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.
Biocham-4 includes
- a notebook on-line
- 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 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 ...
CaSQ: Celldesigner as Sbml-Qual CellDesigner model to SBML-Qual encoded logical model converter, co-developed by Anna Niarakis and Sylvain Soliman.
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No longer maintained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.