Automatically test Design Variations

By using the tc_substituteEmptyModel and tc_substituteOriginalModel, it is possible to systematically remove each regulation from a design and check the results. The python plugin that does just that produces the following result. The code is given below. 

In the example below the input-output relationship is tested as different regulations in a feed-forward network are pruned.

"""

category: Model Variations

name: Try Different Designs Automatically

descr: Try removing each individual regulation one at a time and see how that affects the model

menu: yes

icon: module.png

tool: no

"""

from tinkercell import *

def runAll(indep, start, end, nclusters=0):

    items = tc_allItems()

    listOfModules = []

    moduleNames = []

    for i in range(0, items.length):

        item = tc_getItem(items, i)

        if tc_getParent(item) == 0:

            submodels = tc_listOfPossibleModels(item)

            if submodels.length > 0:

                listOfModules.append(item)

                moduleNames.append(tc_getUniqueName(item))

    n = len(listOfModules)

    if n > 0:

        tc_multiplot(2, int(1+n/2))

        tc_showProgress("Explore design variations", 0)

        for i in range(0,n):

            tc_substituteEmptyModel(listOfModules[i])

            if indep.lower() == "time":

                m = tc_simulateDeterministic(start,end,100)

                tc_plot(m, moduleNames[i] + " removed")

            else:

                m = tc_steadyStateScan(indep, start,end,10)

                tc_plot(m, moduleNames[i] + " removed")

            tc_substituteOriginalModel(listOfModules[i])

            tc_showProgress("Explore design variations", int(100*(i+1)/n))

        tc_showProgress("Explore design variations", 100)

        if nclusters > 1:

            m = tc_clusterPlots(nclusters)

            fout = open("designs.txt","w")

            for i in range(0, nclusters):

                s = "========\nCluster " + str(i+1) + "\n========\n"

                for j in range(0, n):

                    if tc_getMatrixValue(m, j, 0) == i+1:

                        s += " ,  " + moduleNames[j]

                        s += "\n"

                    s += "\n"

                fout.write(s)

            fout.close()

            tc_openUrl("designs.txt")

    else:

        if indep.lower() == "time":

            m = tc_simulateDeterministic(start,end,100)

            tc_plot(m, "steady state scan")

        else:

            m = tc_steadyStateScan(indep, start,end,10)

            tc_plot(m, "simulation")

    return

params = tc_getParametersAndFixedVariables(tc_allItems())

list = fromTC(params.rownames)

list.insert(0,"Time")

inputWindow = tc_createMatrix(3, 1)

tc_setMatrixValue(inputWindow, 0, 0, 0)

tc_setMatrixValue(inputWindow, 1, 0, 0.0)

tc_setMatrixValue(inputWindow, 2, 0, 200.0)

tc_setMatrixValue(inputWindow, 3, 0, 4)

tc_setRowName(inputWindow, 0, "Independent variable")

tc_setRowName(inputWindow, 1, "Start")

tc_setRowName(inputWindow, 2, "Stop")

tc_setRowName(inputWindow, 3, "Clusters")

tc_createInputWindowForScript(inputWindow, "Explore design variations", "runAll")

tc_addInputWindowOptions("Explore design variations", 0, 0, toTC(list))