The Biochemical Abstract Machine BIOCHAM 4

version 4.4.15 October 2020

EP Lifeware, Inria Saclay - Ile de France
http://lifeware.inria.fr/biocham4/
https://gitlab.inria.fr/lifeware/biocham
developpers mailing list: biocham@inria.fr

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 For the sake of reproducible research, Biocham 3 is still active on http://lifeware.inria.fr/biocham3 but no longer maintained.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

• 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).


• Online Jupyter notebook with Biocham kernel 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:

• 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 in Mocassin for importing Matlab models in SBML),
• 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].
• 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],
• synthesizing reaction systems for executing imperative programs or computing real functions presented as solutions of polynomial initial value problems (PIVPs) [FLBP17cmsb],

Download, Installation and Online Notebook Servers

• source files:  https://gitlab.inria.fr/lifeware/biocham.
  The installation then basically proceeds by using the Unix shell script
  ./install.sh


• 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.


• Jupyter notebook with Biocham kernel:
  http://lifeware.inria.fr/biocham4/online/ on mybinder.org: .


• Previous versions (for reproducible research):
  • 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