BIOCHAM 4 web page (original) (raw)

The Biochemical Abstract Machine BIOCHAM 4

version 4.6.26 June 2024

Overview

The Biochemical Abstract Machine (Biocham) is a modelling environment for systems biology and synthetic biology, based on the computational theory of Chemical Reaction Networks (CRN).

Biocham is mainly composed of :

• a rule-based language for modeling biochemical processes with reactions (i.e. CRN, compatible with SBML) and/or influences (compatible with QualSBML),
• a hierarchy of semantics (differential, stochastic, Petri Net, Boolean) to interpret, analyze or synthesize CRNs,
• a temporal logic based language to formalize behaviors of biochemical systems and validate, or synthesize, CRNs with respect to temporal specifications,
• a command line language interfaced with Jupyter for both 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. Biocham is implemented in SWI-Prolog (43000 LOC) and interfaced with several third-party software.

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 CRN implementing a mathematical function (either of time or of some input),
• robustness optimisation with respect to behavior specification in quantitative temporal logic,
• influence systems combined with CRNs. . For the sake of reproducible research, Biocham 3 is still active on http://lifeware.inria.fr/biocham3 but no longer maintained.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.

Feedback on the use of Biocham in applications, research or teaching are particularly welcomed on biocham@inria.fr

Demonstrations

• short tutorial notebook (presented at aSSB 2018)

• Demonstration video (with comments in French) and associated jupyter notebook online doctor in the cell

• historical tutorial notebook (presented at CMSB 2017).

• Jupyter notebook with Biocham kernel (http://lifeware.inria.fr/biocham4/online/) to try the other examples or upload your own ones on our server.

Documentation

• Reference manual in html

Unique features

Biocham implements some unique features for:

• synthesizing reaction systems from mathematical specification of an input/output or time function [FLBP17cmsb][HFS20cmsb][HFS21cmsb]
• 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 [FS08tcs],
• 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] [FR08tcs],
• 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

• Jupyter notebook with Biocham kernel:

  • on Inria serverhttp://lifeware.inria.fr/biocham4/online/
  • on mybinder.org: https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.inria.fr%2Flifeware%2Fbiocham.git/develop

• docker images: https://gitlab.inria.fr/lifeware/biocham/container_registry.
  Launch with
  docker run -p 8888:8888 registry.gitlab.inria.fr/lifeware/biocham:[tag]
  You can add
  start.sh biocham --notebook --NotebookApp.token=''
  if you don't want token-based authentication.

• source files (warning, this currently fails on M1/M2 Macs): https://gitlab.inria.fr/lifeware/biocham.
  The installation then basically proceeds by using the Unix shell script
  ./install.sh

• Previous versions (for reproducible research):

  • on https://gitlab.inria.fr/lifeware/biocham since 2019
  • biocham4.1.9 online notebook for 2017-2019 publications
  • <biocham4.0.zip> for 2016-2017 publications
  • biocham3 for previous publications

Feedback and bug reports:

https://gitlab.inria.fr/lifeware/biocham/issues or mail to biocham@inria.fr