#############################################################################
# #
# Model of Cerebellar Long-Term Depression #
# #
# developed by Gabriela Antunes #
# updated for STEPS 1.3 by Iain Hepburn and Cory Simon #
# #
#############################################################################
# WARNING: THIS SCRIPT RUNS ON STEPS 1.2 and higher.
# Please use file ltd.py if you are using earlier versions of STEPS
# The reactions described in this script have the same identities and are presented in the same order
# as the reactions described in Supplementary Table I.
# Note, however, that some species might be represented by slightly different names.
import datetime
import steps.model as smodel
import math
import sys
import numpy
import numpy as np
from numpy import mean
import steps.solver as swmdirect
import steps.geom as swm
import steps.rng as srng
from pylab import*
DT = 0.05 # time step
INT = 3600 # final time (s) simulated
NITER = 2 # number of runs used to calculate the mean
tinit = 600 # initial time that will be discharged. The initial 10 minutes of all simulations should be discharged to allow the model to reach equilibrium.
# Avogadro constant
Na = 6.02214129e23
########################################################################
# Ca2+ pulse. IMPORTANT: the duration and amplitude of the pulse should be checked directly in the Ca2+ concentration
# The changes in [Ca2+] generated by the pulses are highly stochastic
# altering max_molar alters the maximum molar concentration per second injection (M/s)
# cntr defines the time the pulse is at maximum (s)
# FW100M defines the full-width 100th maximum of the Gaussian (s)
def gaussian_ica(t,max_molar=40.0e-6/0.05,cntr=1200.0,FW100M=3):
c = FW100M/(2*math.sqrt(2*math.log(100)))
return max_molar*np.exp(-(((t-cntr)**2)/(2*c**2)))
########################################################################
def gen_model():
mdl=smodel.Model()
Ca = smodel.Spec('Ca', mdl)
PMCA = smodel.Spec('PMCA', mdl)
Ca1PMCA = smodel.Spec('Ca1PMCA', mdl)
NCX = smodel.Spec('NCX', mdl)
Ca1NCX = smodel.Spec('Ca1NCX', mdl)
Ca2NCX = smodel.Spec('Ca2NCX', mdl)
SERCA = smodel.Spec('SERCA', mdl)
Ca1SERCA = smodel.Spec('Ca1SERCA', mdl)
Ca2SERCA = smodel.Spec('Ca2SERCA', mdl)
PV = smodel.Spec('PV', mdl)
MgPV = smodel.Spec('MgPV', mdl)
CaPV = smodel.Spec('CaPV', mdl)
Mg2PV = smodel.Spec('Mg2PV', mdl)
Ca2PV = smodel.Spec('Ca2PV', mdl)
CBf = smodel.Spec('CBf', mdl)
CaCBf = smodel.Spec('CaCBf', mdl)
Ca2CBf = smodel.Spec('Ca2CBf', mdl)
CBs = smodel.Spec('CBs', mdl)
CaCBs = smodel.Spec('CaCBs', mdl)
Ca2CBs = smodel.Spec('Ca2CBs', mdl)
PKC = smodel.Spec('PKC', mdl)
Ca1PKC = smodel.Spec('Ca1PKC', mdl)
Ca3PKC = smodel.Spec('Ca3PKC', mdl)
AAPKC = smodel.Spec('AAPKC', mdl)
AACa1PKC = smodel.Spec('AACa1PKC', mdl)
AACa3PKC = smodel.Spec('AACa3PKC', mdl)
PKCstar = smodel.Spec('PKCstar', mdl)
PKCstar2 = smodel.Spec('PKCstar2', mdl)
PKCstar4 = smodel.Spec('PKCstar4', mdl)
PKCstar3 = smodel.Spec('PKCstar3', mdl)
Rafact = smodel.Spec('Rafact', mdl)
PKCstarRafact = smodel.Spec('PKCstarRafact', mdl)
PKCstar2Rafact = smodel.Spec('PKCstar2Rafact', mdl)
PKCstar3Rafact = smodel.Spec('PKCstar3Rafact', mdl)
PKCstar4Rafact = smodel.Spec('PKCstar4Rafact', mdl)
Rafactstar = smodel.Spec('Rafactstar', mdl)
Raf = smodel.Spec('Raf', mdl)
RafactstarRaf = smodel.Spec('RafactstarRaf', mdl)
Rafstar = smodel.Spec('Rafstar', mdl)
PP5 = smodel.Spec('PP5', mdl)
PP5Rafstar = smodel.Spec('PP5Rafstar', mdl)
MEK = smodel.Spec('MEK', mdl)
RafstarMEK = smodel.Spec('RafstarMEK', mdl)
MEKp = smodel.Spec('MEKp', mdl)
PP2A = smodel.Spec('PP2A', mdl)
PP2AMEKp = smodel.Spec('PP2AMEKp', mdl)
RafstarMEKp = smodel.Spec('RafstarMEKp', mdl)
MEKstar = smodel.Spec('MEKstar', mdl)
PP2AMEKstar = smodel.Spec('PP2AMEKstar', mdl)
ERK = smodel.Spec('ERK', mdl)
MEKstarERK = smodel.Spec('MEKstarERK', mdl)
ERKp = smodel.Spec('ERKp', mdl)
MKP = smodel.Spec('MKP', mdl)
MKPERKp = smodel.Spec('MKPERKp', mdl)
MEKstarERKp = smodel.Spec('MEKstarERKp', mdl)
ERKstar = smodel.Spec('ERKstar', mdl)
MKPERKstar = smodel.Spec('MKPERKstar', mdl)
PLA2 = smodel.Spec('PLA2', mdl)
Ca1PLA2 = smodel.Spec('Ca1PLA2', mdl)
Ca2PLA2 = smodel.Spec('Ca2PLA2', mdl)
PLA2memb = smodel.Spec('PLA2memb', mdl)
Ca1PLA2memb = smodel.Spec('Ca1PLA2memb', mdl)
PLA2star1 = smodel.Spec('PLA2star1', mdl)
ERKstarPLA2 = smodel.Spec('ERKstarPLA2', mdl)
PLA2star2 = smodel.Spec('PLA2star2', mdl)
Ca1PLA2star2 = smodel.Spec('Ca1PLA2star2', mdl)
Ca2PLA2star2 = smodel.Spec('Ca2PLA2star2', mdl)
PLA2star2memb = smodel.Spec('PLA2star2memb', mdl)
Ca1PLA2star2memb = smodel.Spec('Ca1PLA2star2memb', mdl)
Ca2PLA2star2memb = smodel.Spec('Ca2PLA2star2memb', mdl)
PLA2star1APC = smodel.Spec('PLA2star1APC', mdl)
ERKstarCa1PLA2 = smodel.Spec('ERKstarCa1PLA2', mdl)
ERKstarCa2PLA2 = smodel.Spec('ERKstarCa2PLA2', mdl)
PP2ACa1PLA2star2 = smodel.Spec('PP2ACa1PLA2star2', mdl)
PP2ACa2PLA2star2 = smodel.Spec('PP2ACa2PLA2star2', mdl)
PP1Ca1PLA2star2 = smodel.Spec('PP1Ca1PLA2star2', mdl)
PP1Ca2PLA2star2 = smodel.Spec('PP1Ca2PLA2star2', mdl)
PLA2star2membAPC = smodel.Spec('PLA2star2membAPC', mdl)
Ca1PLA2star2membAPC = smodel.Spec('Ca1PLA2star2membAPC', mdl)
Ca2PLA2star2membAPC = smodel.Spec('Ca2PLA2star2membAPC', mdl)
PP1 = smodel.Spec('PP1', mdl)
PP1PLA2star2 = smodel.Spec('PP1PLA2star2', mdl)
PP2APLA2star2 = smodel.Spec('PP2APLA2star2', mdl)
AA = smodel.Spec('AA', mdl)
AMPAR = smodel.Spec('AMPAR', mdl)
PKCstarAMPAR = smodel.Spec('PKCstarAMPAR', mdl)
PKCstar2AMPAR = smodel.Spec('PKCstar2AMPAR', mdl)
PKCstar4AMPAR = smodel.Spec('PKCstar4AMPAR', mdl)
PKCstar3AMPAR = smodel.Spec('PKCstar3AMPAR', mdl)
AMPAR_P = smodel.Spec('AMPAR_P', mdl)
PP2AAMPAR_P = smodel.Spec('PP2AAMPAR_P', mdl)
AMPARextra = smodel.Spec('AMPARextra', mdl)
AMPARextra_P = smodel.Spec('AMPARextra_P', mdl)
PP2AAMPARextra_P = smodel.Spec('PP2AAMPARextra_P', mdl)
GRIP = smodel.Spec('GRIP', mdl)
GRIPAMPAR = smodel.Spec('GRIPAMPAR', mdl)
GRIPAMPAR_P = smodel.Spec('GRIPAMPAR_P', mdl)
AMPARdend = smodel.Spec('AMPARdend', mdl)
AMPARdend_P = smodel.Spec('AMPARdend_P', mdl)
PP2AAMPARdend_P = smodel.Spec('PP2AAMPARdend_P', mdl)
AMPARcyt = smodel.Spec('AMPARcyt', mdl)
AMPARcyt_P = smodel.Spec('AMPARcyt_P', mdl)
PP2AAMPARcyt_P = smodel.Spec('PP2AAMPARcyt_P', mdl)
extra = smodel.Volsys('extra', mdl)
vsys = smodel.Volsys('vsys', mdl)
s = smodel.Surfsys('memb', mdl)
ERs = smodel.Surfsys('ERmemb', mdl)
cytER = smodel.Volsys('cytER', mdl)
########################################################################
########################################################################
# Reactions
# Ca influx (Ca = calcium)
CainfluxR = smodel.Reac('Cainflux', vsys, rhs=[Ca])
# reaction constant for zero-order reaction units M/s in STEPS 1.2 and above
CainfluxR.kcst = 0.0
# Ca + PMCA <-> Ca1PMCA -> PMCA
Reac1 = smodel.SReac('pump2_f', s, ilhs = [Ca], slhs = [PMCA], srhs = [Ca1PMCA])
Reac1.kcst = 25000e6
Reac2 = smodel.SReac('Reac2', s, slhs = [Ca1PMCA], irhs = [Ca], srhs = [PMCA])
Reac2.kcst = 2000
Reac3 = smodel.SReac('Reac3', s, slhs = [Ca1PMCA], srhs = [PMCA])
Reac3.kcst = 500
# Ca + NCX <-> Ca1NCX + Ca <-> Ca2NCX -> NCX
Reac4 = smodel.SReac('Reac4', s, ilhs = [Ca], slhs = [NCX], srhs = [Ca1NCX])
Reac4.kcst = 93.827e6
Reac5 = smodel.SReac('Reac5', s, slhs = [Ca1NCX], irhs = [Ca], srhs = [NCX])
Reac5.kcst = 612.6
Reac6 = smodel.SReac('Reac6', s, ilhs = [Ca], slhs = [Ca1NCX], srhs = [Ca2NCX])
Reac6.kcst = 93.827e6
Reac7 = smodel.SReac('Reac7', s, slhs = [Ca2NCX], irhs = [Ca], srhs = [Ca1NCX])
Reac7.kcst = 612.6
Reac8 = smodel.SReac('Reac8', s, slhs = [Ca2NCX], srhs = [NCX])
Reac8.kcst = 1000
# Ca + SERCA <-> Ca1SERCA +Ca <-> Ca2SERCA -> SERCA
Reac9 = smodel.SReac('Reac9', ERs, olhs = [Ca], slhs = [SERCA], srhs = [Ca1SERCA])
Reac9.kcst = 17147e6
Reac10 = smodel.SReac('Reac10', ERs, slhs = [Ca1SERCA], orhs = [Ca], srhs = [SERCA])
Reac10.kcst = 8426.3
Reac11 = smodel.SReac('Reac11', ERs, olhs = [Ca], slhs = [Ca1SERCA], srhs = [Ca2SERCA])
Reac11.kcst = 17147e6
Reac12 = smodel.SReac('Reac12', ERs, slhs = [Ca2SERCA], orhs = [Ca], srhs = [Ca1SERCA])
Reac12.kcst = 8426.3
Reac13 = smodel.SReac('Reac13', ERs, slhs = [Ca2SERCA], srhs = [SERCA], irhs = [Ca,Ca])
Reac13.kcst = 250
# Leak
Reac14 = smodel.Reac('Reac14', vsys, rhs = [Ca])
# reaction constant for zero-order reaction units M/s in STEPS 1.2 and above
Reac14.kcst = 1900/(Na*0.08e-15)
# PV + Ca <-> CaPV + Ca <-> Ca2PV
Reac15 = smodel.Reac('Reac15', vsys, lhs = [PV, Ca], rhs = [CaPV])
Reac15.kcst = 107e6
Reac16 = smodel.Reac('Reac16', vsys, lhs = [CaPV], rhs = [PV, Ca])
Reac16.kcst = 0.95
Reac17 = smodel.Reac('Reac17', vsys, lhs = [CaPV, Ca], rhs = [Ca2PV])
Reac17.kcst = 107e6
Reac18 = smodel.Reac('Reac18', vsys, lhs = [Ca2PV], rhs = [Ca, CaPV])
Reac18.kcst = 0.95
# PV + Mg <-> MgPV <-> Mg2PV, apparent rate constants, [Mg] = 590uM
Reac19 = smodel.Reac('Reac19', vsys, lhs = [PV], rhs = [MgPV])
Reac19.kcst = 472
Reac20 = smodel.Reac('Reac20', vsys, lhs = [MgPV], rhs = [PV])
Reac20.kcst = 25
Reac21 = smodel.Reac('Reac21', vsys, lhs = [MgPV], rhs = [Mg2PV])
Reac21.kcst = 472
Reac22 = smodel.Reac('Reac22', vsys, lhs = [Mg2PV], rhs = [MgPV])
Reac22.kcst = 25
# CBs + Ca <-> CaCBs + Ca <-> Ca2CBs, CBs - high affinity site
Reac23 = smodel.Reac('Reac23', vsys, lhs = [CBs, Ca], rhs = [CaCBs])
Reac23.kcst = 5.5e6
Reac24 = smodel.Reac('Reac24', vsys, lhs = [CaCBs], rhs = [CBs, Ca])
Reac24.kcst = 2.6
Reac25 = smodel.Reac('Reac25', vsys, lhs = [CaCBs, Ca], rhs = [Ca2CBs])
Reac25.kcst = 5.5e6
Reac26 = smodel.Reac('Reac26', vsys, lhs = [Ca2CBs], rhs = [CaCBs, Ca])
Reac26.kcst = 2.6
# CBf + Ca <-> CaCBf + Ca <-> Ca2CBf, CBf - medium affinity site
Reac27 = smodel.Reac('Reac27', vsys, lhs = [CBf, Ca], rhs = [CaCBf])
Reac27.kcst = 43.5e6
Reac28 = smodel.Reac('Reac28', vsys, lhs = [CaCBf], rhs = [CBf, Ca])
Reac28.kcst = 35.8
Reac29 = smodel.Reac('Reac29', vsys, lhs = [CaCBf, Ca], rhs = [Ca2CBf])
Reac29.kcst = 43.5e6
Reac30 = smodel.Reac('Reac30', vsys, lhs = [Ca2CBf], rhs = [CaCBf, Ca])
Reac30.kcst = 35.8
# PKC + Ca <-> CaPKC + 2Ca <-> Ca3PKC <-> Ca3PKC* (PKCstar)
Reac31 = smodel.Reac('Reac31', vsys, lhs = [PKC, Ca], rhs = [Ca1PKC])
Reac31.kcst = 13.3e6
Reac32 = smodel.Reac('Reac32', vsys, lhs = [Ca1PKC], rhs = [PKC, Ca])
Reac32.kcst = 12
Reac33 = smodel.Reac('Reac33', vsys, lhs = [Ca1PKC, Ca, Ca], rhs = [Ca3PKC])
Reac33.kcst = 1.e12
Reac34 = smodel.Reac('Reac34', vsys, lhs = [Ca3PKC], rhs = [Ca1PKC, Ca, Ca])
Reac34.kcst = 12
Reac35 = smodel.SReac('Reac35', s, ilhs = [Ca3PKC], srhs = [PKCstar])
Reac35.kcst = 11.3
Reac36 = smodel.SReac('Reac36', s, slhs = [PKCstar], irhs = [Ca3PKC])
Reac36.kcst = 0.23
# PKC + AA <-> AAPKC <-> AAPKC* (PKCstar2)
Reac37 = smodel.Reac('Reac37', vsys, lhs = [PKC, AA], rhs = [AAPKC])
Reac37.kcst = 1e6
Reac38 = smodel.Reac('Reac38', vsys, lhs = [AAPKC], rhs = [PKC, AA])
Reac38.kcst = 10
Reac39 = smodel.SReac('Reac39', s, ilhs = [AAPKC], srhs = [PKCstar2])
Reac39.kcst = 0.017
Reac40 = smodel.SReac('Reac40', s, slhs = [PKCstar2], irhs = [AAPKC])
Reac40.kcst = 0.0055
# Ca1PKC + AA <-> AACa1PKC <-> AACa1PKC* (PKCstar3) + 2Ca <-> AACa3PKC* (PKCstar4)
Reac41 = smodel.Reac('Reac41', vsys, lhs = [Ca1PKC, AA], rhs = [AACa1PKC])
Reac41.kcst = 1e6
Reac42 = smodel.Reac('Reac42', vsys, lhs = [AACa1PKC], rhs = [Ca1PKC, AA])
Reac42.kcst = 10
Reac43 = smodel.SReac('Reac43', s, ilhs = [AACa1PKC], srhs = [PKCstar3])
Reac43.kcst = 0.017
Reac44 = smodel.SReac('Reac44', s, slhs = [PKCstar3], irhs = [AACa1PKC])
Reac44.kcst = 0.0055
Reac45 = smodel.SReac('Reac45', s, slhs = [PKCstar3], ilhs = [Ca, Ca], srhs = [PKCstar4])
Reac45.kcst = 1.0e12
Reac46 = smodel.SReac('Reac46', s, slhs = [PKCstar4], srhs = [PKCstar3], irhs = [Ca, Ca])
Reac46.kcst = 12
# AAPKC + Ca <-> AACa1PKC <-> AACa1PKC + 2Ca <-> AACa3PKC <-> AACa3PKC* (PKCstar4)
Reac47 = smodel.Reac('Reac47', vsys, lhs = [AAPKC, Ca], rhs = [AACa1PKC])
Reac47.kcst = 13.3e6
Reac48 = smodel.Reac('Reac48', vsys, lhs = [AACa1PKC], rhs = [AAPKC, Ca])
Reac48.kcst = 12
Reac49 = smodel.Reac('Reac49', vsys, lhs = [AACa1PKC, Ca, Ca], rhs = [AACa3PKC])
Reac49.kcst = 1.0e12
Reac50 = smodel.Reac('Reac50', vsys, lhs = [AACa3PKC], rhs = [AACa1PKC, Ca, Ca])
Reac50.kcst = 12
Reac51 = smodel.SReac('Reac51', s, ilhs = [AACa3PKC], srhs = [PKCstar4])
Reac51.kcst = 11.3
Reac52 = smodel.SReac('Reac52', s, slhs = [PKCstar4], irhs = [AACa3PKC])
Reac52.kcst = 0.23
# Ca3PKC + AA <-> AACa3PKC
Reac53 = smodel.Reac('Reac53', vsys, lhs = [Ca3PKC, AA], rhs = [AACa3PKC])
Reac53.kcst = 1e6
Reac54 = smodel.Reac('Reac54', vsys, lhs = [AACa3PKC], rhs = [Ca3PKC, AA])
Reac54.kcst = 10
# AAPKC* + Ca <-> AACa1PKC*
Reac55 = smodel.SReac('Reac55', s, slhs = [PKCstar2], ilhs = [Ca], srhs = [PKCstar3])
Reac55.kcst = 13.3e6
Reac56 = smodel.SReac('Reac56', s, slhs = [PKCstar3], srhs = [PKCstar2], irhs = [Ca])
Reac56.kcst = 12
# Ca3PKC* + AA <-> AACa3PKC*
Reac57 = smodel.SReac('Reac57', s, ilhs = [AA], slhs = [PKCstar], srhs = [PKCstar4])
Reac57.kcst = 1e6
Reac58 = smodel.SReac('Reac58', s, slhs = [PKCstar4], irhs = [AA], srhs = [PKCstar])
Reac58.kcst = 10
# Ca3PKC* + Rafact <-> Ca3PKC*.Rafact -> Ca3PKC* + Rafact* (Rafactstar)
Reac59 = smodel.SReac('Reac59', s, ilhs = [Rafact], slhs = [PKCstar], srhs = [PKCstarRafact])
Reac59.kcst = 5.80e6
Reac60 = smodel.SReac('Reac60', s, slhs = [PKCstarRafact], irhs = [Rafact], srhs = [PKCstar])
Reac60.kcst = 3.608
Reac61 = smodel.SReac('Reac61', s, slhs = [PKCstarRafact], srhs = [PKCstar], irhs = [Rafactstar])
Reac61.kcst = 4.7
# AAPKC* + Rafact <-> AAPKC*.Rafact -> AAPKC* + Rafact* (Rafactstar)
Reac62 = smodel.SReac('Reac62', s, ilhs = [Rafact], slhs = [PKCstar2], srhs = [PKCstar2Rafact])
Reac62.kcst = 5.80e6
Reac63 = smodel.SReac('Reac63', s, slhs = [PKCstar2Rafact], irhs = [Rafact], srhs = [PKCstar2])
Reac63.kcst = 3.608
Reac64 = smodel.SReac('Reac64', s, slhs = [PKCstar2Rafact], srhs = [PKCstar2], irhs = [Rafactstar])
Reac64.kcst = 4.7
# AACa1PKC* + Rafact <-> AACa1PKC*.Rafact -> AACa1PKC* + Rafact* (Rafactstar)
Reac65 = smodel.SReac('Reac65', s, ilhs = [Rafact], slhs = [PKCstar3], srhs = [PKCstar3Rafact])
Reac65.kcst = 5.80e6
Reac66 = smodel.SReac('Reac66', s, slhs = [PKCstar3Rafact], irhs = [Rafact], srhs = [PKCstar3])
Reac66.kcst = 3.608
Reac67 = smodel.SReac('Reac67', s, slhs = [PKCstar3Rafact], srhs = [PKCstar3], irhs = [Rafactstar])
Reac67.kcst = 4.7
# AACa3PKC* + Rafact <-> AACa3PKC*.Rafact -> AACa3PKC* + Rafact* (Rafactstar)
Reac68 = smodel.SReac('Reac68', s, ilhs = [Rafact], slhs = [PKCstar4], srhs = [PKCstar4Rafact])
Reac68.kcst = 5.80e6
Reac69 = smodel.SReac('Reac69', s, slhs = [PKCstar4Rafact], irhs = [Rafact], srhs = [PKCstar4])
Reac69.kcst = 3.608
Reac70 = smodel.SReac('Reac70', s, slhs = [PKCstar4Rafact], srhs = [PKCstar4], irhs = [Rafactstar])
Reac70.kcst = 4.7
# Rafact* -> Rafact, deactivation
Reac71 = smodel.Reac('Reac71', vsys, lhs = [Rafactstar], rhs = [Rafact])
Reac71.kcst = 1.
# Rafact* + Raf <-> Rafact*. Raf -> Rafact* + Raf* (Rafstar)
Reac72 = smodel.Reac('Reac72', vsys, lhs = [Rafactstar, Raf], rhs = [RafactstarRaf])
Reac72.kcst = 1e6
Reac73 = smodel.Reac('Reac73', vsys, lhs = [RafactstarRaf], rhs = [Rafactstar, Raf])
Reac73.kcst = 2
Reac74 = smodel.Reac('Reac74', vsys, lhs = [RafactstarRaf], rhs = [Rafactstar, Rafstar])
Reac74.kcst = 1.5
# PP5 (PP) + Raf* <-> PP5.Raf* -> PP5 + Raf
Reac75 = smodel.Reac('Reac75', vsys, lhs = [PP5, Rafstar], rhs = [PP5Rafstar])
Reac75.kcst = .55e6
Reac76 = smodel.Reac('Reac76', vsys, lhs = [PP5Rafstar], rhs = [PP5, Rafstar])
Reac76.kcst = 2
Reac77 = smodel.Reac('Reac77', vsys, lhs = [PP5Rafstar], rhs = [PP5, Raf])
Reac77.kcst = 0.5
# Raf* + MEK <-> Raf*.MEK -> Raf* + MEKp <->Raf*.MEKp -> Raf* + MEK* (MEKstar)
Reac78 = smodel.Reac('Reac78', vsys, lhs = [Rafstar, MEK], rhs = [RafstarMEK])
Reac78.kcst = 0.65e6
Reac79 = smodel.Reac('Reac79', vsys, lhs = [RafstarMEK], rhs = [Rafstar, MEK])
Reac79.kcst = 0.065
Reac80 = smodel.Reac('Reac80', vsys, lhs = [RafstarMEK], rhs = [Rafstar, MEKp])
Reac80.kcst = 1.0
Reac81 = smodel.Reac('Reac81', vsys, lhs = [Rafstar, MEKp], rhs = [RafstarMEKp])
Reac81.kcst = 0.65e6
Reac82 = smodel.Reac('Reac82', vsys, lhs = [RafstarMEKp], rhs = [Rafstar, MEKp])
Reac82.kcst = 0.065
Reac83 = smodel.Reac('Reac83', vsys, lhs = [RafstarMEKp], rhs = [Rafstar, MEKstar])
Reac83.kcst = 1.0
# PP2A + MEK* <-> PP2A.MEK* -> PP2A + MEKp <-> PP2A.MEKp -> PP2A + MEK
Reac84 = smodel.Reac('Reac84', vsys, lhs = [PP2A, MEKstar], rhs = [PP2AMEKstar])
Reac84.kcst = 0.75e6
Reac85 = smodel.Reac('Reac85', vsys, lhs = [PP2AMEKstar], rhs = [PP2A, MEKstar])
Reac85.kcst = 2
Reac86 = smodel.Reac('Reac86', vsys, lhs = [PP2AMEKstar], rhs = [PP2A, MEKp])
Reac86.kcst = 0.5
Reac87 = smodel.Reac('Reac87', vsys, lhs = [PP2A, MEKp], rhs = [PP2AMEKp])
Reac87.kcst = 0.75e6
Reac88 = smodel.Reac('Reac88', vsys, lhs = [PP2AMEKp], rhs = [PP2A, MEKp])
Reac88.kcst = 2
Reac89 = smodel.Reac('Reac89', vsys, lhs = [PP2AMEKp], rhs = [PP2A, MEK])
Reac89.kcst = 0.5
# MEK* + ERK <-> MEK*.ERK -> MEK* + ERKp <-> MEK*.ERKp -> MEK* + ERK* (ERKstar)
Reac90 = smodel.Reac('Reac90', vsys, lhs = [MEKstar, ERK], rhs = [MEKstarERK])
Reac90.kcst = 16.2e6
Reac91 = smodel.Reac('Reac91', vsys, lhs = [MEKstarERK], rhs = [MEKstar, ERK])
Reac91.kcst = 0.6
Reac92 = smodel.Reac('Reac92', vsys, lhs = [MEKstarERK], rhs = [MEKstar, ERKp])
Reac92.kcst = 0.15
Reac93 = smodel.Reac('Reac93', vsys, lhs = [MEKstar, ERKp], rhs = [MEKstarERKp])
Reac93.kcst = 16.2e6
Reac94 = smodel.Reac('Reac94', vsys, lhs = [MEKstarERKp], rhs = [MEKstar, ERKp])
Reac94.kcst = 0.6
Reac95 = smodel.Reac('Reac95', vsys, lhs = [MEKstarERKp], rhs = [MEKstar, ERKstar])
Reac95.kcst = 0.3
# MKP + ERK* <-> MKP.ERK* -> MKP + ERKp <-> MKP.ERKp -> MKP + ERK
Reac96 = smodel.Reac('Reac96', vsys, lhs = [MKP, ERKstar], rhs = [MKPERKstar])
Reac96.kcst = 13e6
Reac97 = smodel.Reac('Reac97', vsys, lhs = [MKPERKstar], rhs = [MKP, ERKstar])
Reac97.kcst = 0.396
Reac98 = smodel.Reac('Reac98', vsys, lhs = [MKPERKstar], rhs = [MKP, ERKp])
Reac98.kcst = 0.099
Reac99 = smodel.Reac('Reac99', vsys, lhs = [MKP, ERKp], rhs = [MKPERKp])
Reac99.kcst = 28e6
Reac100 = smodel.Reac('Reac100', vsys, lhs = [MKPERKp], rhs = [MKP, ERKp])
Reac100.kcst = 0.56
Reac101 = smodel.Reac('Reac101', vsys, lhs = [MKPERKp], rhs = [MKP, ERK])
Reac101.kcst = 0.14
# Ca + PLA2 <-> Ca1PLA2 + Ca <-> Ca2PLA2 <-> Ca2PLA2* (PLA2star1)
Reac102 = smodel.Reac('Reac102', vsys, lhs = [PLA2, Ca], rhs = [Ca1PLA2])
Reac102.kcst = 1.93e6
Reac103 = smodel.Reac('Reac103', vsys, lhs = [Ca1PLA2], rhs = [PLA2, Ca])
Reac103.kcst = 108
Reac104 = smodel.Reac('Reac104', vsys, lhs = [Ca, Ca1PLA2], rhs = [Ca2PLA2])
Reac104.kcst = 10.8e6
Reac105 = smodel.Reac('Reac105', vsys, lhs = [Ca2PLA2], rhs = [Ca1PLA2, Ca])
Reac105.kcst = 108
Reac106 = smodel.SReac('Reac106', s, ilhs = [Ca2PLA2], srhs = [PLA2star1])
Reac106.kcst = 300
Reac107 = smodel.SReac('Reac107', s, slhs = [PLA2star1], irhs = [Ca2PLA2])
Reac107.kcst = 15
# Ca1PLA2 <-> Ca1PLA2memb
Reac108 = smodel.SReac('Reac108', s, ilhs = [Ca1PLA2], srhs = [Ca1PLA2memb])
Reac108.kcst = 30
Reac109 = smodel.SReac('Reac109', s, slhs = [Ca1PLA2memb], irhs = [Ca1PLA2])
Reac109.kcst = 15
# PLA2 <-> PLA2memb
Reac110 = smodel.SReac('Reac110', s, ilhs = [PLA2], srhs = [PLA2memb])
Reac110.kcst = 3
Reac111 = smodel.SReac('Reac111', s, slhs = [PLA2memb], irhs = [PLA2])
Reac111.kcst = 15
# PLA2memb + Ca <-> Ca1PLA2memb + Ca <-> Ca2PLA2* (PLA2star1)
Reac112 = smodel.SReac('Reac112', s, slhs = [PLA2memb], ilhs = [Ca], srhs = [Ca1PLA2memb])
Reac112.kcst = 1.93e6
Reac113 = smodel.SReac('Reac113', s, ilhs = [Ca1PLA2memb], srhs = [PLA2memb], irhs = [Ca])
Reac113.kcst = 0.41
Reac114 = smodel.SReac('Reac114', s, slhs = [Ca1PLA2memb], ilhs = [Ca], srhs = [PLA2star1])
Reac114.kcst = 10.8e6
Reac115 = smodel.SReac('Reac115', s, ilhs = [PLA2star1], srhs = [Ca1PLA2memb], irhs = [Ca])
Reac115.kcst = 2.5
# PLA2star1 <-> PLA2star1APC -> PLA2star1 + AA
Reac116 = smodel.SReac('Reac116', s, slhs = [PLA2star1], srhs = [PLA2star1APC])
Reac116.kcst = 43
Reac117 = smodel.SReac('Reac117', s, slhs = [PLA2star1APC], srhs = [PLA2star1])
Reac117.kcst = 600
Reac118 = smodel.SReac('Reac118', s, slhs = [PLA2star1APC], irhs = [AA], srhs = [PLA2star1])
Reac118.kcst = 450
# ERK* + PLA2 <-> ERK*.PLA2 -> ERK* + PLA2p (PLA2star2)
Reac119 = smodel.Reac('Reac119', vsys, lhs = [ERKstar, PLA2], rhs = [ERKstarPLA2])
Reac119.kcst = 4e6
Reac120 = smodel.Reac('Reac120', vsys, lhs = [ERKstarPLA2], rhs = [ERKstar, PLA2])
Reac120.kcst = 1
Reac121 = smodel.Reac('Reac121', vsys, lhs = [ERKstarPLA2], rhs = [ERKstar, PLA2star2])
Reac121.kcst = 14
# ERK* + Ca1PLA2 <-> ERK*.Ca1PLA2 -> ERK* + Ca1PLA2p (Ca1PLA2star2)
Reac122 = smodel.Reac('Reac122', vsys, lhs = [ERKstar, Ca1PLA2], rhs = [ERKstarCa1PLA2])
Reac122.kcst = 4e6
Reac123 = smodel.Reac('Reac123', vsys, lhs = [ERKstarCa1PLA2], rhs = [ERKstar, Ca1PLA2])
Reac123.kcst = 1
Reac124 = smodel.Reac('Reac124', vsys, lhs = [ERKstarCa1PLA2], rhs = [ERKstar, Ca1PLA2star2])
Reac124.kcst = 14
# ERK* + Ca2PLA2 <-> ERK*.Ca2PLA2 -> ERK* + Ca2PLA2p (Ca2PLA2star2)
Reac125 = smodel.Reac('Reac125', vsys, lhs = [ERKstar, Ca2PLA2], rhs = [ERKstarCa2PLA2])
Reac125.kcst = 4e6
Reac126 = smodel.Reac('Reac126', vsys, lhs = [ERKstarCa2PLA2], rhs = [ERKstar, Ca2PLA2])
Reac126.kcst = 1
Reac127 = smodel.Reac('Reac127', vsys, lhs = [ERKstarCa2PLA2], rhs = [ERKstar, Ca2PLA2star2])
Reac127.kcst = 14
# PP2A + PLA2p <-> PP2A.PLA2p -> PP2A + PLA2
Reac128 = smodel.Reac('Reac128', vsys, lhs = [PP2A, PLA2star2], rhs = [PP2APLA2star2])
Reac128.kcst = 1.4e6
Reac129 = smodel.Reac('Reac129', vsys, lhs = [PP2APLA2star2], rhs = [PP2A, PLA2star2])
Reac129.kcst = 1.5
Reac130 = smodel.Reac('Reac130', vsys, lhs = [PP2APLA2star2], rhs = [PLA2, PP2A])
Reac130.kcst = 2.5
# PP2A + Ca1PLA2p <-> PP2A.Ca1PLA2p -> PP2A + Ca1PLA2
Reac131 = smodel.Reac('Reac131', vsys, lhs = [PP2A, Ca1PLA2star2], rhs = [PP2ACa1PLA2star2])
Reac131.kcst = 1.4e6
Reac132 = smodel.Reac('Reac132', vsys, lhs = [PP2ACa1PLA2star2], rhs = [PP2A, Ca1PLA2star2])
Reac132.kcst = 1.5
Reac133 = smodel.Reac('Reac133', vsys, lhs = [PP2ACa1PLA2star2], rhs = [PP2A, Ca1PLA2])
Reac133.kcst = 2.5
# PP2A + Ca2PLA2p <-> PP2A.Ca2PLA2p -> PP2A + Ca2PLA2
Reac134 = smodel.Reac('Reac134', vsys, lhs = [PP2A, Ca2PLA2star2], rhs = [PP2ACa2PLA2star2])
Reac134.kcst = 1.4e6
Reac135 = smodel.Reac('Reac135', vsys, lhs = [PP2ACa2PLA2star2], rhs = [PP2A, Ca2PLA2star2])
Reac135.kcst = 1.5
Reac136 = smodel.Reac('Reac136', vsys, lhs = [PP2ACa2PLA2star2], rhs = [PP2A, Ca2PLA2])
Reac136.kcst = 2.5
# PP1 + PLA2p <-> PP1.PLA2p -> PP1 + PLA2
Reac137 = smodel.Reac('Reac137', vsys, lhs = [PP1, PLA2star2], rhs = [PP1PLA2star2])
Reac137.kcst = 1.4e6
Reac138 = smodel.Reac('Reac138', vsys, lhs = [PP1PLA2star2], rhs = [PP1, PLA2star2])
Reac138.kcst = 1.5
Reac139 = smodel.Reac('Reac139', vsys, lhs = [PP1PLA2star2], rhs = [PLA2, PP1])
Reac139.kcst = 2.5
# PP1 + Ca1PLA2p <-> PP1.Ca1PLA2p -> PP1 + Ca1PLA2
Reac140 = smodel.Reac('Reac140', vsys, lhs = [PP1, Ca1PLA2star2], rhs = [PP1Ca1PLA2star2])
Reac140.kcst = 1.4e6
Reac141 = smodel.Reac('Reac141', vsys, lhs = [PP1Ca1PLA2star2], rhs = [PP1, Ca1PLA2star2])
Reac141.kcst = 1.5
Reac142 = smodel.Reac('Reac142', vsys, lhs = [PP1Ca1PLA2star2], rhs = [PP1, Ca1PLA2])
Reac142.kcst = 2.5
# PP1 + Ca2PLA2p <-> PP1.Ca2PLA2p -> PP1 + Ca2PLA2
Reac143 = smodel.Reac('Reac143', vsys, lhs = [PP1, Ca2PLA2star2], rhs = [PP1Ca2PLA2star2])
Reac143.kcst = 1.4e6
Reac144 = smodel.Reac('Reac144', vsys, lhs = [PP1Ca2PLA2star2], rhs = [PP1, Ca2PLA2star2])
Reac144.kcst = 1.5
Reac145 = smodel.Reac('Reac145', vsys, lhs = [PP1Ca2PLA2star2], rhs = [PP1, Ca2PLA2])
Reac145.kcst = 2.5
# PLA2p <-> PLA2** (PLA2star2memb) <-> PLA2**APC -> PLA2** + AA
Reac146 = smodel.SReac('Reac146', s, ilhs = [PLA2star2], srhs = [PLA2star2memb])
Reac146.kcst = 50
Reac147 = smodel.SReac('Reac147', s, slhs = [PLA2star2memb], irhs = [PLA2star2])
Reac147.kcst = 15
Reac148 = smodel.SReac('Reac148', s, slhs = [PLA2star2memb], srhs = [PLA2star2membAPC])
Reac148.kcst = 43
Reac149 = smodel.SReac('Reac149', s, slhs = [PLA2star2membAPC], srhs = [PLA2star2memb])
Reac149.kcst = 600
Reac150 = smodel.SReac('Reac150', s, slhs = [PLA2star2membAPC], srhs = [PLA2star2memb], irhs = [AA])
Reac150.kcst = 3600
# Ca1PLA2p <-> Ca1PLA2** (Ca1PLA2star2memb) <-> Ca1PLA2**APC -> Ca1PLA2** + AA
Reac151 = smodel.SReac('Reac151', s, ilhs = [Ca1PLA2star2], srhs = [Ca1PLA2star2memb])
Reac151.kcst = 30
Reac152 = smodel.SReac('Reac152', s, slhs = [Ca1PLA2star2memb], irhs = [Ca1PLA2star2])
Reac152.kcst = 15
Reac153 = smodel.SReac('Reac153', s, slhs = [Ca1PLA2star2memb], srhs = [Ca1PLA2star2membAPC])
Reac153.kcst = 43
Reac154 = smodel.SReac('Reac154', s, slhs = [Ca1PLA2star2membAPC], srhs = [Ca1PLA2star2memb])
Reac154.kcst = 600
Reac155 = smodel.SReac('Reac155', s, slhs = [Ca1PLA2star2membAPC], srhs = [Ca1PLA2star2memb], irhs = [AA])
Reac155.kcst = 3600
# Ca2PLA2p <-> Ca2PLA2** (Ca2PLA2star2memb) <-> Ca2PLA2**APC -> Ca2PLA2** + AA
Reac156 = smodel.SReac('Reac156', s, ilhs = [Ca2PLA2star2], srhs = [Ca2PLA2star2memb])
Reac156.kcst = 300
Reac157 = smodel.SReac('Reac157', s, slhs = [Ca2PLA2star2memb], irhs = [Ca2PLA2star2])
Reac157.kcst = 15
Reac158 = smodel.SReac('Reac158', s, slhs = [Ca2PLA2star2memb], srhs = [Ca2PLA2star2membAPC])
Reac158.kcst = 43
Reac159 = smodel.SReac('Reac159', s, slhs = [Ca2PLA2star2membAPC], srhs = [Ca2PLA2star2memb])
Reac159.kcst = 600
Reac160 = smodel.SReac('Reac160', s, slhs = [Ca2PLA2star2membAPC], srhs = [Ca2PLA2star2memb], irhs = [AA])
Reac160.kcst = 3600
# Ca + PLA2p <-> Ca1PLA2p
Reac161 = smodel.Reac('Reac161', vsys, lhs = [PLA2star2, Ca], rhs = [Ca1PLA2star2])
Reac161.kcst = 1.93e6
Reac162 = smodel.Reac('Reac162', vsys, lhs = [Ca1PLA2star2], rhs = [PLA2star2, Ca])
Reac162.kcst = 108
# Ca + PLA2** <-> Ca1PLA2**
Reac163 = smodel.SReac('Reac163', s, slhs = [PLA2star2memb], ilhs = [Ca], srhs = [Ca1PLA2star2memb])
Reac163.kcst = 1.93e6
Reac164 = smodel.SReac('Reac164', s, ilhs = [Ca1PLA2star2memb], srhs = [PLA2star2memb], irhs = [Ca])
Reac164.kcst = 0.41
# Ca + Ca1PLA2p <-> Ca2PLA2p
Reac165 = smodel.Reac('Reac165', vsys, lhs = [Ca, Ca1PLA2star2], rhs = [Ca2PLA2star2])
Reac165.kcst = 10.8e6
Reac166 = smodel.Reac('Reac166', vsys, lhs = [Ca2PLA2star2], rhs = [Ca1PLA2star2, Ca])
Reac166.kcst = 108
# Ca + Ca1PLA2** <-> Ca2PLA2**
Reac167 = smodel.SReac('Reac167', s, slhs = [Ca1PLA2star2memb], ilhs = [Ca], srhs = [Ca2PLA2star2memb])
Reac167.kcst = 10.8e6
Reac168 = smodel.SReac('Reac168', s, ilhs = [Ca2PLA2star2memb], srhs = [Ca1PLA2star2memb], irhs = [Ca])
Reac168.kcst = 2.5
# AA -> 0 ,degradation
Reac169 = smodel.SReac('Reac169', s, ilhs = [AA])
Reac169.kcst = .4
# Ca3PKC* + AMPAR <-> Ca3PKC*.AMPAR -> Ca3PKC* + AMPARp
Reac170 = smodel.SReac('Reac170', s, slhs = [PKCstar, AMPAR], srhs = [PKCstarAMPAR])
# units for 2D reaction based on square meters in STEPS 1.2 and above
# units for 2nd-order reaction are m^2/mol.s
Reac170.kcst = 0.4e6*(1.02e-12/1.87e-19)
Reac171 = smodel.SReac('Reac171', s, slhs = [PKCstarAMPAR], srhs = [PKCstar, AMPAR])
Reac171.kcst = 0.8
Reac172 = smodel.SReac('Reac172', s, slhs = [PKCstarAMPAR], srhs = [PKCstar, AMPAR_P])
Reac172.kcst = 0.3
# AAPKC* + AMPAR <-> AAPKC*.AMPAR -> AAPKC* + AMPARp
Reac173 = smodel.SReac('Reac173', s, slhs = [PKCstar2, AMPAR], srhs = [PKCstar2AMPAR])
# units for 2D reaction based on square meters in STEPS 1.2 and above
# units for 2nd-order reaction are m^2/mol.s
Reac173.kcst = 0.4e6*(1.02e-12/1.87e-19)
Reac174 = smodel.SReac('Reac174', s, slhs = [PKCstar2AMPAR], srhs = [PKCstar2, AMPAR])
Reac174.kcst = 0.8
Reac175 = smodel.SReac('Reac175', s, slhs = [PKCstar2AMPAR], srhs = [PKCstar2, AMPAR_P])
Reac175.kcst = 0.3
# AACa1PKC* + AMPAR <-> AACa1PKC*.AMPAR -> AACa1PKC* + AMPARp
Reac176 = smodel.SReac('Reac176', s, slhs = [PKCstar3, AMPAR], srhs = [PKCstar3AMPAR])
# units for 2D reaction based on square meters in STEPS 1.2 and above
# units for 2nd-order reaction are m^2/mol.s
Reac176.kcst = 0.4e6*(1.02e-12/1.87e-19)
Reac177 = smodel.SReac('Reac177', s, slhs = [PKCstar3AMPAR], srhs = [PKCstar3, AMPAR])
Reac177.kcst = 0.8
Reac178 = smodel.SReac('Reac178', s, slhs = [PKCstar3AMPAR], srhs = [PKCstar3, AMPAR_P])
Reac178.kcst = 0.3
# AACa3PKC* + AMPAR <-> AACa3PKC*.AMPAR -> AACa3PKC* + AMPARp
Reac179 = smodel.SReac('Reac179', s, slhs = [PKCstar4, AMPAR], srhs = [PKCstar4AMPAR])
# units for 2D reaction based on square meters in STEPS 1.2 and above
# units for 2nd-order reaction are m^2/mol.s
Reac179.kcst = 0.4e6*(1.02e-12/1.87e-19)
Reac180 = smodel.SReac('Reac180', s, slhs = [PKCstar4AMPAR], srhs = [PKCstar4, AMPAR])
Reac180.kcst = 0.8
Reac181 = smodel.SReac('Reac181', s, slhs = [PKCstar4AMPAR], srhs = [PKCstar4, AMPAR_P])
Reac181.kcst = 0.3
# PP2A + AMPARp <-> PP2A.AMPARp -> PP2A + AMPAR
Reac182 = smodel.SReac('Reac182', s, ilhs = [PP2A], slhs = [AMPAR_P], srhs = [PP2AAMPAR_P])
Reac182.kcst = 0.6e6
Reac183 = smodel.SReac('Reac183', s, slhs = [PP2AAMPAR_P], irhs = [PP2A], srhs = [AMPAR_P])
Reac183.kcst = 0.17
Reac184 = smodel.SReac('Reac184', s, slhs = [PP2AAMPAR_P], srhs = [AMPAR], irhs = [PP2A])
Reac184.kcst = 0.25
# AMPAR + GRIP <-> GRIP.AMPA
Reac185 = smodel.SReac('Reac185', s, slhs = [AMPAR, GRIP], srhs = [GRIPAMPAR])
# units for 2D reaction based on square meters in STEPS 1.2 and above
# units for 2nd-order reaction are m^2/mol.s
Reac185.kcst = 1e6*(1.02e-12/1.87e-19)
Reac186 = smodel.SReac('Reac186', s, slhs = [GRIPAMPAR], srhs = [GRIP, AMPAR])
Reac186.kcst = 7
# AMPARp + GRIP <-> GRIP.AMPAp (AMPAR = synaptic AMPAR)
Reac187 = smodel.SReac('Reac187', s, slhs = [AMPAR_P, GRIP], srhs = [GRIPAMPAR_P])
# units for 2D reaction based on square meters in STEPS 1.2 and above
# units for 2nd-order reaction are m^2/mol.s
Reac187.kcst = 1e6*(1.02e-12/1.87e-19)
Reac188 = smodel.SReac('Reac188', s, slhs = [GRIPAMPAR_P], srhs = [GRIP, AMPAR_P])
Reac188.kcst = 70
# AMPAR <-> AMPARextra (AMPARextra = extra-synaptic AMPAR)
Reac189 = smodel.SReac('Reac189', s, slhs = [AMPAR], srhs = [AMPARextra])
Reac189.kcst = 0.1
Reac190 = smodel.SReac('Reac190', s, slhs = [AMPARextra], srhs = [AMPAR])
Reac190.kcst = 0.02
# AMPARp <-> AMPARextra_P
Reac191 = smodel.SReac('Reac191', s, slhs = [AMPAR_P], srhs = [AMPARextra_P])
Reac191.kcst = 0.1
Reac192 = smodel.SReac('Reac192', s, slhs = [AMPARextra_P], srhs = [AMPAR_P])
Reac192.kcst = 0.02
# PP2A + AMPARextra_P <-> PP2A.AMPARextra_P -> PP2A + AMPARextra
Reac193 = smodel.SReac('Reac193', s, ilhs = [PP2A], slhs = [AMPARextra_P], srhs = [PP2AAMPARextra_P])
Reac193.kcst = 0.6e6
Reac194 = smodel.SReac('Reac194', s, slhs = [PP2AAMPARextra_P], irhs = [PP2A], srhs = [AMPARextra_P])
Reac194.kcst = 0.17
Reac195 = smodel.SReac('Reac195', s, slhs = [PP2AAMPARextra_P], srhs = [AMPARextra], irhs = [PP2A])
Reac195.kcst = 0.25
# AMPARextra <-> AMPARdend (AMPARdend = dendritic AMPAR)
Reac196 = smodel.SReac('Reac196', s, slhs = [AMPARextra], srhs = [AMPARdend])
Reac196.kcst = 0.02
Reac197 = smodel.SReac('Reac197', s, slhs = [AMPARdend], srhs = [AMPARextra])
Reac197.kcst = 0.00025
# AMPARextra_P <-> AMPARdend_P
Reac198 = smodel.SReac('Reac198', s, slhs = [AMPARextra_P], srhs = [AMPARdend_P])
Reac198.kcst = 0.02
Reac199 = smodel.SReac('Reac199', s, slhs = [AMPARdend_P], srhs = [AMPARextra_P])
Reac199.kcst = 0.00025
# PP2A + AMPARp_dend <-> PP2A.AMPARp_dend -> PP2A + AMPAR_dend
Reac200 = smodel.SReac('Reac200', s, ilhs = [PP2A], slhs = [AMPARdend_P], srhs = [PP2AAMPARdend_P])
Reac200.kcst = 0.6e6
Reac201 = smodel.SReac('Reac201', s, slhs = [PP2AAMPARdend_P], irhs = [PP2A], srhs = [AMPARdend_P])
Reac201.kcst = 0.17
Reac202 = smodel.SReac('Reac202', s, slhs = [PP2AAMPARdend_P], srhs = [AMPARdend], irhs = [PP2A])
Reac202.kcst = 0.25
# AMPARdend_P <-> AMPARcyt_P (AMPARcyt = cytosolic AMPAR)
Reac203 = smodel.SReac('Reac203', s, slhs = [AMPARdend_P], irhs = [AMPARcyt_P])
Reac203.kcst = 0.003
Reac204 = smodel.SReac('Reac204', s, ilhs = [AMPARcyt_P], srhs = [AMPARdend_P])
Reac204.kcst = 0.002
# PP2A + AMPARcyt_P <-> PP2A.AMPARcyt_P -> PP2A + AMPARcyt
Reac205 = smodel.Reac('Reac205', vsys, lhs = [PP2A, AMPARcyt_P], rhs = [PP2AAMPARcyt_P])
Reac205.kcst = 0.6e6
Reac206 = smodel.Reac('Reac206', vsys, lhs = [PP2AAMPARcyt_P], rhs = [PP2A, AMPARcyt_P])
Reac206.kcst = 0.17
Reac207 = smodel.Reac('Reac207', vsys, lhs = [PP2AAMPARcyt_P], rhs = [AMPARcyt, PP2A])
Reac207.kcst = 0.25
return mdl
########################################################################
# Geometric properties of the model: To change the size of the model, all volumetric compartments must be altered by the same ratio
# and all the areas must be scaled considering a spherical shape.
# Alterations in the size of the compartments will change automatically the population
# of species given in concentration (initial condition), but the species given in number of molecules must be altered manually by the same ratio
# to keep the balance among all the components of the model.
def gen_geom():
g = swm.Geom()
c = swm.Comp('vsys', g)
c.addVolsys('vsys')
c.vol = 0.08e-18
extra = swm.Comp('extra', g)
extra.addVolsys('extra')
extra.vol = 1.87e-22
s = swm.Patch('memb', g, icomp = c, ocomp = extra)
s.addSurfsys('memb')
s.area = 1.02e-12
cytER = swm.Comp('cytER', g)
cytER.addVolsys('cytER')
cytER.vol = 0.017e-18
ERs = swm.Patch('ERmemb', g, icomp = cytER, ocomp = c)
ERs.addSurfsys('ERmemb')
ERs.area = 0.32e-12
return g
######################################################################
def run_gauss_mean():
rng=srng.create('mt19937',512)
m=gen_model()
g=gen_geom()
tpnts=np.arange(0.0,INT,DT)
ntpnts=tpnts.shape[0]
# initialize arrays for storage at each time point and at each run.
Ca = numpy.zeros((NITER, ntpnts))
PMCA = numpy.zeros((NITER, ntpnts))
Ca1PMCA = numpy.zeros((NITER, ntpnts))
NCX = numpy.zeros((NITER, ntpnts))
Ca1NCX = numpy.zeros((NITER, ntpnts))
Ca2NCX = numpy.zeros((NITER, ntpnts))
SERCA = numpy.zeros((NITER, ntpnts))
Ca1SERCA = numpy.zeros((NITER, ntpnts))
Ca2SERCA = numpy.zeros((NITER, ntpnts))
CBf = numpy.zeros((NITER, ntpnts))
CaCBf = numpy.zeros((NITER, ntpnts))
Ca2CBf = numpy.zeros((NITER, ntpnts))
CBs = numpy.zeros((NITER, ntpnts))
CaCBs = numpy.zeros((NITER, ntpnts))
Ca2CBs = numpy.zeros((NITER, ntpnts))
PV = numpy.zeros((NITER, ntpnts))
CaPV = numpy.zeros((NITER, ntpnts))
MgPV = numpy.zeros((NITER, ntpnts))
Ca2PV = numpy.zeros((NITER, ntpnts))
Mg2PV = numpy.zeros((NITER, ntpnts))
PP2A = numpy.zeros((NITER, ntpnts))
PKC = numpy.zeros((NITER, ntpnts))
Ca1PKC = numpy.zeros((NITER, ntpnts))
Ca3PKC = numpy.zeros((NITER, ntpnts))
AAPKC = numpy.zeros((NITER, ntpnts))
AACa1PKC = numpy.zeros((NITER, ntpnts))
AACa3PKC = numpy.zeros((NITER, ntpnts))
PKCstar = numpy.zeros((NITER, ntpnts))
PKCstar2 = numpy.zeros((NITER, ntpnts))
PKCstar4 = numpy.zeros((NITER, ntpnts))
PKCstar3 = numpy.zeros((NITER, ntpnts))
Rafact = numpy.zeros((NITER, ntpnts))
PKCstarRafact = numpy.zeros((NITER, ntpnts))
PKCstar2Rafact = numpy.zeros((NITER, ntpnts))
PKCstar3Rafact = numpy.zeros((NITER, ntpnts))
PKCstar4Rafact = numpy.zeros((NITER, ntpnts))
Rafactstar = numpy.zeros((NITER, ntpnts))
Raf = numpy.zeros((NITER, ntpnts))
RafactstarRaf = numpy.zeros((NITER, ntpnts))
Rafstar = numpy.zeros((NITER, ntpnts))
PP5Rafstar = numpy.zeros((NITER, ntpnts))
PP5 = numpy.zeros((NITER, ntpnts))
MEK = numpy.zeros((NITER, ntpnts))
RafstarMEK = numpy.zeros((NITER, ntpnts))
MEKp = numpy.zeros((NITER, ntpnts))
PP2AMEKp = numpy.zeros((NITER, ntpnts))
RafstarMEKp = numpy.zeros((NITER, ntpnts))
MEKstar = numpy.zeros((NITER, ntpnts))
PP2AMEKstar = numpy.zeros((NITER, ntpnts))
ERK = numpy.zeros((NITER, ntpnts))
MEKstarERK = numpy.zeros((NITER, ntpnts))
ERKp = numpy.zeros((NITER, ntpnts))
MKP = numpy.zeros((NITER, ntpnts))
MKPERKp = numpy.zeros((NITER, ntpnts))
MEKstarERKp = numpy.zeros((NITER, ntpnts))
ERKstar = numpy.zeros((NITER, ntpnts))
MKPERKstar = numpy.zeros((NITER, ntpnts))
Ca1PLA2 = numpy.zeros((NITER, ntpnts))
Ca2PLA2 = numpy.zeros((NITER, ntpnts))
PLA2 = numpy.zeros((NITER, ntpnts))
PLA2memb = numpy.zeros((NITER, ntpnts))
Ca1PLA2memb = numpy.zeros((NITER, ntpnts))
PLA2star1 = numpy.zeros((NITER, ntpnts))
ERKstarPLA2 = numpy.zeros((NITER, ntpnts))
PLA2star2 = numpy.zeros((NITER, ntpnts))
AA = numpy.zeros((NITER, ntpnts))
Ca1PLA2star2 = numpy.zeros((NITER, ntpnts))
Ca2PLA2star2 = numpy.zeros((NITER, ntpnts))
PLA2star2memb = numpy.zeros((NITER, ntpnts))
Ca1PLA2star2memb = numpy.zeros((NITER, ntpnts))
Ca2PLA2star2memb = numpy.zeros((NITER, ntpnts))
PLA2star1APC = numpy.zeros((NITER, ntpnts))
ERKstarCa1PLA2 = numpy.zeros((NITER, ntpnts))
ERKstarCa2PLA2 = numpy.zeros((NITER, ntpnts))
PP2ACa1PLA2star2 = numpy.zeros((NITER, ntpnts))
PP2ACa2PLA2star2 = numpy.zeros((NITER, ntpnts))
PP1Ca1PLA2star2 = numpy.zeros((NITER, ntpnts))
PP1Ca2PLA2star2 = numpy.zeros((NITER, ntpnts))
PLA2star2membAPC = numpy.zeros((NITER, ntpnts))
Ca1PLA2star2membAPC = numpy.zeros((NITER, ntpnts))
Ca2PLA2star2membAPC = numpy.zeros((NITER, ntpnts))
PP1PLA2star2 = numpy.zeros((NITER, ntpnts))
PP1 = numpy.zeros((NITER, ntpnts))
PP2APLA2star2 = numpy.zeros((NITER, ntpnts))
PKCstarAMPAR = numpy.zeros((NITER, ntpnts))
PKCstar2AMPAR = numpy.zeros((NITER, ntpnts))
PKCstar4AMPAR = numpy.zeros((NITER, ntpnts))
PKCstar3AMPAR = numpy.zeros((NITER, ntpnts))
AMPAR = numpy.zeros((NITER, ntpnts))
AMPAR_P = numpy.zeros((NITER, ntpnts))
PP2AAMPAR_P = numpy.zeros((NITER, ntpnts))
AMPARextra = numpy.zeros((NITER, ntpnts))
AMPARextra_P = numpy.zeros((NITER, ntpnts))
PP2AAMPARextra_P = numpy.zeros((NITER, ntpnts))
GRIP = numpy.zeros((NITER, ntpnts))
GRIPAMPAR_P = numpy.zeros((NITER, ntpnts))
GRIPAMPAR = numpy.zeros((NITER, ntpnts))
AMPARdend = numpy.zeros((NITER, ntpnts))
AMPARdend_P = numpy.zeros((NITER, ntpnts))
PP2AAMPARdend_P = numpy.zeros((NITER, ntpnts))
AMPARcyt = numpy.zeros((NITER, ntpnts))
AMPARcyt_P = numpy.zeros((NITER, ntpnts))
PP2AAMPARcyt_P = numpy.zeros((NITER, ntpnts))
ica=gaussian_ica(tpnts)
sim = swmdirect.Wmdirect(m, g, rng)
for j in arange(NITER):
print "Run number {0}".format(j)
rng.initialize(datetime.datetime.now().microsecond)
sim.reset()
# initial conditions
sim.setCompConc('vsys', 'Ca', 0.045e-6)
sim.setCompConc('vsys', 'CBf', 37.775e-6)
sim.setCompConc('vsys', 'CaCBf', 2.1e-6)
sim.setCompConc('vsys', 'Ca2CBf', 0.125e-6)
sim.setCompConc('vsys', 'CBs', 36.25e-6)
sim.setCompConc('vsys', 'CaCBs', 3.4e-6)
sim.setCompConc('vsys', 'Ca2CBs', 0.125e-6)
sim.setCompConc('vsys', 'PV', 1.15e-6)
sim.setCompConc('vsys', 'CaPV', 8.4e-6)
sim.setCompConc('vsys', 'MgPV', 30.45e-6)
sim.setCompCount('vsys', 'PKC', 48)
sim.setCompConc('vsys', 'Raf',0.1e-6)
sim.setCompConc('vsys', 'Rafact', 0.5e-6)
sim.setCompConc('vsys', 'MEK',1.5e-6)
sim.setCompConc('vsys', 'ERK',1.0e-6)
sim.setCompConc('vsys', 'MKP',0.26e-6)
sim.setCompConc('vsys', 'PP5', 1.0e-6)
sim.setCompConc('vsys', 'PP2A', 1.5e-6)
sim.setCompConc('vsys', 'PLA2',0.4e-6)
sim.setCompCount('vsys', 'PP1', 30)
sim.setPatchCount('memb', 'PMCA',10)
sim.setPatchCount('memb', 'NCX',3)
sim.setPatchCount('ERmemb', 'SERCA', 100)
sim.setCompConc('cytER', 'Ca', 150e-6)
sim.setCompClamped('cytER', 'Ca', True) # clamped means the conc won't change as simulation runs.
sim.setPatchCount('memb', 'AMPAR', 3)
sim.setPatchCount('memb', 'AMPARextra', 16)
sim.setPatchCount('memb', 'GRIP', 22)
sim.setPatchCount('memb', 'GRIPAMPAR', 119)
sim.setPatchCount('memb', 'AMPARdend', 1600)
for i in range(ntpnts):
sim.run(tpnts[i])
print "percent done",(tpnts[i]/INT*100)
Ca[j,i] = sim.getCompConc('vsys', 'Ca')
CBf[j,i] = sim.getCompConc('vsys', 'CBf')
CaCBf[j,i] = sim.getCompConc('vsys', 'CaCBf')
Ca2CBf[j,i] = sim.getCompConc('vsys', 'Ca2CBf')
CaCBs[j,i] = sim.getCompConc('vsys', 'CaCBs')
Ca2CBs[j,i] = sim.getCompConc('vsys', 'Ca2CBs')
PV[j,i] = sim.getCompConc('vsys', 'PV')
CaPV[j,i] = sim.getCompConc('vsys', 'CaPV')
MgPV[j,i] = sim.getCompConc('vsys', 'MgPV')
Ca2PV[j,i] = sim.getCompConc('vsys', 'Ca2PV')
Mg2PV[j,i] = sim.getCompConc('vsys', 'Mg2PV')
PP2A[j,i] = sim.getCompCount('vsys', 'PP2A')
PP5[j,i] = sim.getCompCount('vsys', 'PP5')
PKC[j,i] = sim.getCompCount('vsys', 'PKC')
Ca3PKC[j,i] = sim.getCompCount('vsys', 'Ca3PKC')
Ca1PKC[j,i] = sim.getCompCount('vsys', 'Ca1PKC')
AAPKC[j,i] = sim.getCompCount('vsys', 'AAPKC')
AACa1PKC[j,i] = sim.getCompCount('vsys', 'AACa1PKC')
AACa3PKC[j,i] = sim.getCompCount('vsys', 'AACa3PKC')
PKCstar[j,i] = sim.getPatchCount('memb', 'PKCstar')
PKCstar2[j,i] = sim.getPatchCount('memb', 'PKCstar2')
PKCstar3[j,i] = sim.getPatchCount('memb', 'PKCstar3')
PKCstar4[j,i] = sim.getPatchCount('memb', 'PKCstar4')
Rafact[j,i] = sim.getCompConc('vsys', 'Rafact')
PKCstarRafact[j,i] = sim.getPatchCount('memb', 'PKCstarRafact')
PKCstar2Rafact[j,i] = sim.getPatchCount('memb', 'PKCstar2Rafact')
PKCstar3Rafact[j,i] = sim.getPatchCount('memb', 'PKCstar3Rafact')
PKCstar4Rafact[j,i] = sim.getPatchCount('memb', 'PKCstar4Rafact')
Rafactstar[j,i] = sim.getCompCount('vsys', 'Rafactstar')
RafactstarRaf[j,i] = sim.getCompCount('vsys', 'RafactstarRaf')
Raf[j,i] = sim.getCompCount('vsys', 'Raf')
Rafstar[j,i] = sim.getCompCount('vsys', 'Rafstar')
PP5Rafstar[j,i] = sim.getCompCount('vsys', 'PP5Rafstar')
MEK[j,i] = sim.getCompCount('vsys', 'MEK')
RafstarMEK[j,i] = sim.getCompCount('vsys', 'RafstarMEK')
MEKp[j,i] = sim.getCompCount('vsys', 'MEKp')
PP2AMEKp[j,i] = sim.getCompCount('vsys', 'PP2AMEKp')
RafstarMEKp[j,i] = sim.getCompCount('vsys', 'RafstarMEKp')
MEKstar[j,i] = sim.getCompCount('vsys', 'MEKstar')
RafstarMEKp[j,i] = sim.getCompCount('vsys', 'RafstarMEKp')
ERK[j,i] = sim.getCompCount('vsys', 'ERK')
MEKstarERK[j,i] = sim.getCompCount('vsys', 'MEKstarERK')
ERKp[j,i] = sim.getCompCount('vsys', 'ERKp')
MKP[j,i] = sim.getCompCount('vsys', 'MKP')
MKPERKp[j,i] = sim.getCompCount('vsys', 'MKPERKp')
MEKstarERKp[j,i] = sim.getCompCount('vsys', 'MEKstarERKp')
ERKstar[j,i] = sim.getCompCount('vsys', 'ERKstar')
MKPERKstar[j,i] = sim.getCompCount('vsys', 'MKPERKstar')
PP2A[j,i] = sim.getCompCount('vsys', 'PP2A')
PLA2[j,i] = sim.getCompCount('vsys', 'PLA2')
Ca1PLA2[j,i] = sim.getCompCount('vsys', 'Ca1PLA2')
Ca2PLA2[j,i] = sim.getCompCount('vsys', 'Ca2PLA2')
PLA2memb[j,i] = sim.getPatchCount('memb', 'PLA2memb')
Ca1PLA2memb[j,i] = sim.getPatchCount('memb', 'Ca1PLA2memb')
PLA2star1[j,i] = sim.getPatchCount('memb', 'PLA2star1')
ERKstarPLA2[j,i] = sim.getCompCount('vsys', 'ERKstarPLA2')
PLA2star2[j,i] = sim.getCompCount('vsys', 'PLA2star2')
Ca1PLA2star2[j,i] = sim.getCompCount('vsys', 'Ca1PLA2star2')
Ca2PLA2star2[j,i] = sim.getCompCount('vsys', 'Ca2PLA2star2')
PLA2star2memb[j,i] = sim.getPatchCount('memb', 'PLA2star2memb')
Ca1PLA2star2memb[j,i] = sim.getPatchCount('memb', 'Ca1PLA2star2memb')
Ca2PLA2star2memb[j,i] = sim.getPatchCount('memb', 'Ca2PLA2star2memb')
AA[j,i] = sim.getCompConc('vsys', 'AA')
PP2APLA2star2[j,i] = sim.getCompCount('vsys', 'PP2APLA2star2')
PP1[j,i] = sim.getCompCount('vsys','PP1')
PP1PLA2star2[j,i] = sim.getCompCount('vsys', 'PP1PLA2star2')
PLA2star1APC[j,i] = sim.getPatchCount('memb', 'PLA2star1APC')
ERKstarCa1PLA2[j,i] = sim.getCompConc('vsys', 'ERKstarCa1PLA2')
ERKstarCa2PLA2[j,i] = sim.getCompConc('vsys', 'ERKstarCa2PLA2')
PP2ACa1PLA2star2[j,i] = sim.getCompConc('vsys', 'PP2ACa1PLA2star2')
PP2ACa2PLA2star2[j,i] = sim.getCompConc('vsys', 'PP2ACa2PLA2star2')
PP1Ca1PLA2star2[j,i] = sim.getCompConc('vsys', 'PP1Ca1PLA2star2')
PP1Ca2PLA2star2[j,i] = sim.getCompConc('vsys', 'PP1Ca2PLA2star2')
PLA2star2membAPC[j,i] = sim.getPatchCount('memb', 'PLA2star2membAPC')
Ca1PLA2star2membAPC[j,i] = sim.getPatchCount('memb', 'Ca1PLA2star2membAPC')
Ca2PLA2star2membAPC[j,i] = sim.getPatchCount('memb', 'Ca2PLA2star2membAPC')
Ca1PMCA[j,i] = sim.getPatchCount('memb', 'Ca1PMCA')
PMCA[j,i] = sim.getPatchCount('memb', 'PMCA')
NCX[j,i] = sim.getPatchCount('memb', 'NCX')
Ca1NCX[j,i] = sim.getPatchCount('memb', 'Ca1NCX')
Ca2NCX[j,i] = sim.getPatchCount('memb', 'Ca2NCX')
SERCA[j,i] = sim.getPatchCount('ERmemb', 'SERCA')
Ca1SERCA[j,i] = sim.getPatchCount('ERmemb', 'Ca1SERCA')
Ca2SERCA[j,i] = sim.getPatchCount('ERmemb', 'Ca2SERCA')
PP1PLA2star2[j,i] = sim.getCompConc('vsys', 'PP1PLA2star2')
AMPAR[j,i] = sim.getPatchCount('memb', 'AMPAR')
AMPAR_P[j,i] = sim.getPatchCount('memb', 'AMPAR_P')
PP2AAMPAR_P[j,i] = sim.getPatchCount('memb', 'PP2AAMPAR_P')
AMPARextra[j,i] = sim.getPatchCount('memb', 'AMPARextra')
AMPARextra_P[j,i] = sim.getPatchCount('memb', 'AMPARextra_P')
PP2AAMPARextra_P[j,i] = sim.getPatchCount('memb', 'PP2AAMPARextra_P')
GRIP[j,i] = sim.getPatchCount('memb', 'GRIP')
GRIPAMPAR[j,i] = sim.getPatchCount('memb', 'GRIPAMPAR')
GRIPAMPAR_P[j,i] = sim.getPatchCount('memb', 'GRIPAMPAR_P')
PKCstarAMPAR[j,i] = sim.getPatchCount('memb', 'PKCstarAMPAR')
PKCstar2AMPAR[j,i] = sim.getPatchCount('memb', 'PKCstar2AMPAR')
PKCstar3AMPAR[j,i] = sim.getPatchCount('memb', 'PKCstar3AMPAR')
PKCstar4AMPAR[j,i] = sim.getPatchCount('memb', 'PKCstar4AMPAR')
AMPARdend[j,i] = sim.getPatchCount('memb', 'AMPARdend')
AMPARdend_P[j,i] = sim.getPatchCount('memb', 'AMPARdend_P')
PP2AAMPARdend_P[j,i] = sim.getPatchCount('memb', 'PP2AAMPARdend_P')
AMPARcyt[j,i] = sim.getCompCount('vsys','AMPARcyt')
AMPARcyt_P[j,i] = sim.getCompCount('vsys', 'AMPARcyt_P')
PP2AAMPARcyt_P[j,i] = sim.getCompCount('vsys', 'PP2AAMPARcyt_P')
sim.setCompReacK('vsys', 'Cainflux', ica[i]) # changes reaction constant to be ...
####################################################################################
# Plot Calcium: these lines must be commented if pylab is not installed
Ca_mean = mean(Ca, axis=0)
plot(linspace(0,INT-tinit,(INT-tinit)/DT),Ca_mean[tinit/DT-1:INT/DT-1]*1e6,'k')
xlabel('Time (s)')
ylabel('Calcium (umol.L^-^1)')
show()
# Plot PKC: these lines must be commented if pylab is not installed
PKCstar_mean = mean(PKCstar, axis=0)
PKCstar2_mean = mean(PKCstar2, axis=0)
PKCstar3_mean = mean(PKCstar3, axis=0)
PKCstar4_mean = mean(PKCstar4, axis=0)
PKCstarRafact_mean = mean(PKCstarRafact, axis=0)
PKCstar2Rafact_mean = mean(PKCstar2Rafact, axis=0)
PKCstar3Rafact_mean = mean(PKCstar3Rafact, axis=0)
PKCstar4Rafact_mean = mean(PKCstar4Rafact, axis=0)
PKCstarAMPAR_mean = mean(PKCstarAMPAR, axis=0)
PKCstar2AMPAR_mean = mean(PKCstar2AMPAR, axis=0)
PKCstar3AMPAR_mean = mean(PKCstar3AMPAR, axis=0)
PKCstar4AMPAR_mean = mean(PKCstar4AMPAR, axis=0)
PKC_mean=PKCstar_mean+PKCstar2_mean+PKCstar3_mean+PKCstar4_mean+PKCstarRafact_mean+PKCstar2Rafact_mean+PKCstar3Rafact_mean+PKCstar4Rafact_mean+PKCstarAMPAR_mean+PKCstar2AMPAR_mean+PKCstar3AMPAR_mean+PKCstar4AMPAR_mean
plot(linspace(0,INT-tinit,(INT-tinit)/DT), PKC_mean[tinit/DT-1:INT/DT-1], 'r')
xlabel('Time (s)')
ylabel('PKC (#)')
show()
# Plot ERK: these lines must be commented if pylab is not installed
ERKstar_mean = mean(ERKstar, axis=0)
MKPERKstar_mean = mean(MKPERKstar, axis=0)
ERKstarPLA2_mean = mean(ERKstarPLA2, axis=0)
ERKstarCa1PLA2_mean = mean(ERKstarCa1PLA2, axis=0)
ERKstarCa2PLA2_mean = mean(ERKstarCa2PLA2, axis=0)
ERK_mean=ERKstar_mean+MKPERKstar_mean+ERKstarPLA2_mean+ERKstarCa1PLA2_mean+ERKstarCa2PLA2_mean;
plot(linspace(0,INT-tinit,(INT-tinit)/DT), ERK_mean[tinit/DT-1:INT/DT-1],'c')
xlabel('Time (s)')
ylabel('ERK (#)')
show()
# Plot cPLA2: these lines must be commented if pylab is not installed
PLA2star1_mean = mean(PLA2star1, axis=0)
PLA2star1APC_mean = mean(PLA2star1APC, axis=0)
PLA2star2_mean = mean(PLA2star2, axis=0)
Ca1PLA2star2_mean = mean(Ca1PLA2star2, axis=0)
Ca2PLA2star2_mean = mean(Ca2PLA2star2, axis=0)
Ca1PLA2star2memb_mean = mean(Ca1PLA2star2memb, axis=0)
Ca2PLA2star2memb_mean = mean(Ca2PLA2star2memb, axis=0)
Ca1PLA2star2membAPC_mean = mean(Ca1PLA2star2membAPC, axis=0)
Ca2PLA2star2membAPC_mean = mean(Ca2PLA2star2membAPC, axis=0)
PP1PLA2star2_mean = mean(PP1PLA2star2, axis=0)
PP1Ca1PLA2star2_mean = mean(PP1Ca1PLA2star2, axis=0)
PP1Ca2PLA2star2_mean = mean(PP1Ca2PLA2star2, axis=0)
PP2APLA2star2_mean = mean(PP1PLA2star2, axis=0)
PP2ACa1PLA2star2_mean = mean(PP2ACa1PLA2star2, axis=0)
PP2ACa2PLA2star2_mean = mean(PP2ACa2PLA2star2, axis=0)
PLA2_mean=PLA2star1_mean+PLA2star1APC_mean+PLA2star2_mean+Ca1PLA2star2_mean+Ca2PLA2star2_mean+Ca1PLA2star2memb_mean+Ca2PLA2star2memb_mean+Ca1PLA2star2membAPC_mean+Ca2PLA2star2membAPC_mean+PP1PLA2star2_mean+PP1Ca1PLA2star2_mean+PP1Ca2PLA2star2_mean+PP2APLA2star2_mean+PP2ACa1PLA2star2_mean+PP2ACa2PLA2star2_mean;
plot(linspace(0,INT-tinit,(INT-tinit)/DT), PLA2_mean[tinit/DT-1:INT/DT-1], 'b')
xlabel('Time (s)')
ylabel('cPLA2 (#)')
show()
# Plot Synaptic AMPAR: these lines must be commented if pylab is not installed
AMPAR_mean = mean(AMPAR, axis=0)
AMPAR_P_mean = mean(AMPAR_P, axis=0)
PP2AAMPAR_P_mean = mean(PP2AAMPAR_P, axis=0)
GRIPAMPAR_mean = mean(GRIPAMPAR, axis=0)
GRIPAMPAR_P_mean = mean(GRIPAMPAR_P, axis=0)
PKCstarAMPAR_mean = mean(PKCstarAMPAR, axis=0)
PKCstar2AMPAR_mean = mean(PKCstar2AMPAR, axis=0)
PKCstar3AMPAR_mean = mean(PKCstar3AMPAR, axis=0)
PKCstar4AMPAR_mean = mean(PKCstar4AMPAR, axis=0)
AMPAR_syn_mean=AMPAR_mean+AMPAR_P_mean+PP2AAMPAR_P_mean+GRIPAMPAR_mean+GRIPAMPAR_P_mean+PKCstarAMPAR_mean+PKCstar2AMPAR_mean+PKCstar3AMPAR_mean+PKCstar4AMPAR_mean;
plot(linspace(0,INT-tinit,(INT-tinit)/DT), AMPAR_syn_mean[tinit/DT-1:INT/DT-1], 'g')
xlabel('Time (s)')
ylabel('Synaptic AMPAR (#)')
show()
return AMPAR_syn_mean
ampar_syn_mean = run_gauss_mean()