IGEM:Imperial/2010/Modelling

Have a look at this link: Synthetic Biology (Spring2008): Computer Modelling Practicals

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.

TEV is used at both stages of amplification	At each stage of amplification a distinct protease is being used
TEV is used at both stages of amplification	At each stage of amplification a distinct protease is being used

Second attempt

Model improved to account for the enzymes (protease action)

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	?	?	?
production rate in B.sub	?	?	?	?