SoftwaresThe "formal bioinfo" project has developed a number of tools for modeling genetic regulatory networks:
HyMBioNet: Hybrid Modeling for Biological Network
- HyMBioNet is a trace simulator of hybrid models of gene networks.
- see book chapter Hybrid Gene Networks: a new Framework and a Software Environment (2016).
HHLforBioNet: Hybrid Hoare Logic for Biological Networks
- HHLforBioNet allows the construction of constraints on the parameters of a hybrid model of gene network based on a chronometric discrete trace. This tool uses techniques based on Hoare logic to build the constraints leading to a model presenting the specified trace.
- See article A hybrid Hoare logic for gene network models (ArXiv, 2016).
SMBioNet: Selection of Models of Biological Networks
- helps genetic network modeling as part of the discrete theory of R. Thomas. This tool allows you to select models that meet a specification expressed in CTL.