[Biopredyn_pi] BioPreDyn - focus groups

Dear BioPreDyn Partners, As agreed during the BioPreDyn meeting, one of our first actions should be to define benchmark models for our algorithms. For this purpose, we have defined the following focus groups: - E. coli: metabolic & regulatory network (Pedro) - Yeast: metabolic & regulatory network (Pedro, Fluxome) - Chinese Hamster Ovary (CHO) Cells: metabolic, regulatory & signaling network model (Diego, Insilico, Julio S, Pedro) - Developmental Gene Regulatory Networks in animal systems (Yogi, Jaap) We need to establish for each of these benchmark problems what kind of data are available for modeling. This should be done as soon as possible. I would suggest that each focus group compiles the available data sets and writes a brief report on the nature and quality (completeness, technical accuracy etc.) of the data. I think we should aim at collecting such reports for each problem in February. To facilitate information exchange, we have set up folders on our Alfresco sharing platform (see Olaf's last email for information on how to access it) for each Focus Group. This allows you to store and share your contributions centrally. The idea is that each partner in a focus group contributes descriptions of those data sets they know about. The different WP leaders can then collect this information for the specific modeling tasks in each work package. Let me know if you have any problems/questions. I will try to provide an example report for the animal development focus group as soon as possible, and will be bugging you some more about this in the near future. Happy holidays! Best, Yogi -- Dr. Johannes Jaeger EMBL/CRG Research Unit in Systems Biology CRG - Centre de Regulació Genòmica Dr. Aiguader 88 08003 Barcelona, Spain Phone: +34 93 316 02 85 Fax: +34 93 396 99 83 Email: yogi.jaeger(a)crg.es or yoginho(a)gmail.com URL: http://www.crg.es/johannes_jaeger