Software development
 "La simplicité est la sophistication suprême." Léonard de Vinci
 Biocham the Biochemical Abstract Machine for modeling, analyzing and synthesizing chemical reaction networks (CRN) in both perspectives of systems biology and synthetic biology. Biocham 4 is a complete rewriting of Biocham 3 for easier maintenance. It includes
 a notebook online,
 a short tutorial ( video with comments in French) ,
 an historical tutorial
 new features for
 compiling mathematical functions or programs in chemical reaction networks (CRN)
 influence systems with forces
 in addition to Biocham features for
 differential simulation, stochastic simulation, Boolean modelchecking and Boolean attractors
 specifying semiqualitative semiquantitative behaviors in quantitative temporal logic
 new features for
 verifying such behaviors, estimating parameter sensitivity and robustness
 searching and optimizing parameter values in high dimension
 detecting model reductions by subgraph epimorphisms
 various static analyses: dimension analysis, multistability, tropicalisation ...
 CaSQ: Celldesigner as SbmlQual CellDesigner model to SBMLQual encoded logical model converter, codeveloped by Anna Niarakis and Sylvain Soliman.
Aghamiri, Sara Sadat, Singh, Vidisha, Naldi, Aurélien, Helikar, Tomas, Soliman, Sylvain and Niarakis, Anna. Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics, 2020. [ preprint ]
 Trappist a tool for computing minimal trap spaces of a Boolean model, developed by Sylvain Soliman.
Trinh, VanGiang, Benhamou, Belaid, Soliman, Sylvain. Trap spaces of Boolean networks are conflictfree siphons of their Petri net encoding. Theoretical Computer Science, 971:114073, 2023. [ preprint ]
 Pack modeling a SWIProlog pack for mathematical modellng with constraints on subscripted variables, developed by François Fages.
François Fages. A Constraintbased Mathematical Modeling Library in Prolog with Answer Constraint Semantics. In 17th International Symposium on Functional and Logic Programming, FLOPS 2024, volume 14659 of LNCS. SpringerVerlag, 2024. [ preprint ]
No longer maintained
 BIOCHAM 3.7 is a previous version of the Biochemical Abstract Machine software for modelilng and analysing biochemical reaction networks. BIOCHAMweb allows you to try it online 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 modelchecking, and estimating parameter sensitivity and robustness,
 searching parameter values under temporal logic constraints.
 FOCTL is a constraint solver for full FirstOrder Computation Tree Logic with linear arithmetic over the reals, FOCTL(ℝlin), in Constrained Transition Systems.
 ClpZinc a Horn clause frontend for the MiniZInc modelling language for expressing search strategies by constraints
 MiniZincCMAES a stochastic optimization backend for the MiniZinc modelling language
 Rules2CP a general purpose rulebased modelling language for constraint solving.
 CLPGUI a generic graphical user interface for constraint logic programming.
Public data, models, notebooks and benchmarks related to publications.
 TCS 23
 Companion notebook to upload on BIOCHAM Jupyter notebook (alternatively see result in pdf,html or upload Biocham bc files)

Thibault Greugny, Eléa, Fages, François and Radulescu, Ovidiu, Szmolyan, Peter, Stamatas, Georgios. A Skin Microbiome Model with AMP interactions and Analysis of QuasiStability vs Stability in Population Dynamics. Theoretical Computer Science, 983:114294, 2023. [ preprint ]
 CMSB 2022
 Companion notebook to upload on BIOCHAM Jupyter notebook (alternatively see result in html or upload biocham bc files)

Mathieu Hemery, François Fages. Algebraic Biochemistry: a Framework for Analog Online Computation in Cells. In CMSB'22: Proceedings of the twentieth international conference on Computational Methods in Systems Biology, volume 13447 of LNCS. SpringerVerlag, 2022. [ preprint ] [ slides ] [ video ]
 CMSB 2022b
 Companion notebook to upload on BIOCHAM Jupyter notebook (alternatively see result in pdf,html or upload Biocham bc files)

Eléa Thibault Greugny, Georgios N Stamatas and François Fages. Stability versus Metastability in a Skin Microbiome Model. In CMSB'22: Proceedings of the twentieth international conference on Computational Methods in Systems Biology, volume 13447 of LNCS. SpringerVerlag, 2022. [ preprint ] [ slides ]
 CMSB 2021
 Companion notebook to save as local file and upload on BIOCHAM Jupyter notebook with v4.5.14 kernel

Mathieu Hemery, François Fages, Sylvain Soliman. Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs. In CMSB'21: Proceedings of the nineteenth international conference on Computational Methods in Systems Biology, volume 12881 of LNCS. SpringerVerlag, 2021. [ preprint ]
 CMSB 2020a
 Benchmark (zip file) and BIOCHAM notebooks for minimizing either number of species or the number of reactions

Mathieu Hemery, François Fages, Sylvain Soliman. On the Complexity of Quadratization for Polynomial Differential Equations. In CMSB'20: Proceedings of the eighteenth international conference on Computational Methods in Systems Biology, LNCS. SpringerVerlag, 2020. [ preprint ]
 CMSB 2020b
 Benchmark and Examples as a BIOCHAM notebook

Elisabeth Degrand, François Fages, Sylvain Soliman. Graphical Conditions for Rate Independence in Chemical Reaction Networks. In CMSB'20: Proceedings of the eighteenth international conference on Computational Methods in Systems Biology, volume 12314 of LNCS. SpringerVerlag, 2020. [ preprint ] [ slides ] [ video ]
 ICML workshop CB 2019
 source code
 used for the implementation of

Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages. A Statistical Unsupervised Learning Algorithm for Inferring Reaction Networks from Time Series Data. In ICML Workshop on Computational Biology, 2019. [ preprint ]
 CMSB 2019a
 source code
 used for the implementation of

Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages. On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics. In CMSB'19: Proceedings of the seventeenth international conference on Computational Methods in Systems Biology, volume 11773 of LNCS. SpringerVerlag, 2019. [ preprint ]
 CMSB 2019b
 Biocham4 notebook of examples of evolved CRNs
 to upload on http://lifeware.inria.fr/biocham4/online/

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, volume 11773 of LNCS. SpringerVerlag, 2019. [ preprint ]
 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 BIOCHAM4 notebooks online

Fages, François, Soliman, Sylvain. On Robustness Computation and Optimization in BIOCHAM4. In CMSB'18: Proceedings of the sixteenth international conference on Computational Methods in Systems Biology, LNCS. SpringerVerlag, 2018. [ preprint ]
 CMSB 2017a
 companion BIOCHAM4 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 AnalogDigital Programs. In CMSB'17: Proceedings of the fiveteen international conference on Computational Methods in Systems Biology, pages 108–127, volume 10545 of LNCS. SpringerVerlag, 2017. [ preprint ]
 CMSB 2017b
 companion BIOCHAM4 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 TimeSeries 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 LotkaVolterra.ipynb, CircadianClock.ipynb, p53Mdm2.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. Modelbased Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErbalpha UpRegulation during Mitosis. Biosystems, 149:59–69, 2016. [ preprint ]
 TCS 2015, CMSB 2012
 Automatic rewriting in SBML of the curated part of biomodels.net 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 Petrinets. In Proceedings of CP'2012, 18th International Conference on Principles and Practice of Constraint Programming, pages 798–814, volume 7514 of LNCS. SpringerVerlag, 2012. [ preprint ] [ slides ] [ poster ]
No longer maintained:
 CellStar image tracker as part of the Yeast Image Toolkit a collective effort for automatic tracking of yeast cells in timelapse microscopy.
 STSE SpatioTemporal Simulation environment: a platform facilitating spatial, microscopybased 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 in Prolog.