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Computational Modelling

The modelling in our 2009 iGEM project, BacMan, can be split into a number of sections - the Stochastic Switch, Degradation system, Metal Intake, Sporulation Tuning and Population Simulation. We are particularly proud of our Population Simulation Model as it combines distributed computing, agent based and cellular models.

For computational modelling, we are using a number of technologies, including Java, Matlab, Amazon EC2, Microbase, SBML and CellML.

Sub-projects

Stochastic Switch

See Stochastic Switch Model

We have modelled our stochastic switch.

We also designed an inducible protein degradation system for our switch.

See Degradation Model

Population Modelling

See Population Simulation

One of the models which we are producing is one concerning the population numbers of our bacteria. It looks at how our additions to the DNA may affect the growth of the bacterial population.

Sporulation Tuning

The KinA Expression model describes how KinA is expressed.

See KinA Expression Model

Building on the KinA Expression model, the phosphorelay is implented into our model, using the expression of KinA to induce sporulation.

See Sporulation Tuning Model

The Sin Operon model is used to repress sporulation, in view of making our model more realistic.

See Sin Operon Model

Metal Intake

See Metal Intake Model

Another of our models looks at metal intake. Specifically this looks at Cadmium transport throughout our bacteria.