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	:'''2. Optimization of parameters'''		:'''2. Optimization of parameters'''
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		+	Now we have an idea of which parameters affect the response the most. But we don't know which value of the range is represnts the behave od the system.
	:'''3.Screening'''		:'''3.Screening'''

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Revision as of 19:51, 21 September 2012

Team Colombia @ 2012 iGEM

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Parameters of the equations

When we want to model a biological process, it is necessary to write the differential equation that model the system which requires a number of constants. If the real value for the constants are unknown, the system can not have any biological sense. These entries are called parameters and they are crucial elements in the mathematical model made in this project.

There are three possible ways to find this parameters:

i) Literature. There are a lot of studies trying to find biological parameters, such as basal rate of protein production, kinetic constants, Monod's constants, etc. Moreover, there are so many biological systems and only a few of them have been characterized. Thus, it is difficult to find the parameters that are needed.

ii) Experimental way. If an experiment is made using the biological system of interest, it is possible to find the parameters for the equations that models the whole system. For this project, it was necessary to model the biological system first. Thus, experiments couldn't be performed to find the constant for the differential equations.

iii) Screening of parameters. Sometimes we don't have the exact number that we need, but we have a range where it could be or the parameter for a similar biological system, then we can perfom a screening of parameter, where we try to find the value that perfectly fits the reponse of our circuit.

How did we do it?

For our biological system we use options i) and iii). In the literature it was possible to find the parameters for the complete CI activation box and for the rest of values we found an aproximately range where they could be, so we proceeded to step iii).

Once the ranges of the parameters was set, we proceed to do the screening. We tried a lot of techniques and most of the failed, here we present the steps of the succesful one:

1.Sensitivity Analysis

2. Optimization of parameters

Now we have an idea of which parameters affect the response the most. But we don't know which value of the range is represnts the behave od the system.

3.Screening