The Biochemical Abstract Machine BIOCHAM
version 4.1.5 March 2018
Biocham 4 was released in September
2017. Biocham 4 is a complete rewriting of Biocham 3 for easier maintenance.
It integrates new features, in particular concerning influence systems, the synthesis of reaction systems, and robustness optimisation.
It also lacks some features of Biocham 3 concerning model comparisons (by subgraph epimorphisms), sensitivity analyses and the graphical user interface.
For these reasons Biocham 3 is still active on http://lifeware.inria.fr/biocham3 but no longer maintained.
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 the temporal behaviors of biochemical systems and validate models with respect to such specifications.
Biocham implements some unique features for:
-
combining reaction and influence systems [FMRS18tcbb] and interpreting them in a hierarchy of continuous, stochastic, discrete and Boolean semantics related by abstraction [FS088tcs] or approximation relationships,
-
infering reaction systems from ODEs [FGS15tcs] (used for importing Matlab models in SBML within Mocassin),
-
synthesizing reaction systems for computing real functions presented as solutions of polynomial initial value problems (PIVPs) [FLBP17cmsb],
-
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,
-
solving tropical equilibration problems for reasoning about orders of magnitudes in quantitative models [SFR14amb],
-
(in Biocham 3, available in Biocham 4 in Fall 2018) the detection of model reductions within model repositories such as biomodels [FS10bi] , based on the structure of the reaction graphs (subgraph epimorphisms [GFMSS14dam]).
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.
Biocham notebook online
Try the tutorial notebook (presented at aSSB 2018) or the historical tutorial notebook (presented at CMSB 2017)
Try the other examples, or upload your own ones, on our online notebook.
Documentation
Reference manual in html
Download and Installation
Source version:
biocham.zip.
The installation then basically proceeds by using the Unix shell script
./install.sh
Previous versions:
biocham4.0.zip, biocham3.
Feedback and bug reports:
Mail to biocham@inria.fr
