diff --git a/ipynb/Examples/egfr-simple.ipynb b/ipynb/Examples/egfr-simple.ipynb new file mode 100644 index 000000000..f227771fa --- /dev/null +++ b/ipynb/Examples/egfr-simple.ipynb @@ -0,0 +1,371 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Simple EGFR model\n", + "\n", + "- http://bionetgen.org/index.php/Simple_EGFR_model\n", + "- M.L. Blinov, J.R. Faeder, B. Goldstein, W.S. Hlavacek, \"A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity.\", Biosystems, 83(2-3), 136-151, 2006." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "%matplotlib inline\n", + "from ecell4 import *" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "NA = 6.02e23 # Avogadro's number (molecules/mol)\n", + "f = 1 # Fraction of the cell to simulate\n", + "Vo = f * 1.0e-10 # Extracellular volume=1/cell_density (L)\n", + "V = f * 3.0e-12 # Cytoplasmic volume (L)\n", + "\n", + "EGF_init = 20 * 1e-9 * NA * Vo # Initial amount of ligand (20 nM) converted to copies per cell\n", + "\n", + "# Initial amounts of cellular components (copies per cell)\n", + "EGFR_init = f * 1.8e5\n", + "Grb2_init = f * 1.5e5\n", + "Sos1_init = f * 6.2e4\n", + "\n", + "# Rate constants\n", + "# Divide by NA*V to convert bimolecular rate constants\n", + "# from /M/sec to /(molecule/cell)/sec\n", + "kp1 = 9.0e7 / (NA * Vo) # ligand-monomer binding\n", + "km1 = 0.06 # ligand-monomer dissociation\n", + "kp2 = 1.0e7 / (NA * V) # aggregation of bound monomers\n", + "km2 = 0.1 # dissociation of bound monomers\n", + "kp3 = 0.5 # dimer transphosphorylation\n", + "km3 = 4.505 # dimer dephosphorylation\n", + "kp4 = 1.5e6 / (NA * V) # binding of Grb2 to receptor\n", + "km4 = 0.05 # dissociation of Grb2 from receptor\n", + "kp5 = 1.0e7 / (NA * V) # binding of Grb2 to Sos1\n", + "km5 = 0.06 # dissociation of Grb2 from Sos1\n", + "deg = 0.01 # degradation of receptor dimers" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "with reaction_rules():\n", + " # R1: Ligand-receptor binding\n", + " EGFR(L, CR1) + EGF(R) == EGFR(L^1, CR1).EGF(R^1) | (kp1, km1)\n", + " \n", + " # R2: Receptor-aggregation\n", + " EGFR(L^_, CR1) + EGFR(L^_, CR1) == EGFR(L^_,CR1^1).EGFR(L^_,CR1^1) | (kp2, km2)\n", + " \n", + " # R3: Transphosphorylation of EGFR by RTK\n", + " EGFR(CR1^_, Y1068=U) > EGFR(CR1^_, Y1068=P) | kp3\n", + " \n", + " # R4: Dephosphorylation\n", + " EGFR(Y1068=P) > EGFR(Y1068=U) | km3\n", + " \n", + " # R5: Grb2 binding to pY1068\n", + " EGFR(Y1068=P) + Grb2(SH2) == EGFR(Y1068=P^1).Grb2(SH2^1) | (kp4, km4)\n", + " \n", + " # R6: Grb2 binding to Sos1\n", + " Grb2(SH3) + Sos1(PxxP) == Grb2(SH3^1).Sos1(PxxP^1) | (kp5, km5)\n", + " \n", + " # R7: Receptor dimer internalization/degradation\n", + " (EGF(R^1).EGF(R^2).EGFR(L^1,CR1^3).EGFR(L^2,CR1^3) > ~EmptySet | deg\n", + " | _policy(ReactionRule.STRICT | ReactionRule.DESTROY))\n", + "\n", + "m = get_model(is_netfree=True, effective=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "y0 = {\"EGF(R)\": EGF_init, \"EGFR(L, CR1, Y1068=U)\": EGFR_init, \"Grb2(SH2, SH3)\": Grb2_init, \"Sos1(PxxP)\": Sos1_init}" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "newm = m.expand([Species(serial) for serial in y0.keys()])" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "22 species and 86 reactions were generated.\n", + "1: EGF(R)\n", + "2: EGF(R^1).EGFR(CR1,L^1,Y1068=P)\n", + "3: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)\n", + "4: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)\n", + "5: EGF(R^1).EGFR(CR1,L^1,Y1068=U)\n", + "6: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)\n", + "7: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)\n", + "8: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)\n", + "9: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)\n", + "10: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3)\n", + "11: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)\n", + "12: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3^6).Sos1(PxxP^6).Grb2(SH2^3,SH3^7).Sos1(PxxP^7)\n", + "13: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)\n", + "14: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)\n", + "15: EGF(R^1).EGFR(CR1^2,L^1,Y1068=U).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)\n", + "16: EGFR(CR1,L,Y1068=P)\n", + "17: EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3)\n", + "18: EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3^2).Sos1(PxxP^2)\n", + "19: EGFR(CR1,L,Y1068=U)\n", + "20: Grb2(SH2,SH3)\n", + "21: Grb2(SH2,SH3^1).Sos1(PxxP^1)\n", + "22: Sos1(PxxP)\n", + "1: EGF(R)+EGFR(CR1,L,Y1068=U)>EGF(R^1).EGFR(CR1,L^1,Y1068=U)|1.49502e-06\n", + "2: Grb2(SH2,SH3)+Sos1(PxxP)>Grb2(SH2,SH3^1).Sos1(PxxP^1)|5.5371e-06\n", + "3: EGF(R^1).EGFR(CR1,L^1,Y1068=U)>EGF(R)+EGFR(CR1,L,Y1068=U)|0.06\n", + "4: EGF(R^1).EGFR(CR1,L^1,Y1068=U)+EGF(R^1).EGFR(CR1,L^1,Y1068=U)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=U).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)|2.76855e-06\n", + "5: Grb2(SH2,SH3^1).Sos1(PxxP^1)>Grb2(SH2,SH3)+Sos1(PxxP)|0.06\n", + "6: EGF(R^1).EGFR(CR1^2,L^1,Y1068=U).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)>EGF(R^1).EGFR(CR1,L^1,Y1068=U)+EGF(R^1).EGFR(CR1,L^1,Y1068=U)|0.1\n", + "7: EGF(R^1).EGFR(CR1^2,L^1,Y1068=U).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)|1\n", + "8: EGF(R^1).EGFR(CR1^2,L^1,Y1068=U).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)>|0.01\n", + "9: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P)+EGF(R^1).EGFR(CR1,L^1,Y1068=U)|0.1\n", + "10: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)|0.5\n", + "11: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=U).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)|4.505\n", + "12: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)+Grb2(SH2,SH3^1).Sos1(PxxP^1)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)|8.30565e-07\n", + "13: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)+Grb2(SH2,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)|8.30565e-07\n", + "14: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)>|0.01\n", + "15: EGF(R^1).EGFR(CR1,L^1,Y1068=P)>EGF(R)+EGFR(CR1,L,Y1068=P)|0.06\n", + "16: EGF(R^1).EGFR(CR1,L^1,Y1068=P)+EGF(R^1).EGFR(CR1,L^1,Y1068=P)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)|2.76855e-06\n", + "17: EGF(R^1).EGFR(CR1,L^1,Y1068=P)+EGF(R^1).EGFR(CR1,L^1,Y1068=U)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)|5.5371e-06\n", + "18: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P)+EGF(R^1).EGFR(CR1,L^1,Y1068=P)|0.1\n", + "19: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)+EGF(R^1).EGFR(CR1,L^1,Y1068=U)|0.1\n", + "20: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)+EGF(R^1).EGFR(CR1,L^1,Y1068=U)|0.1\n", + "21: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)|0.5\n", + "22: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)|0.5\n", + "23: EGF(R^1).EGFR(CR1,L^1,Y1068=P)>EGF(R^1).EGFR(CR1,L^1,Y1068=U)|4.505\n", + "24: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)|9.01\n", + "25: EGF(R^1).EGFR(CR1,L^1,Y1068=P)+Grb2(SH2,SH3^1).Sos1(PxxP^1)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)|8.30565e-07\n", + "26: EGF(R^1).EGFR(CR1,L^1,Y1068=P)+Grb2(SH2,SH3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)|8.30565e-07\n", + "27: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)+Grb2(SH2,SH3^1).Sos1(PxxP^1)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)|1.66113e-06\n", + "28: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)+Grb2(SH2,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)|1.66113e-06\n", + "29: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)+Grb2(SH2,SH3^1).Sos1(PxxP^1)|0.05\n", + "30: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=U).EGF(R^3)+Grb2(SH2,SH3)|0.05\n", + "31: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)+Sos1(PxxP)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)|5.5371e-06\n", + "32: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)+Sos1(PxxP)|0.06\n", + "33: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)>|0.01\n", + "34: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)>|0.01\n", + "35: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)>|0.01\n", + "36: EGF(R)+EGFR(CR1,L,Y1068=P)>EGF(R^1).EGFR(CR1,L^1,Y1068=P)|1.49502e-06\n", + "37: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)>EGF(R)+EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3^2).Sos1(PxxP^2)|0.06\n", + "38: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)>EGF(R)+EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3)|0.06\n", + "39: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3^6).Sos1(PxxP^6).Grb2(SH2^3,SH3^7).Sos1(PxxP^7)|2.76855e-06\n", + "40: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)|5.5371e-06\n", + "41: EGF(R^1).EGFR(CR1,L^1,Y1068=P)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)|5.5371e-06\n", + "42: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)+EGF(R^1).EGFR(CR1,L^1,Y1068=U)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)|5.5371e-06\n", + "43: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3)|2.76855e-06\n", + "44: EGF(R^1).EGFR(CR1,L^1,Y1068=P)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)|5.5371e-06\n", + "45: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)+EGF(R^1).EGFR(CR1,L^1,Y1068=U)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)|5.5371e-06\n", + "46: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)>EGF(R^1).EGFR(CR1,L^1,Y1068=P)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)|0.1\n", + "47: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)|0.1\n", + "48: EGFR(CR1,L,Y1068=P)>EGFR(CR1,L,Y1068=U)|4.505\n", + "49: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3^5).Sos1(PxxP^5)|4.505\n", + "50: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=U).EGF(R^4).Grb2(SH2^3,SH3)|4.505\n", + "51: EGFR(CR1,L,Y1068=P)+Grb2(SH2,SH3^1).Sos1(PxxP^1)>EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3^2).Sos1(PxxP^2)|8.30565e-07\n", + "52: EGFR(CR1,L,Y1068=P)+Grb2(SH2,SH3)>EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3)|8.30565e-07\n", + "53: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)+Grb2(SH2,SH3^1).Sos1(PxxP^1)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3^6).Sos1(PxxP^6).Grb2(SH2^3,SH3^7).Sos1(PxxP^7)|8.30565e-07\n", + "54: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)+Grb2(SH2,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)|8.30565e-07\n", + "55: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)+Grb2(SH2,SH3^1).Sos1(PxxP^1)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)|8.30565e-07\n", + "56: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)+Grb2(SH2,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3)|8.30565e-07\n", + "57: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P)+Grb2(SH2,SH3^1).Sos1(PxxP^1)|0.05\n", + "58: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P)+Grb2(SH2,SH3)|0.05\n", + "59: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)+Grb2(SH2,SH3^1).Sos1(PxxP^1)|0.05\n", + "60: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P).EGF(R^3)+Grb2(SH2,SH3)|0.05\n", + "61: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)+Sos1(PxxP)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)|5.5371e-06\n", + "62: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)+Sos1(PxxP)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)|5.5371e-06\n", + "63: EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)+Sos1(PxxP)|0.06\n", + "64: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)+Sos1(PxxP)|0.06\n", + "65: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)>|0.01\n", + "66: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)>|0.01\n", + "67: EGF(R)+EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3^2).Sos1(PxxP^2)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)|1.49502e-06\n", + "68: EGF(R)+EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)|1.49502e-06\n", + "69: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3^6).Sos1(PxxP^6).Grb2(SH2^3,SH3^7).Sos1(PxxP^7)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)|0.1\n", + "70: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3^3).Sos1(PxxP^3)|0.1\n", + "71: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3)>EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)+EGF(R^1).EGFR(CR1,L^1,Y1068=P^2).Grb2(SH2^2,SH3)|0.1\n", + "72: EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3^2).Sos1(PxxP^2)>EGFR(CR1,L,Y1068=P)+Grb2(SH2,SH3^1).Sos1(PxxP^1)|0.05\n", + "73: EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3)>EGFR(CR1,L,Y1068=P)+Grb2(SH2,SH3)|0.05\n", + "74: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3^6).Sos1(PxxP^6).Grb2(SH2^3,SH3^7).Sos1(PxxP^7)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)+Grb2(SH2,SH3^1).Sos1(PxxP^1)|0.1\n", + "75: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)+Grb2(SH2,SH3^1).Sos1(PxxP^1)|0.05\n", + "76: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3^5).Sos1(PxxP^5)+Grb2(SH2,SH3)|0.05\n", + "77: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P).EGFR(CR1^2,L^3,Y1068=P^4).EGF(R^3).Grb2(SH2^4,SH3)+Grb2(SH2,SH3)|0.1\n", + "78: EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3)+Sos1(PxxP)>EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3^2).Sos1(PxxP^2)|5.5371e-06\n", + "79: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)+Sos1(PxxP)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3^6).Sos1(PxxP^6).Grb2(SH2^3,SH3^7).Sos1(PxxP^7)|5.5371e-06\n", + "80: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3)+Sos1(PxxP)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)|1.10742e-05\n", + "81: EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3^2).Sos1(PxxP^2)>EGFR(CR1,L,Y1068=P^1).Grb2(SH2^1,SH3)+Sos1(PxxP)|0.06\n", + "82: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3^6).Sos1(PxxP^6).Grb2(SH2^3,SH3^7).Sos1(PxxP^7)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)+Sos1(PxxP)|0.12\n", + "83: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)>EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3)+Sos1(PxxP)|0.06\n", + "84: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3^6).Sos1(PxxP^6).Grb2(SH2^3,SH3^7).Sos1(PxxP^7)>|0.01\n", + "85: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3^6).Sos1(PxxP^6)>|0.01\n", + "86: EGF(R^1).EGFR(CR1^2,L^1,Y1068=P^3).EGFR(CR1^2,L^4,Y1068=P^5).EGF(R^4).Grb2(SH2^5,SH3).Grb2(SH2^3,SH3)>|0.01\n" + ] + } + ], + "source": [ + "print(\"{} species and {} reactions were generated.\".format(len(newm.list_species()), len(newm.reaction_rules())))\n", + "\n", + "for i, sp in enumerate(newm.list_species()):\n", + " print(\"{}: {}\".format(i + 1, sp.serial()))\n", + "\n", + "for i, rr in enumerate(newm.reaction_rules()):\n", + " print(\"{}: {}\".format(i + 1, rr.as_string()))" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + "
\n", + " \n", + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "species_list = [\"EGFR\",\n", + " \"EGF(R)\",\n", + " \"EGFR(CR1^_)\",\n", + " \"EGFR(Y1068=P^_0)\",\n", + " \"Grb2(SH2, SH3^1).Sos1(PxxP^1)\",\n", + " \"EGFR(Y1068^1).Grb2(SH2^1, SH3^2).Sos1(PxxP^2)\"]\n", + "run_simulation(120, model=newm, y0=y0, species_list=species_list,\n", + " opt_kwargs={'interactive': True, 'to_png': True})" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.4.3" + } + }, + "nbformat": 4, + "nbformat_minor": 0 +}