Sample python script for doing perturbation experiments

# we are just going to change all the parameters that begin with the phrase 'synthconst'

items = tc_allItems()

params = tc_getParameters(items)

p = ""   #parameter name

#just count how many there are

total = 0  

for i in range(0,params.rows):

    p = tc_getRowName(params, i)

    if p.count('synthconst') > 0:

    total += 1

#for each parameter

j = 0

for i in range(0,params.rows):

    p = tc_getRowName(params, i)

    if p.count('synthconst') > 0:   #check parameter name

        tc_showProgress("DREAM automation", int((100.0 * j)/total))  #progress meter

        j += 1

        #perturb

        s = ""

        FILE = open(p + '.perturb.txt','w+')  #save to file

        p0 = tc_getMatrixValue(params, i, 0)  #original parameter value

        for q in [100, 10, 2, 1]:        #perturbations

            tc_setMatrixValue(params, i, 0, p0/q)

            tc_setParameters(params,0)

            m = tc_getSteadyState() #steady state

            s += str(p0/q)

            for i in range(0,m.rows):  #for each output value

                if tc_getRowName(m,i).count('m') > 0: #if name starts with m

                    s += "\t"

                    s += str(tc_getMatrixValue(m, i, 0))

                    s += "\n"

            FILE.write(s)

            FILE.close()

#done

tc_showProgress("DREAM automation", 100)  #close progress meter