[BioC] Student project at European Bioinformatics Institute

[Gabriella Rustici]

Dear all,
the following student project is available at the EBI, Cambridge, UK. 
The project description is reproduced below.
Regards,
Gabriella

--------------------------------------
Project title:  Interface for Human Gene Expression Map

Project Description:

Thousands of microarray experiments are performed every year to estimate 
the relative abundance of different RNA molecules in different 
biological conditions. Most of these experiments concentrate on 
comparing a small number of biological conditions such as a particular 
disease state compared to a normal condition. However, many more 
different biological states, such as rare diseases or particular cell 
subtypes exist. It is impractical for a single dedicated experiment to 
generate a comprehensive expression data set covering all biological 
conditions but we can achieve this by using computational integration of 
the wealth of experiments that have already been performed and are 
available from public databases.

We collected, from the public microarray repositories GEO1 and 
ArrayExpress2, over 9000 raw data files generated from the human gene 
expression array Affymetrix U133A and derived a global Human Gene 
Expression Map by integrating raw data and harmonizing annotations from 
thousands of samples. For each gene we then computed its expression 
profile characterizing its expression under each of the studied 
biological conditions and sample classes. This project is part of an 
ongoing effort of integrative analysis across very large collections of 
microarray datasets, which has resulted in the release of a new 
database, the Gene Expression Atlas2.

This project aims at implementing, based on the current prototype, a 
public interface for the Human Gene Expression Map. Through this 
interface, users will be able to visualize the map, explore expression 
profiles and differentially expressed genes under particular 
experimental and biological conditions, and link to other bioinformatics 
resources providing genes functional annotation.

Project Learning Summary:

The student will acquire experience in the development of web interfaces 
for explorative bioinformatics analysis, a deeper understanding of 
microarray data analysis, as well as meta-analytical approaches and 
statistical methods for data mining of large-scale datasets. The student 
will also gain insights into the production process of a large European 
transcriptomics database.

Objectives:

  1. Further develop visualization and browsing features in the
     existing prototype (http://wwwdev.ebi.ac.uk/microarray/hge/HGE.jsp);
  2. Implement a more advanced interface for exploring the Human Gene
     Expression Map;
  3. Implement basic descriptive statistics for data exploration; and
  4. Retrieve or link information about gene annotation from other
     bioinformatics resources


Required Student Knowledge:

  1. Good to expert level of programming ability with Java and R;
  2. Familiarity with some of the aspects of bioinformatics would be
     advantageous, especially transcriptomics and microarray data
     analysis; and
  3. Ability to document code and work progress

Please note that candidates must be registered at a university 
throughout the entire duration of their stay at EBI and the work 
completed at EBI should form part of the candidate's final year studies.

Project duration:

approx. 6 months

Please email a cv and a cover letter to Gabriella Rustici, gabry at ebi.ac.uk

-- 
Gabriella Rustici, PhD

Microarray Informatics Team
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD
United Kingdom

Email: gabry at ebi.ac.uk

Tel: +44 (0)1223 492539
Fax: +44 (0)1223 494468