TIM/WIM: a set of tools to interface modelling in biology

Modelling in biology is a complex task. Many types of information are used by biologists but there is a lack of tools for integrating heterogeneous data in a core interface. TIM (Tools to Input Models) is a tool which allows to put in the same interface data which describe biological objects like enzymes, metabolites, DNA, ... and information about biological process modelling like those coming from NMR (Nuclear Magnetic Resonance) experiments and used to simulate flux through metabolic networks. TIM is able to manage the widely used database format, PGDB (BioCyc format), and uses a large part of a biological ontology, BioPAX format, to store information about biological processes. To manage all these data, WIM (Web Interface for Modelling) provides a set of web pages. The WIM package generates dynamic html sources using CL-WHO library and integrates an Hunchen-toot web server. At present, the application is used by a biologist group to store data about the carbon metabolism of the tomato fruit. They have released the first version of the TomaCyc database and currently used the WIM interface to create automatically input files for softwares that simulate the activity of their metabolism network.