Software development © Inria / Photo C. Morel

  • Biocham 4 the Biochemical Abstract Machine: this new version (see video) 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 mathematical functions and programs 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 2019b
Biocham-4 notebook of examples of evolved CRNs
to upload on

Elisabeth Degrand, Mathieu Hemery, François Fages. On Chemical Reaction Network Design by a Nested Evolution Algorithm. In CMSB'19: Proceedings of the seventeenth international conference on Computational Methods in Systems Biology, Lecture Notes in BioInformatics. Springer-Verlag, 2019. [ preprint ]

CMSB 2019a
source code
used for the implementation of
Julien Martinelli, Jérémy Grignard, François Fages and Sylvain Soliman : A Statistical Learning Algorithm for Inferring Reaction Systems from Data Time Series [submitted]

JTB 2018
source code
used for the implementation of

Adrien Baudier, François Fages, Sylvain Soliman. Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels. Journal of Theoretical Biology, 459:79–89, 2018. [ preprint ]

CMSB 2018
companion BIOCHAM-4 notebooks online

Fages, François, Soliman, Sylvain. On Robustness Computation and Optimization in BIOCHAM-4. In CMSB'18: Proceedings of the sixteenth international conference on Computational Methods in Systems Biology, Lecture Notes in BioInformatics. Springer-Verlag, 2018. [ preprint ]

CMSB 2017a
companion BIOCHAM-4 notebooks online (zip file of models and notebooks for Biocham v4.0)

Fages, François, Le Guludec, Guillaume and Bournez, Olivier, Pouly, Amaury. Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs. In CMSB'17: Proceedings of the fiveteen international conference on Computational Methods in Systems Biology, pages 108–127, volume 10545 of Lecture Notes in Computer Science. Springer-Verlag, 2017. [ preprint ]

CMSB 2017b
companion BIOCHAM-4 notebooks online (original Python code and examples implementing trace generation and PAC learning, the corresponding biocham commands can also be used directly in Biocham v4)

Carcano, Arthur, Fages, François, Soliman, Sylvain. Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data. In CMSB'17: Proceedings of the fifteenth international conference on Computational Methods in Systems Biology, pages 74–90, volume 10545 of , 2017. [ preprint ]

TCBB 2018
Models in Biocham v4.0
companion notebooks Lotka-Volterra.ipynb, Circadian-Clock.ipynb, p53-Mdm2.ipynb and MAPK.ipynb for Biocham v4.0

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 ]

Biosystems 2016
Files containing models and behavior specification in quantitative temporal logic with BIOCHAM 3.7.5commands for parameter sensitivity and search

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 ]

TCS 2015, CMSB 2012
Automatic rewriting in SBML of the curated part of from their ODE semantics, and associated graphs.

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

Constraints 2015, CP 2012
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 ]

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.