A Case Study in Model-driven Synthetic Biology

A Case Study in Model-driven Synthetic Biology

Model Status

Reproduces results as placed online by the iGEM07 Glasgow team, as at February 2007. Unit formulation here is such that the equations are dimensionally consistent.

Model Structure

This model is a Cellml version of the Glasgow team's award-winning entry into iGEM07. Details of their formulation and model output can be found here.

Here the Cellml aims to reproduce the original equations as faithfully as possible. As such, this is not described using 'standard parts' Cellml. At the time of writing, standard parts Cellml is under development.

Some modularity considerations have been observed. The basic architecture of the model has been broken up into four main components. One for each 'device' or promoter-to-double terminator DNA segment, and one for each 'bioenvironment' centered on a specific reaction (TFS association in one case, PYO formation from PCA in another). Degradation reactions are housed in the appropriate BioEnvironment component.

The component architecture of the Cellml formulation.

This Cellml formulation could be easily extended in at least two ways: (1) Use Cellml 1.1 functionality and place the separate components in different files via imports. (2) Tease apart the Bioenvironment components into species-specific components. At the moment, there is no reason to do this but it would make the model more extensible.

Model Curation
  • Curation Status c3
  • JSim c0
  • COR c3
  • OpenCell c0
Derived from workspace Gilbert, Heiner, Rosser, Fulton, Gu, Trybilo, 2007 at changeset fae19ce2621b.
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This work is licensed under a Creative Commons Attribution 3.0 Unported License.