Biochemical Space language software tool

Systems biology provides multiple formalisms for modelling of biochemical processes among which rule-based approach seems to be one of the most suitable as it allows compact mechanistic description of complex processes. The rule-based language called Biochemical Space Language (BCSL) combines advantages of different approaches and makes thus an effort to overcome several problems of existing solutions. BCSgen is a software providing basic functionality to write, maintain, and analyse models written in BCSL.

BCSL is a part of a general framework developed for comprehensive modelling in systems biology. BCSL relies on the formal basis of the rule-based methodology while preserving user-friendly syntax of plain chemical equations. BCSL combines the following aspects:

  • human-readability improving user-friendly usability of the language,
  • executability allowing unique formal analysis and consistency checking at the level of the language,
  • universality allowing integration of different biochemical mechanisms,
  • scalability and compactness of the specification,
  • hierarchical specification and composability of chemical entities,
  • support for genome-scale annotation.

The key features of the Biochemical Space Language software tool (BSCgen) are:

  • Interactive editor - create and load models, which can be edited with automatic syntax highlighting and errors reporting.
  • Transition system analysis - it is possible to generate transition system for a given model and consequently analyse it (e.g. perform reachability analysis).
  • Simulation - a model with defined kinetic rates can be simulated in particular setting using either deterministic or stochastic approach.
  • Visualisation - simulated data can be visualised in a interactive plot chart and transition systems can be view in a web-based visualisation for exploration of whole space.