CompBioMed Software – Visual GEC

Software Project
Visual GEC is a software tool for designing engineered cells and simulating biochemical interactions. The Genetic Engineering of Cells (GEC) software, developed by the Biological Computation team at Microsoft Research (Cambridge, UK), is a modelling tool that can be used to design and simulate synthetic genetic circuits. At the core is a domain-specific programming language for biochemical systems (LBS), originally developed at the University of Edinburgh. The tool supports stochastic and deterministic simulation of the temporal dynamics of chemical reaction networks, but also spatio-temporal dynamics via reaction-diffusion equations. Parameter inference can also be performed using Metropolis-Hastings Markov chain Monte Carlo with time-series data.

Offered By



Use scenario
Synthetic biology, Computational biology.

HPC motivation
Parameter inference, Stochastic simulation, Deterministic simulation, Reaction-diffusion simulation.

Relevant links

Related Articles

  • Pedersen, M., & Phillips, A. (2009). Towards programming languages for genetic engineering of living cells. Journal of the Royal Society Interface, rsif-2008.
  • Pedersen, M., & Plotkin, G. D. (2010). A language for biochemical systems: design and formal specification. In Transactions on computational systems biology XII (pp. 77-145). Springer, Berlin, Heidelberg.
  • Dalchau, N., Smith, M. J., Martin, S., Brown, J. R., Emmott, S., & Phillips, A. (2012). Towards the rational design of synthetic cells with prescribed population dynamics. Journal of the Royal Society Interface, 9(76), 2883-2898.
  • Yordanov, B., Dalchau, N., Grant, P. K., Pedersen, M., Emmott, S., Haseloff, J., & Phillips, A. (2014). A computational method for automated characterization of genetic components. ACS synthetic biology, 3(8), 578-588.