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