

Date:

Tuesday, May 28, 2013 - Thursday, May 30, 2013

Organisers:

Gabriella Rustici

Admin support:

Frank O'Donnell

Registration Opens Date:

Friday, March 1, 2013

Registration Deadline:

Friday, April 26, 2013

Participation:

First come, first served

Overview:

This course is intended to give life scientists training in two major areas: analysis of next generation sequencing data (NGS) as well as interactions and network analysis.

The first two days are designed to familiarize participants with NGS data analysis and to provide hands-on computational experience in analysis of such data using common analytical approaches for ChIP-seq and RNA-Seq data handling.

The third day provides an introduction to the study of Protein-Protein Interaction (PPI) networks, their importance and the techniques that are used to build and analyze them. Data resources related to pathways will also be covered.

What will I learn?

• What are the fundamental principles in the analysis of RNA-Seq and ChIP-Seq data. Topics will include: data quality, alignment, data handling and visualization, region identification, transcriptome analysis and basis statistical analysis.

• To explore the ENCODE data, the Encyclopedia of DNA Elements, a project aimed at identifying all regions of transcription, transcription factor association, chromatin structure and histone modification in the human genome sequence.

• To understand what is to be found in a molecular interaction database, alternative data formats and the various tools designed to work with them.

• To learn how to explore reactions and pathways.

Programme:

Time	Topic
Day 1 - 28 May - RNA-seq data analysis
09:00 - 09:10	Welcome and introduction
09:10 - 10:15	Lecture: Transcriptome assembly and differential expression analysis	Myrto Kostadima/Remco Loos
10:15 - 10:30	Tea/coffee break
10:30 - 12:00	Practical: Reference guided transcriptome assembly	Myrto Kostadima/Remco Loos
12:00 - 13:00	Lunch
13:00 - 15:15	Practical: Differential expression analysis	Myrto Kostadima/Remco Loos
15:15 - 15:30	Tea/coffee break
15:30 - 17:00	Lecture/Practical: Downstream analysis	Myrto Kostadima/Remco Loos
Day 2 - 29 May - ENCODE & ChIP-seq data analysis
09:00 - 10:00	Introduction to ENCODE data	Ian Dunham/Steven Wilder
10:00 - 10:15	Tea/coffee break
10:15 - 12:00	Working with ENCODE data	Ian Dunham/Steven Wilder
12:00 - 13:00	Lunch
13:00 - 14:00	Introduction to ChIP-seq	Myrto Kostadima/Remco Loos
14:00 - 15:30	Practical: ChIP-seq analysis - peak calling and annotation	Myrto Kostadima/Remco Loos
15:30 - 15:45	Tea/coffee break
15:45 - 17:00	Practical: ChIP-seq analysis - motif analysis	Myrto Kostadima/Remco Loos
Day 3 - 30 May - Interactions and Network analysis
09:00 - 10:00	Introduction to protein-protein interactions (PPIs) and networks	Sandra Orchard
10:00 - 10:15	Tea/coffee break
10:15 - 12:30	A PPIs database: IntAct. Description and hands-on session. Includes a brief introduction to Cytscape	Sandra Orchard
12:30 - 13:30	PPI data integration: PSICQUIC. Description and hands-on session with PSICQUICView	Sandra Orchard
13:30 - 14:30	Lunch
14:30 - 15:30	Reactome - description and hands-on	Sandra Orchard
15:30 - 16:00	Tea/coffee break
16:00 - 17:00	Reactome - description and hands-on (cont.)	Sandra Orchard