1-PROGRAMME
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- 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.fr/) 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 (http://oncora1.lyon.fnclcc.fr/englis...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 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 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 a computer scientist with thorough bioinformatics experience
• be in charge of the computer resources maintenance (job pending, backups ...)
• be a major player in providing the organization and implementing the procedures to develop the facility in accordance with high quality insurance standard. She/he will continually search for and evaluate new technologies which may be of interest in the facility.
• bring her/his expertise in analyzing data to address specific requests from the collaborating research teams.
• collaborate with investigators trained in mathematics, statistics, informatics and genomics and with the collaborating sequence production teams, methods for the efficient processing and analysis of nucleotide sequences, adapted to the huge volume of data produced by genomic technologies and notably by new high throughput DNA sequencing methods (quality control, identification and analysis of correlations, genome reconstruction and characterization algorithms).
2- REQUIRED QUALIFICATION
2.1 Education:
Advanced university degree (Masters, PhD) in computer science.
• Skills
• Capacity of contributing the computer methods of interest for bioinformatics analysis especially distributed calculus.
• proficiency at administering large computing facility including clusters working such as linux/unix system
• knowledge of web interfaces for biological databases (secure access, large load of data retrieval, handy browsing for biologists ...)
• advanced knowledge of major script, programming and markup languages (shell, awk, perl, python, php, ruby, ajax, javascript, java, c, c++, XML).
• Statistical analysis and/or programming experience in a bioinformatics context would be advantageous.
• knowledge of the major genomic databases and their interfaces.
Previous experience in the cancer field would be appreciated.
2.3 Professional experience
At least two years of relevant professional experience at the international level in the field of bioinformatics 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- CONTRACT AND SUBMISSION PROCEDURE
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 : [email protected] before February 6th 2010 . 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.
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- 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.fr/) 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 (http://oncora1.lyon.fnclcc.fr/englis...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 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 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 a computer scientist with thorough bioinformatics experience
• be in charge of the computer resources maintenance (job pending, backups ...)
• be a major player in providing the organization and implementing the procedures to develop the facility in accordance with high quality insurance standard. She/he will continually search for and evaluate new technologies which may be of interest in the facility.
• bring her/his expertise in analyzing data to address specific requests from the collaborating research teams.
• collaborate with investigators trained in mathematics, statistics, informatics and genomics and with the collaborating sequence production teams, methods for the efficient processing and analysis of nucleotide sequences, adapted to the huge volume of data produced by genomic technologies and notably by new high throughput DNA sequencing methods (quality control, identification and analysis of correlations, genome reconstruction and characterization algorithms).
2- REQUIRED QUALIFICATION
2.1 Education:
Advanced university degree (Masters, PhD) in computer science.
• Skills
• Capacity of contributing the computer methods of interest for bioinformatics analysis especially distributed calculus.
• proficiency at administering large computing facility including clusters working such as linux/unix system
• knowledge of web interfaces for biological databases (secure access, large load of data retrieval, handy browsing for biologists ...)
• advanced knowledge of major script, programming and markup languages (shell, awk, perl, python, php, ruby, ajax, javascript, java, c, c++, XML).
• Statistical analysis and/or programming experience in a bioinformatics context would be advantageous.
• knowledge of the major genomic databases and their interfaces.
Previous experience in the cancer field would be appreciated.
2.3 Professional experience
At least two years of relevant professional experience at the international level in the field of bioinformatics 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- CONTRACT AND SUBMISSION PROCEDURE
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 : [email protected] before February 6th 2010 . 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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