Chemical Reaction Networks

Neil Dalchau, Andrew Phillips, Colin Gravill
Jan 1, 2013
crn-engine

Chemical Reaction Networks Engine (CRN-Engine) is an open source repository that enables programming and analysis of (bio)chemical systems.

The implementation for several domain-specific programming languages (DSLs) are included, and have been published previously in web tools and the scientific literature:

The languages compile to chemical reaction networks, which is a mathematical object that defines parameterised chemical systems. Several analysis methods are provided, which can be applied to all CRN-compatible languages:

  • Stochastic simulation (Gillespie’s Direct Method)
  • Moment closure techniques (Approximate simulation of stochastic dynamics)
  • Integration of the chemical master equation
  • Satisfiability analysis for stable systems, using the Z3 theorem prover
  • Parameter inference from observation data, using Markov chain Monte Carlo (MCMC).
Dynamical Systems DNA Computing Synthetic Biology
Neil Dalchau

Mathematical and computational biologist

Andrew Phillips

Innovator and leader in molecular and genetic programming

Colin Gravill

Software Developer