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Jobs : Experienced bioinformatician specialized in biological databases aurelielaugraud Academic/Non-Profit Jobs 0 08-09-2009 11:35 PM

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Old 01-25-2010, 04:36 AM   #1
Location: lyon

Join Date: Aug 2009
Posts: 37
Default Experienced bioinformatician specialized in biological databases


1.1- Background
Recognizing the new opportunities offered by next generation sequencing technologies in the field of cancer genomics, the French National Cancer Institute (INCa) has pledged to provide a major contribution to the International Cancer Genome Consortium (ICGC- through the study of two cancer types (hepatocellular carcinoma and HER2 amplified breast tumors). In the near future, INCa is considering contributing more tumor types. The entire sequencing of multiple pairs of tumor and matched germline DNAs has already been completed in France and other pairs are rapidly following. In order to overcome the challenges raised by the massive amount of sequence data that has been and will be generated by such programs, INCa and the Lyon community through the Synergie Lyon Cancer Foundation ( are joining efforts to create a dedicated bioinformatics facility. The objective of the bioinformatics facility will be to empower the biomedical teams working in the field of cancer to best exploit the data generated through large scale genomic projects, notably those funded by INCa and in the first place those taking place within the ICGC.

1.2 Context
The INCa-Synergie facility is located in a major French comprehensive cancer center (Centre Leon Berard) with a very active research department ( It is in close proximity to the International Agency for Research on Cancer, IARC. The facility is integrated into the "Pole Rhone-Alpes de Bioinformatique, PRABI (, which federates major bioinformatic teams. Thus the facility benefits both from strong biomedical and bioinformatics environments. It is acquiring a large HPC equipment. The facility is completing the recruitment of its staff by opening two additional positions for experienced bioinformaticians who will work under the supervision of the facility director, Pr. Gilles Thomas. This job description corresponds to one of these two positions.

1.3 Description of duties
Working in a team of experienced bioinformaticians and in close collaboration with French partner groups and international research centers, the candidate will :
be in charge of

- the design, development, implementation and maintenance of a high performance storage database enabling the integration of very large volumes of heterogeneous genomic data using different technologies (row storage, column storage, xml, key-value ) while respecting accepted standards. This database, interconnected and in communication with the major genomic databases of the scientific community, will be the core of a platform dedicated to data mining for both local and distant research teams. In addition, the database will offer interfaces (API) which will permit the development of innovative analytic tools.
- the development of ETL (Extract-Transform-Load) tools in order to import or export data in an automatic or semi-automatic manner.
- the evaluation of algorithms and softwares which may be of interest in the scientific field.

- the management of specific requests from the collaborating research teams aiming at improving the integration of biological knowledge and at performing data mining.


2.1 Education:
Advanced university degree (Masters, PhD) in bioinformatics.

2.2 Skills
design and development of databases for the management and analysis of large heterogeneous data sets.
modeling schemes for databases (relational databases, entity-association models, UML, ) and associated programs.
implementation and optimization of relational database management systems (Oracle, Postgres, MySql, ).
knowledge of the major genomic databases and their interfaces.
knowledge of querying languages such as SQL.
major script, programming and markup languages (shell, awk, perl, python, php, ruby, ajax, javascript, java, c, c++, XML).

2.3 Professional experience
At least two years of relevant professional experience at the international level in the field of bioinformatics and/or data base management is required. Prior experience in quality assurance procedures will be highly appreciated.

2.4 Complementary information:
Communication in French is not required but English language, excellent communication and interpersonal skills are essential. The candidate should be self motivated, capable of working both independently and within a closely interacting team of scientists and be able to deliver a quality product with fixed deadlines.


3.1 Contract :
Fixed term appointment (two years, renewable once) will be offered to the successful candidate. At the end of a 4 year period and depending on circumstances, a long term position may be considered. Starting date will depend on availability of the successful candidate. It may be as early as February 2010. The salary will be calculated according to the french public research institution salary (IR level) and slightly adjusted according to the successful candidate experience.

3.2 Work location :
Lyon, France

3.3 Submission procedure :
Letter of motivation, curriculum vitae and addresses of three referees are to be provided in electronic form to the following e-mail address : before Fabruary 6th. Acknowledgement of receipt will be forwarded to each candidate. Selected candidates will be invited to come to Lyon, France for an interview. General enquiries about the open position may be sent to the same e-mail address.
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