The Biochemical Abstract Machine BIOCHAM 4
version 4.5.17 June 2021
Biocham 4 was first released in September 2017.
Biocham 4 is a complete rewriting of Biocham 3 for easier maintenance.
It integrates new features, in particular concerning the synthesis of reaction systems, robustness optimisation and influence systems.
For the sake of reproducible research, Biocham 3 is still active on http://lifeware.inria.fr/biocham3 but no longer maintained. Biocham 0 was first released in 2002.
Overview
The Biochemical Abstract Machine (Biocham) is a modelling
environment for systems biology and synthetic biology.
Biocham is mainly composed of :
- a rule-based language for modeling biochemical processes
with reactions (compatible with SBML) and/or influences (compatible with QualSBML),
- a hierarchy of semantics (differential, stochastic, Petri Net, Boolean) to interpret and analyze such models,
- a temporal logic based language to formalize behaviors of biochemical systems and validate or synthesize models with respect to such specifications.
- a command line language interfaced with Jupyter for notebook (i.e. time line view of the commands) and graphical user interface (i.e. static view of the commands) uses.
Biocham is a free software protected by the GNU General Public License
GPL version 2. This is an Open Source license that allows free
usage
of this software.
Feedback on the use of Biocham in applications, research or teaching
are particularly welcomed.
Demonstrations
Documentation
Unique features
Biocham implements some unique features for:
-
synthesizing reaction systems from mathematical specification of an input/output or time function [FLBP17cmsb][HFS20cmsb]
-
infering reaction systems from ODEs [FGS15tcs] (used in Mocassin for importing Matlab models in SBML),
-
combining reaction and influence systems [FMRS18tcbb] and interpreting them in a hierarchy of continuous, stochastic, discrete and Boolean semantics related by abstraction [FS088tcs],
-
detecting model reductions between reaction models and in model repositories such as biomodels [FS10bi] , based on reaction graph structures (concept of subgraph epimorphisms [GFMSS14dam]).
-
checking necessary conditions for multistationarity in reaction systems [BFS18jtb],
or sufficient conditions for rate independence [DFS20cmsbcmsb].
-
checking or enumerating temporal properties of the (asynchronous non-deterministic) Boolean dynamics in Computation Tree Logic (CTL) using a symbolic model-checker [CF03cmsb],
-
reducing reaction systems with a CTL specification of their behavior [CCFS06tcsb],
-
analyzing numerical traces in First-Order Linear Time Logic with constraints over the reals, FO-LTL(Rlin) [FT14book],
-
measuring the satisfaction, sensitivity and robustness of FO-LTL(Rlin) properties w.r.t. parameter distributions in differential or stochastic models [RBFS11tcs] [RBFS09bi],
-
optimizing model parameters for satisfying FO-LTL(Rlin) constraints including robustness constraints [FS18cmsb],
-
solving tropical equilibration problems for reasoning about orders of magnitudes in quantitative models [SFR14amb],
-
synthesizing reaction systems for executing imperative programs or computing real functions presented as solutions of polynomial initial value problems (PIVPs) [FLBP17cmsb],
Online access to notebook - Docker image download - Installation from source files
Feedback and bug reports:
https://gitlab.inria.fr/lifeware/biocham/issues or mail to biocham@inria.fr
https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.inria.fr%2Flifeware%2Fbiocham.git/develop