IGEM:Imperial/2010/Modelling
Have a look at this link: Synthetic Biology (Spring2008): Computer Modelling Practicals
Have a look at Cell Designer to easily generate images of the system.
Example on how Valencia 2006 team used SimulLink to simulate their project: Valencia 2006 PowerPoint presentation
Output amplification model
First attempt
Is it better to use TEV all the way or HIV1? Modelling should allows us to take decision which design is more efficient. If taken further, it will allow us to determine number of amplification steps that are most favourable.
Second attempt
Kinetic constants
Quality | GFP | TEV | split TEV | split GFP |
---|---|---|---|---|
Km and Kcat | Doesn't apply | TEV constants (Km and kcat) | 40% of whole TEV | Doesn't apply |
half-life or degradation rate | Half-life of GFP in Bacillus = 1.5 hours - ref. Chris | ? | ? | Half-life shorter than GFP |
production rate in B.sub | ? | ? | ? | ? |
Conclusions
We couldn't obtain all the necessary constants. Hence, we decided to make educated guesses about possible relative values between the constants as well as varying them and observing the change in output.
As the result, we concluded that the amplification happens at each amplification level proposed. It's magnitude varies depending on the constants. There doesn’t seem to be much difference in substitution of TEV with HIV1.