Software
TotemBioNet:
Computer aided methodology for modeling of Biological Networks
- TotemBioNet is a platform dedicated to the identification of parameters for the discrete modeling framework of René Thomas. TotemBioNet exploits the complementarity of approaches based on Hoare logic and temporal logic. The benefit is twofold. On the one hand, the power of expression is reinforced. For the same case study, it is possible to express reachability properties such as multi-stationarity or homeostasis by temporal logic, as well as path properties by Hoare logic. On the other hand, the performances are improved because the weakest precondition calculated by Hoare logic serves to reduce the search space for the settings.
Holmes BioNet:
HOare Logic for Modeling Experiments in Biological Networks
- Holmes BioNet allows the construction of constraints on the parameters of a hybrid model of gene regulatory 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).
DyMBioNet:
Dynamical Models of Biological Networks (not yet available)
- includes SMBioNet (selection of models that meet a CTL specification) but adds a simulator and fair model-checking.
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).
SMBioNet:
Selection of Models of Biological Networks (is now a part of TotemBioNet)
- 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.