- BIOCHAM (the Biochemical Abstract Machine) is a software environment for modeling and analyzing biochemical reaction systems, performing various static analyses, specifying behaviors in temporal logic, searching parameter values, and making simulations. BIOCHAM-web allows you to try it on-line through a web service.
Biocham v4 is a complete rewriting of Biocham with new features for compiling behaviour specifications into reactions systems. It is still not released yet.
- CellStar image tracker as part of the Yeast Image Toolkit a collective effort for automatic tracking of yeast cells in time-lapse microscopy.
- FO-CTL is a constraint solver for full First-Order Computation Tree Logic with linear arithmetic over the reals, FO-CTL(ℝlin), in Constrained Transition Systems.
- ClpZinc a Horn clause front-end for the MiniZInc modelling language for expressing search strategies by constraints
- MiniZinc-CMAES a stochastic optimization backend for the MiniZinc modelling language
Public data and benchmarks related to publications.
- Automatic rewriting in SBML of the curated part of biomodels.net from their ODE semantics, and associated graphs.
- Enumerating Minimal Siphons in Petri nets using CLP and SAT solvers (source code)
Faten Nabli, François Fages, Thierry Martinez, Sylvain Soliman. A Boolean Model for Enumerating Minimal Siphons and Traps in Petri-nets. In Proceedings of CP'2012, 18th International Conference on Principles and Practice of Constraint Programming, pages 798–814, volume 7514 of Lecture Notes in Computer Science. Springer-Verlag, 2012. [ preprint ] [ slides ] [ poster ]
- STSE Spatio-Temporal Simulation environment: a platform facilitating spatial, microscopy-based simulation in biology
- CHRat a modular version of Constraint Handling Rules with ask and tell
- Rules2CP a modelling language for constraint programming
- CLPGUI is a graphical user interface for constraint logic programming.
- GNU Prolog RH is a version of GNU Prolog extended with attributed variables, coroutines and CLP(R) constraints.
- TCLP is a type checker for constraint logic programming.