Thursday, April 7, 2011

Trying different versions of a model

From Python or Octave, it is relatively simple to try different versions of the same network architecture. For example, the diagram below shows a protein regulating itself. The regulation type is "transcription regulation", i.e. it does not specify whether it is positive or negative regulation. The code below the figure simulates both positive and negative feedback using the tc_substituteModel command.

j = tc_find("tr1")

file1 = "/home/deepak/Documents/TinkerCell/Modules/transcription_activation/Equilibrium_Model.tic"

file2 = "/home/deepak/Documents/TinkerCell/Modules/transcription_repression/Equilibrium_Model.tic"


tc_substituteModel(j, file1)

m1 = tc_simulateDeterministic(0,100,100)

tc_plot(m1, "using file 1")

tc_substituteModel(j, file2)

m2 = tc_simulateDeterministic(0,100,100)

tc_plot(m2, "using file 2")

It is also possible to practically remove a component from the model by substituting "empty" for the model, e.g. tc_substituteModel(j, "empty")

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