Gigabase: Synthetic Biology Cell Modeling Project
Developing a visual environment for designing and simulating virtual cells.
- Substrate, s.
- Metabolism converting substrate s into product p.
- Substrate and product transporter.
- DNA synthesis.
- Protein synthesis and degratation.
- Lipid synthesis.
The lipid membrane separates the inside of the cell from the outside environment, allowing for unequal substrate and product concentrations inside and outside the cell (s#in, p#in and s#ext, p#ext respectively). Each of the components is associated with a cellular process (e.g. molecule synthesis or substrate conversion), which is modeled by one or more differential equations. The proposed model describes an av- erage cell in a growing population of cells. Ordinary Differential Equations (ODEs) in this model describe the change of molecule concentrations in time.
