BACKGROUND

The « UMR de GENETIQUE VEGETALE » Gif-sur-Yvette (France, 30 min. south of Paris) is a pioneering laboratory in plant proteomics. Using state-of-the-art high-throughput technologies, the group produces large volumes of data (2-D gel electrophoresis and mass spectrometry) [1] To manage and mine these data, we have developed the PROTICdb database ([2], [3]. The data model of this database extends from experimental design description to protein identification by mass spectrometry and also includes full description of protein separation by electrophoresis. Data are submitted to the database by the end-user through a web interface wizard that automatically recognizes the type of submitted data (ie, output file from gel image analysis, output file from mass spectrometry analysis, etc.) and asks the user for additional information not available in the submitted file. A plug-in system allows for fast extension of this system to new proteomics software output or new file format. A tight quality control on data is also automatically conducted, including consistency with ontologies. Data can be queried, visualized and analysed with the help of an annotated 2-D gel browser, a graphical 2-D gel comparator and a query builder. This database is used in several laboratories [4-6]. The last version will be released under the GPL license this spring and is fully compliant with the Proteomics Initiative Standards [7] for data representation.

RESPONSIBILITIES

While basic requirements for proteomics data management and query are now fulfilled by PROTICdb, we still need to address several requirements like curation, statistical analysis and integration of data. To this end we will develop a bioinformatics environment around the PROTICdb database in the frame of the PROTIC workshop project, funded for three years by the french national Agency of Research. This programme, which has started in 2008, gathers 4 french bioinformatics and proteomics groups and is led by our team. Our group will develop new modules for automatic annotation of protein, updates and curation of data as well as data integration with federative databases (World Page 2D) or others OMICs databases such as métaboP (metabolomics).

REQUIREMENTS

In this context, we are opening a two-year position for an engineer in computer science or holder of a master's degree in bioinformatics. A first experience in oriented Web development project is strongly desired as well as being familiar with Java/JSP and/or PHP5. Good Knowledge of the SQL DBMS PostgreSQL,UML, and Web services would be an advantage.

COMPENSATION

€ 1800/Mo

HOW TO APPLY

Please send your application (CV, contact information for three references and cover letter) to Johann Joets by e-mail (joets[at]moulon.inra.fr). A Candidate will be selected in May and position will start on September 1st, 2008.

DEADLINE

15 May 2008