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Hw-1-pPro-ref-steady-state.py
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Hw-1-pPro-ref-steady-state.py
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# -*- coding: utf-8 -*-
"""
Created on Thu Apr 09 08:30:18 2015
@author: Raandrew
"""
import tellurium as te
import math
def simulate(antModelStr, constants):
rr = te.loada(antModelStr.format(**constants))
rr.simulate(0, 800000, 100)
rr.plot()
print "P =", rr.P
kinittxn = 0.12
kpol = 25.0
ORF = 678.0
kinittrans = 2.0
ktrans = 21.0
kobsminus = 0 / 60
kobsplus = 0 / 60
kfold = 0;
RNAthalf = (1.2 * 60)
Proteinthalf = (72.0 * (60 * 60))
d = 250
k1 = 0.12
k2 = (math.log(2) / (0.5 * (d / kpol)))
k3 = (math.log(2) / (0.5 * (d / kpol)))
k4 = (math.log(2) / (0.5 * 1200))
k5 = (math.log(2) / (0.5 * (d / ktrans)))
k6 = (kfold)
k7 = (kobsminus)
k8 = (kobsplus)
k9 = (math.log(2) / RNAthalf)
k10 = (0.1745 * k9)
k11 = (math.log(2) / Proteinthalf)
constants = {'k1': str(k1), 'k2': str(k2), 'k3': str(k3), 'k4': str(k4),
'k5': str(k5), 'k6': str(k6), 'k7': str(k7), 'k8': str(k8), 'k9': str(k9),
'k10': str(k10), 'k11': str(k11)}
antModel = """
-> I; k1
I -> Uppp; k2 * I
Uppp -> Rppp; k3 * Uppp
UOH -> ROH; k3 * UOH
Upppf ->Rpppf; k3 * Upppf
Uppp -> Uppp + T; k4 * Uppp
Upppf -> Upppf + T; k4 * Upppf
UOH -> UOH + T; k4 * UOH
Rppp -> Rppp + T; k4 * Rppp
Rpppf -> Rpppf + T; k4 * Rpppf
ROH -> ROH + T; k4 * ROH
T -> P; k5 * T
Uppp -> Upppf; k6 * Uppp
Upppf -> UOH; k7 * Upppf
Upppf -> UOH; k8 * Upppf
Rppp -> Rpppf; k6 * Rppp
Rpppf -> ROH; k7 * Rpppf
Rpppf -> ROH; k8 * Rpppf
Uppp -> ; k9 * Uppp
Upppf -> ; k9 * Upppf
Rppp -> ; k9 * Rppp
Rpppf -> ; k9 * Rpppf
UOH -> ; k10 * UOH
ROH -> ; k10 * ROH
P -> ; k11 * P
I = 0;
Uppp = 0;
Upppf = 0;
Rppp = 0;
Rpppf = 0;
UOH = 0;
ROH = 0;
P = 0;
k1 = {k1}; k2 = {k2}; k3 = {k3}; k4 = {k4}; k5 = {k5};
k6 = {k6}; k7 = {k7}; k8 = {k8}; k9 = {k9}; k10 = {k10};
k11 = {k11}"""
simulate(antModel, constants)