Team Symbiose

Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Other Grants and Activities
Dissemination
Bibliography

Section: Overall Objectives

A Bioinformatics center

Symbiose is a bioinformatics research project. It focuses on methodological research at the interface between computer science and molecular biology, excluding "standard" informatics (“biocomputing”) for routine management of biological data. However, it is hard to achieve in depth research in this domain without participating to biology-oriented developments. In order to favor cooperative studies with biological labs we have decided to create a Bioinformatics Center, with a research team, Symbiose, leaning back against a bioinformatics core facility GenOuest (or the converse...). This report is mainly focused on the research project. Our research specificities include our interest in large scale studies (genomes, proteomes or regulation networks) and discrete methods necessary to handle the associated complexity. Our methods relate on discrete optimization, analysis of systems of qualitative equations and formal language modeling. Our goal is to push forward their range of applicability by exploring the impact of specialized machines or algorithms.

The bioinformatics resource center GenOuest acts as a facility and software tool provider for the analysis of genomic data generated by numerous laboratories (55) of Biogenouest®. The resource center provides at first computing power but also a comprehensive list of software dedicated to sequence analysis. On a national level, the platform is developing an expertise in the field of pattern matching and pattern discovery tool. It received a national RIO label in 2003 and 2006 and is supported by national and regional contracts. The platform is a mediator between computer science and biological labs. This leads to consulting, partnership and transfer actions. This activity is described in the section 5.1 .


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