Section: New Software and Platforms

New tools for integrative biology

Participants : Anne Siegel [contact] , Jeanne Cambefort [contact] , Guillaume Collet, Damien Eveillard, Sylvain Prigent, Marie Chevallier.

The tools MeMap and MeMerge were complemented with new tools in order to analyze reference networks from litterature database and to vizualize the product of reconstructed metabolic networks.

Unifier. [input: SBML file with Palsson's metabolites identifiers output: sbml file with standard identifiers for metabolites]. This software is a Decision Support Tool to help biologists to normalize a file, containing Palsson's identifiers to refer to reactions and metabolites, using well known identifiers. Submit a list of Palsson identifiers to retrieve the corresponding database entries. Typically it maps with Metacyc identifiers but it would be used with Kegg or other databases later. A Unifier web service will be soon available.

NetWikiMaker. This tool generates (half) automatically a wiki on our reconstruction workflow. It contains information and data about the network reconstruction process such as different versions of draft metabolic networks files, parameters of tools, log files. It also displays the reactions, genes and metabolites that the workflow has found to be involved in the metabolic network, and provides a powerful search tool.