Thursday, April 21, 2011
by Herbert M Sauro
published at analogmachine.org
318 pages, 94 illustrations and 75 exercises
This new monograph introduces students to basic reaction kinetics, including enzyme kinetics, cooperativity, allostery and gene regulatory kinetics. The text introduces a number of modern concepts such as generalized rate laws, elasticities and systems biology thermodynamic quantities. The text is suitable for junior undergraduate level in the US and 2nd year undergraduates in the UK. The text can also be used as a reference text for graduates and other researchers. Click here for the Google books preview.
Tuesday, April 19, 2011
The simulation tools now display an animated "fire" on top of items after a simulation. The purpose of the fire is to highlight upregulated and downregulated molecules. The size of the fire is proportional to the final output in the simulation.
Saturday, April 16, 2011
Events can be inserted using the clock icon in the "Inputs" tab at the top. The events table is stored as part of the "global item", which can be accessed in the command-line using "_". The clock icon can be used to edit the Events. In this screenshot, an event is used with the toggle-switch model to try to switch the toggle-switch from one state to the other (didn't work in this model, because the states are quite robust).
Wednesday, April 13, 2011
A user can write any Python function and optimize it using CrossEntropy. Here is template code:
#objective function for CrossEntropy
error = 0.0
#do something here, e.g. call tc_getSteadyState or tc_simulateDeterministic
minimize = False
maxruns = 100
numPoints = 100
title = "My Optimization Function"
result = CrossEntropy.OptimizeParameters(FitFormula_Objective, title, maxruns, numPoints, minimize)
mu = result
sigma = result
paramnames = result
CrossEntropy.DoPCA(mu, sigma, paramnames)
#set the optimized parameters in the model if you want
n = len(mu)
params = tc_createMatrix(n, 1)
for i in range(0,n):
tc_setMatrixValue(params, i, 0, mu[i])
tc_setRowName(params, i, paramnames[i])
CrossEntropy.DoPCA will generate a summary file such as the one below.
Thursday, April 7, 2011
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"
m1 = tc_simulateDeterministic(0,100,100)
tc_plot(m1, "using file 1")
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")