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The teams

The Bioinformatics Center of the Synergie Lyon Cancer Foundation places its expertise and human and technological resources at the service of the structure and interpretation of cancer genomic data.

Anthony Ferrari, bioinformatics specialist

Bioinformatics center

Anthony Ferrari has been a bioinformatics specialist for the Synergie Lyon Cancer Foundation since September 2010. He has gained specific expertise in the development of software pipelines for the processing of research databases.

As part of the International Cancer Genome Consortium (ICGC), a joint European project, Anthony Ferrari acts as an interface between the Synergie Lyon Cancer Foundation and the Sanger Institute, British partner of the bioinformatics platform involved in the sequencing of certain types of breast cancer (HER2+). He monitors the progress of the various scientific operations, verifies the quality of the samples, interacts with the scientists, collects and analyses the data obtained … The partnership focuses, above and beyond the services provided, on a wide-range of scientific aspects: “We exchange information and share our experience regarding the genomic modifications identified and listed by both teams, and regarding the optimisation of data analysis procedures”, explains Anthony Ferrari.

The bioinformatics specialist works on the development of a software pipeline, in other words a software infrastructure enabling platform engineers to analyse large genomic databases in a sequential and automated manner. “I create the software architecture necessary for meticulously laying the various bricks, which will constitute the major steps towards data processing. To confirm the reliability and strength of the system, I test all of the pipelines in their actual configuration ensuring that each step is valid, that the system takes into account the correct parameters, that it has access to sufficient material resources in order to function properly… I also have to safeguard the memory of the computer system, so that an earlier version of the pipeline can be used straightforwardly, even in several years from now”. Finally, Anthony Ferrari manages the computer cluster* of the platform and collaborates with the suppliers of that equipment in order to guarantee the reliability of its performances.

The platform of the Synergie Lyon Cancer Foundation: a group of bioinformatics specialists working closely together and sharing complementary skills so that each and everyone can benefit from the knowledge and expertise of the others

Anthony Ferrari chose to follow a bioinformatics course at the French Educational Institution in Informatics and Applied Mathematics of Grenoble (“Ecole nationale supérieure d’informatique et de mathématiques appliqués” or the ENSIMAG) in 2003. After having completed his final year project at the Structural Biology Institute (“Institut de Biologie structurelle” or IBS) in Grenoble, he was taken on by the Paoli-Calmette Institute, at the Cancer Research Centre of Marseille (“Centre de Recherches en Cancérologie”). While creating and managing bioinformatics tools, he also played a central role, as “database manager”, in initiating dialogue between the scientists, developers and hospital centres taking part in an INCa (“Institut National du Cancer” or French National Cancer Institute) project. “After having worked alone on several scientific issues for 4 years, I wanted to join a group of ‘people like myself’ in order to benefit from meaningful discussions, support and creative competition”, remembers Anthony Ferrari. “Not only was I motivated by the project, but I also regarded working under the supervision of Gilles Thomas as a great honour. I knew I was entering a work environment where my career would be able to evolve favourably”.

* The connection of several computers in order to increase the data processing performance.