Saturday, February 12, 2011

Testing different modeling methods easily

The following Python code was tested on the ComK_ComS example file. It generates all possible modeling methods for connections ta1 and pp2, which are transcription regulation and protein production connections.

ta1 = tc_find("ta1")

pp2 = tc_find("pp2")

models1 = tc_listOfPossibleModels(ta1)

models2 = tc_listOfPossibleModels(pp2)

tc_multiplot(models2.length, models1.length)

for i in range(0,models1.length):

tc_substituteModel(ta1, tc_getString(models1,i))

for j in range(0,models2.length):

tc_substituteModel(pp2, tc_getString(models2,j))

m = tc_simulateDeterministic(0,100,100)

tc_plot(m, "sys" + str(i*j+1))

There are two different ways to model transcription regulation in the current TinkerCell repository. There are three different ways to model protein production in the current repository. So, there are 6 possible combinations. The following graphs were the output of the python code.

Tuesday, February 1, 2011

Operator sites

"Operator" has been added as a new part type. It has sub-families called "Activator Binding Site" and "Repressor Binding Site". An Inducible Promoter is defined as a combination of an Activator Binding Site and a Promoter part. A Repressible Promoter is defined as a combination of Repressor Binding Site and Promoter. Only one transcription factor is allowed to bind to a single operator site -- this makes modeling much more convenient, but it also makes sense physically.