Hello all,
Forwarding this from SFBI list.
Dave C
---------- Forwarded message ----------
From: <etienne.thevenot(a)cea.fr>
Date: Tue, Apr 15, 2014 at 1:07 AM
Subject: [bioinfo] Post-doctoral position in computational mass
spectrometry at CEA Saclay (France, Paris area)
To: bioinfo(a)sfbi.fr
Innovative algorithms and software tools for spectra interpretation and
structure elucidation in metabolomics
Background
The Laboratory for Data Analysis and Smart Systems (LADIS) at CEA
(French Alternative Energies and Atomic Energy Commission) has strong
expertise in processing and analysis of mass spectrometry (MS) data and has
a longstanding partnership with Laboratory of Drug Metabolism (LEMM) which
is specialized in LC-MS metabolomics. Together with three INRA platforms
(PFEM, BMP and MetaToul at Clermont-Ferrand, Bordeaux and Toulouse,
respectively), we develop the bioinformatics tools for MetaboHUB, the
national infrastructure in metabolomics and fluxomics (www.metabohub.fr/en).
The three main tasks are: 1) developing a Galaxy workflow for data
processing, analysis and annotation (in collaboration with the French
Institute for Bioinformatics), 2) building a reference database for
compounds and spectra (NMR and MS) with the corresponding tools for spectra
visualization, matching and interpretation, and 3) managing the data and
metadata resulting from the analysis of samples from large cohorts
on the four platforms.
As metabolomics is increasingly used for biomarker discovery,
high-throughput annotation of MS peak signals is critical. Within task 2,
the development of efficient algorithms for mass spectra interpretation is
tightly coupled to the building of a comprehensive database of high quality
spectra. Whereas software tools exist for the determination of the chemical
formula (based on mass accuracy, analysis of isotope distribution, etc.),
the elucidation of de novo structures (i.e. from unknown compounds) through
interpretation of fragmentation spectra (MS/MS) remains challenging due to
the chemical diversity of metabolites. Such a task requires the ability to
develop efficient combinatorial algorithms and interactive visualization
tools in addition to a good knowledge of both the rules of ionization and
fragmentation in the gas phase.
Project
Within the MetaboHUB project, the post holder will develop the software
tools to interpret MS/MS spectra and determine the structure of previously
uncharacterized compounds. He/she will work with Pr. Jean-Claude Tabet to
automate the process of spectrum interpretation by 1) determining the
metadata regarding spectrum acquisition to be stored in the database, 2)
designing and implementing the algorithms for MS and MS/MS spectra
matching, chemical structure elucidation and visualization, and 3)
integrating the tools in the MetaboHUB database. In addition, the post
holder will contribute to task 3 by benchmarking software tools and
architecture solutions for collaborative management of the huge amount of
raw and processed data generated simultaneously by the four MetaboHUB
platforms.
Profile
The successful candidate should hold a PhD in cheminformatics,
bioinformatics or computer science and have a strong understanding of
organic chemistry. The candidate is expected to have experience with Java
and C++, with database management systems (MySQL) and with web content
management systems (jQuery). The candidate should have presented his/her
Ph.D. thesis for less than two years before the starting date and should
have a good record of scientific publications.
Our offer
1-year contract (renewable once).
Net salary: about 2200 €/month, depending on experience.
Application
Please send your CV and your letter of motivation to:
Etienne Thévenot
Laboratory for Data Analysis and Smart Systems
CEA, Saclay Center, build. 565 (DRT/LIST/DM2I/LADIS)
F-91191 Gif-sur-Yvette Cedex, France
Mail: etienne.thevenot(a)cea.fr
Website: http://www-centre-saclay.cea.fr/en
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