[Employment] Bioinformatics Programmer (INRA, France)

[joets from moulon.inra.fr]

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

DEADLINE: 30th April 2008

SALARY AND BENEFITS: € 1800/Mo

For more information, please contact Johann Joets
(joets from moulon.inra.fr)

References :
[1]	D. Vincent et coll., “Water Deficits Affect Caffeate O-
Methyltransferase, Lignification, and Related Enzymes in Maize Leaves.
A Proteomic Investigation,” Plant Physiol., vol. 137, Mar. 2005, pp.
949-960.
[2]	H. Ferry-Dumazet et coll., “PROTICdb: a web-based application to
store, track, query, and compare plant proteome data,” Proteomics,
vol. 5, Mai. 2005, pp. 2069-81.
[3]	O. Langella, M. Zivy, et J. Joets, “Plant Proteomics: Methods and
Protocols,” H. Thiellement et coll., éd., Humana press, Totowa, New
Jersey, U.S.A, 2006, pp. 279-304.
[4]	W. Albertin et coll., “Differential regulation of gene products in
newly synthesized Brassica napus allotetraploids is not related to
protein function nor subcellular localization,” BMC genomics, vol. 8,
2007, p. 56.
[5]	J.A. Paiva et coll., “Molecular and phenotypic profiling from the
base to the crown in maritime pine wood-forming tissue,” New
Phytologist, vol. 178, Avr. 2008, pp. 283-301.
[6]	S. ALVAREZ et coll., “Metabolomic and proteomic changes in the
xylem sap of maize under drought,” Plant, Cell & Environment, vol. 31,
Mar. 2008, pp. 325-340.
[7]	S. Orchard et coll., “Proteomic data exchange and storage: the
need for common standards and public repositories,” Methods in
molecular biology (Clifton, N.J.), vol. 367, 2007, pp. 261-70.