TREMPPI - Toolkit for Reverse Engineering of Molecular Pathways through Parameter Identification
TREMPPI is a Systems Biology toolkit for research in gene regulation and molecular signalling. This fully integrated, visual toolkit is well suited for the analysis of complex functional modules, e.g. circadian clock. TREMPPI supports multiple ways of encoding various biological knowledge about the system. The goal is to provide as much information as possible about how the structure of the system is likely to look. Such an approach is most valuable if the precise mechanics of the module in question are not known. In this scenario we simply consider all the possibilities for how the components of the module may interact and analyse them one by one and therefore we utilize a very coarse-grained modelling framework of logical networks, focusing solely on qualitative features of a model.