EdiGEM12 is the team from Edinburgh University taking part in the synthetic biology competition iGEM 2012. Part of EdiGEM's project is to implement the MtrCAB electron transfer system from Shewanella oneidensis in E. coli.
We model the electron transfer system in E.coli by using the stochastic, agent-based language Kappa and its implementation KaSim 3.0 (*). The whole process is divided into sub-processes which we try to model separately at first and combine at the end. The sub-processes can roughly be described in the following way:
1_TCA.ka // Glucose -> TCA cycle -> Quinol
2_NapC.ka // Quinol -> NapC
3_MtrABC.ka // NapC -> MtrA-> MtrB or Fe soluble
4_UFe.ka // MtrC -> Flavins -> Fe insoluble
5.ka // Combines 3. and 4.
The file "Electron Transfer - Process Description.pdf" contains a detailed description of the used information and assumptions in the modelling.
(*) More about Kappa and rule-based modelling can be found at http://kappalanguage.org/.