Experienced bioinformatician specialized in biological databases : Lyon, France

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-
http://www.icgc.org/) 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 (http://www.synergielyoncancer.com/) 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.

2 Context
The INCa-Synergie facility is located in a major French comprehensive
cancer center (Centre Leon Berard) with a very active research
department (http://oncora1.lyon.fnclcc.fr/english_version/index_eng.html).
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 (http://www.prabi.fr/), 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 will open over the coming months four
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 positions.

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.
• be a major player in providing the organization and implementing the
procedures to develop the facility in accordance with the ISO
9001:2000 standard.
• develop tools such as ETL (Extract-Transform-Load) in order to
import or export data in an automatic or semi-automatic manner.
• continually evaluate, in the context of the platform, new
technologies which may be of interest in the scientific field.
• bring her/his expertise in managing data to specific requests from
the collaborating research teams.


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

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).

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.

4 Complementary information:
Communication in French is not required but advanced 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.


How to apply
Letter of motivation, curriculum vitae and addresses of three referees
are to be provided in electronic form to the following e-mail address
: synergie_vacancies@prabi.fr, prior to September 15, 2009.
Acknowledgement of receipt will be forwarded to each candidate.
Selected candidates will be invited to come to Lyon, France for an
interview. Prior to the closing date, general enquiries about the open
position may be sent to the same e-mail address.


Email Resume To
synergie_vacancies@prabi.fr