Software development

  • 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.


Older stuff:

  • 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.