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SLING Bioinformatics Roadshow, 18–20 May 2010

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The Bioinformatics Roadshow is a collaborative effort that is funded by the European Commission as part of the SLING Integrating Activity. The Bioinformatics Roadshow is coordinated by the European Bioinformatics Institute – Europe’s main provider of biological data – and is run in collaboration with our SLING partners, the Swiss Institute of Bioinformatics (SIB), the European Patent Office and the BRENDA project.


The course will provide hands-on training on some of the bioinformatics tools and databases developed by EBI. We will concentrate especially on various EBI datasources for functional genomics.


Day 1 will concentrate on human functional genomics using Ensembl and ArrayExpress

Day 2 will concentrate on microbe and plant genomics using Ensembl Genomes and Biomart

Day 3 will concentrate on protein structures using PDBe


Please note:

Days are largely independent and you can register for one or more days as you wish.


A brief overview on subjects covered in each session:



Ensembl Functional Genomics:

  • How the Ensembl project annotates functional genomics / regulatory data

  • How to browse and retrieve functional genomics / regulatory data in Ensembl

  • About our future plans with regard to the annotation of functional genomics / regulatory data

  • Mapping of microarray probes

Note: these data are for the largest part only available for human.

Link: http://www.ensembl.org


ArrayExpress:

  • How to browse and retrieve data from the ArrayExpress public repository of transcriptomics data
  • How to submit data to ArrayExpress

Link: http://www.ebi.ac.uk/microarray-as/ae/


Ensembl genomes:

  • How to navigate Ensembl Genomes and retrieve information.

Note: these data are mostly for plants and microbes

Link: http://www.ensemblgenomes.org/


PDBe:

  • To understand the fundamentals of protein structures - tertiary and quaternary structures and structure quality.

  • To learn how to search, retrieve, visualise and analyse structures and their bound inhibitor, or drug molecule environments.

  • To analyse similar structures, small structural motifs and similar interfaces.

Link: http://www.ebi.ac.uk/pdbe/

Program

18 th May

09:30-10:00    Registration & coffee
10:00-11:00    Ensembl Functional Genomics presentation and demo
11:00-11:30    Break
11:30-12:30    Ensembl Functional Genomics hands-on
12:30-13:30    Lunch break
13:30-15:00    Array Express
15:00-15:30    Tea break
15:30-17:00    Array Express

19th May

09:00-09:30    Registration & coffee  
09:30-11:00    Introduction to Ensembl Genomes (Browser hands on example (Protists or plants)
11:00-11:30    Break
11:30-12:30    Biomart
12:30-13:30    Lunch break
13:30-14:30    Variation
14:30-15:00    Tea break
15:00-16:30    Comparative Genomics

20th May

09:00-09:30    Registration & coffee
09:30-10:30    PDBe
10:30-10:45    Break
10:45-12:15    PDBe
12:15-13:00    Lunch break
13:00-14:30    PDBe
14:30-14:45    Tea break
14:45-16:15    PDBe
Date: 18.05.2010 10:00 - 20.05.2010 17:00
Location: Premises of CSC at Keilaranta 14, Espoo, Finland.
Language: English
Lecturers: Emma Hastings, Bert Overduin, Jeff Almeida-King, Gaurav Sahni
Price: 50 EUR (+ VAT) per day
The fee covers course materials, lunches as well as morning and afternoon coffees

Registration

Registration has expired 18.04.2010
All course days are now full. Some seats may become available if there are cancellations. Please inquire by email. There are 24 seats available. As there are less computers than seats in the course room, participants are encouraged to bring their own laptop if possible. The registration may be canceled until the last day of registration. Thereafter the full fee will be invoiced. The course will be organized only if there is at least 15 registrations per session.

Additional information

Ari-Matti Saren (09-457 2282, Ari-Matti.Saren [at] csc.fi)