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.
© Inria / Photo C. Morel

Biocham-4 includes

  • 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 model-checking and Boolean attractors
    • specifying semi-qualitative semi-quantitative behaviors in quantitative temporal logic
    • 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, multi-stability, tropicalisation ...

  • Trappist a tool for computing minimal trap spaces of a Boolean model, developed by Sylvain Soliman.

  • MetaLo an opensource Python package that enables the coupling of Boolean models inferred from process description molecular interaction maps with generic core metabolic networks. Developed by Sylvain Soliman, Sahar Aghakhani and Anna Niarakis.

  • Pack modeling a SWI-Prolog pack for mathematical modellng with constraints on subscripted variables defined by set comprehension in Prolog, developed by François Fages.

No longer maintained

  • BIOCHAM 3.7 is a previous version of the Biochemical Abstract Machine software for modelilng and analysing 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.
  • 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

  • Rules2CP a general purpose rule-based 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)

CMSB 2022
Companion notebook to upload on BIOCHAM Jupyter notebook (alternatively see result in html or upload biocham bc files)

CMSB 2022b
Companion notebook to upload on BIOCHAM Jupyter notebook (alternatively see result in pdf,html or upload Biocham bc files)

CMSB 2021
Companion notebook to save as local file and upload on BIOCHAM Jupyter notebook with v4.5.14 kernel

CMSB 2020a
Benchmark (zip file) and BIOCHAM notebooks for minimizing either number of species or the number of reactions

CMSB 2020b
Benchmark and Examples as a BIOCHAM notebook

ICML workshop CB 2019
source code
used for the implementation of

CMSB 2019a
source code
used for the implementation of

CMSB 2019b
Biocham-4 notebook of examples of evolved CRNs
to upload on http://lifeware.inria.fr/biocham4/online/

JTB 2018
source code
used for the implementation of

CMSB 2018
companion BIOCHAM-4 notebooks online

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

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

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

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

Constraints 2015, CP 2012
source code.

No longer maintained:

  • CellStar image tracker as part of the Yeast Image Toolkit a collective effort for automatic tracking of yeast cells in time-lapse microscopy.

  • 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 in Prolog.