Software development

  • New version: Biocham 4 is a complete rewriting of Biocham 3 for easier maintenance. It includes a notebook,a short tutorial an historical tutorial and new features for
    • influence networks with forces
    • compiling functions in CRNs
    • learning models from data.

      However some features of BIocham 3 are still under development for Biocham 4, especially concerning
    • detecting model reductions by subgraph epimorphisms
    • hybrid simulations
    • the graphical user interface view of the notebook

  • BIOCHAM 3.7 (the Biochemical Abstract Machine) is a software environment for modeling, analyzing and synthesizing biochemical reaction networks. BIOCHAM-web allows you to try it on-line through a web service. Beyond making simulations of different kinds, BIOCHAM provides unique features for
  • importing and exporting biochemical reaction networks (CRNs) s in different formalisms and formats,
  • performing various static analyses of CRNs,
  • specifying behaviors in (quantitative) temporal logic,
  • verifying tempoal properties by model-checking, and estimating parameter sensitivity and robustness,
  • searching parameter values under temporal logic constraints.
  • 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, models, notebooks and benchmarks related to publications.

CMSB 2018
tool paper artifact submission On Robustness Computation and Optimization in BIOCHAM 4
BIOCHAM-4 notebook online

CMSB 2017
Strong Turing completeness of continuous chemical reaction systems and compilation of mixed analog-digital programs
Models and Notebooks for Biocham v4.0, executable online
CMSB 2017
Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data
Python code and examples implementing trace generation and PAC learning. The corresponding biocham commands can also be used directly in Biocham v4, locally or online

TCBB 2018

François Fages, Thierry Martinez, David Rosenblueth, Sylvain Soliman. Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018. [ preprint ]

Models in Biocham v4.0
Notebooks Lotka-Volterra.ipynb, Circadian-Clock.ipynb, p53-Mdm2.ipynb and MAPK.ipynb for Biocham v4.0

Biosystems 2016

Pauline Traynard, Céline Feillet, Sylvain Soliman, Franck Delaunay, François Fages. Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-alpha Up-Regulation during Mitosis. Biosystems, 149:59–69, 2016. [ preprint ]

Files containing models and behavior specification in quantitative temporal logic with BIOCHAM 3.7.5commands for parameter sensitivity and search

TCS 2015, CMSB 2012

François Fages, Steven Gay, Sylvain Soliman. Inferring Reaction Systems from Ordinary Differential Equations. Theoretical Computer Science, 599:64–78, 2015. [ preprint ]

Automatic rewriting in SBML of the curated part of from their ODE semantics, and associated graphs.

Constraints 2015, CP 2012

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 ]

source code.

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.