From f9e3464e60b9dea89365687783ab850092ca5b6a Mon Sep 17 00:00:00 2001 From: jrfaeder Date: Thu, 22 Feb 2024 17:32:43 -0500 Subject: [PATCH] File changes on NFsim issue --- .DS_Store | Bin 6148 -> 6148 bytes Issues/.DS_Store | Bin 6148 -> 6148 bytes Issues/nfsim_indrani/.gitignore | 3 + Issues/nfsim_indrani/deleteMolecules.bngl | 22 + .../2024_02_07__16_11_07/deleteMolecules.bngl | 22 + .../2024_02_07__16_11_47/deleteMolecules.bngl | 22 + .../2024_02_07__16_11_47/deleteMolecules.net | 14 + .../deleteMolecules_test.bngl | 20 + .../deleteMolecules_changed.bngl | 25 + Issues/nfsim_indrani/run_nf.ipynb | 1196 +++++++++++++++++ Issues/nfsim_indrani/run_pybng.ipynb | 86 ++ Issues/nfsim_indrani/run_pybng.py | 8 + .../nfsim_indrani/test_deleteMolecules.bngl | 31 + Issues/nfsim_indrani/test_deleteMolecules.xml | 171 +++ .../test_deleteMolecules_changed.bngl | 21 + .../test_deleteMolecules_simple.bngl | 31 + Issues/nfsim_indrani/test_totalRate.bngl | 31 + Issues/nfsim_indrani/test_totalRate.xml | 174 +++ .../nfsim_indrani/test_totalRate_changed.bngl | 24 + Issues/paramchange_rama/param_change.ipynb | 160 +++ Issues/paramchange_rama/simple.bngl | 16 + .../simple/2024_02_13__09_14_02/simple.bngl | 22 + Issues/paramchange_rama/simple_sbml.xml | 70 + 23 files changed, 2169 insertions(+) create mode 100644 Issues/nfsim_indrani/.gitignore create mode 100644 Issues/nfsim_indrani/deleteMolecules.bngl create mode 100644 Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules.bngl create mode 100644 Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.bngl create mode 100644 Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.net create mode 100644 Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules_test.bngl create mode 100644 Issues/nfsim_indrani/deleteMolecules_changed.bngl create mode 100644 Issues/nfsim_indrani/run_nf.ipynb create mode 100644 Issues/nfsim_indrani/run_pybng.ipynb create mode 100644 Issues/nfsim_indrani/run_pybng.py create mode 100644 Issues/nfsim_indrani/test_deleteMolecules.bngl create mode 100644 Issues/nfsim_indrani/test_deleteMolecules.xml create mode 100644 Issues/nfsim_indrani/test_deleteMolecules_changed.bngl create mode 100644 Issues/nfsim_indrani/test_deleteMolecules_simple.bngl create mode 100644 Issues/nfsim_indrani/test_totalRate.bngl create mode 100644 Issues/nfsim_indrani/test_totalRate.xml create mode 100644 Issues/nfsim_indrani/test_totalRate_changed.bngl create mode 100644 Issues/paramchange_rama/param_change.ipynb create mode 100644 Issues/paramchange_rama/simple.bngl create mode 100644 Issues/paramchange_rama/simple/2024_02_13__09_14_02/simple.bngl create mode 100644 Issues/paramchange_rama/simple_sbml.xml diff --git a/.DS_Store b/.DS_Store index 875187b664a1b15180a40b063bbf1bb93d3e0f67..8b9ef2d25dbda507e52aba0a7c3bc9a1be8a3f80 100644 GIT binary patch delta 21 ccmZoMXffC@hmpg~(nLqW$jD&x62=5E07p0m4*&oF delta 21 ccmZoMXffC@hmph7!cs@U$lQGM62=5E07s(+9smFU diff --git a/Issues/.DS_Store b/Issues/.DS_Store index 12fecd2df758e1b5e1d2622545201b4aa52937ee..1349b565d68f6700c9725faa84f9814fbb5e04ae 100644 GIT binary patch delta 21 ccmZoMXffEZiiyL_(nLqW$jD&xCZ-@!07yj!9smFU delta 21 ccmZoMXffEZiiyM2!cs@U$lQGMCZ-@!07$R~EdT%j diff --git a/Issues/nfsim_indrani/.gitignore b/Issues/nfsim_indrani/.gitignore new file mode 100644 index 00000000..3a136634 --- /dev/null +++ b/Issues/nfsim_indrani/.gitignore @@ -0,0 +1,3 @@ +!*.gdat +!*.net +BioModel* diff --git a/Issues/nfsim_indrani/deleteMolecules.bngl b/Issues/nfsim_indrani/deleteMolecules.bngl new file mode 100644 index 00000000..2561dc48 --- /dev/null +++ b/Issues/nfsim_indrani/deleteMolecules.bngl @@ -0,0 +1,22 @@ +begin parameters + d 1 + kdeg_Ste2_PO4 1 +end parameters + +begin molecule types + CELL() + Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4) + Pheromone(Ste2_site) +end molecule types + +begin seed species + Pheromone(Ste2_site!1).Ste2(Pheromone_site!1,Gpa1_site,Sst2_site,Yck_site,S338_S339~PO4) 1 +end seed species + +begin reaction rules +# Ste2(S338_S339~PO4) -> CELL() kdeg_Ste2_PO4 DeleteMolecules + Ste2(S338_S339~PO4) -> CELL() 100 DeleteMolecules +end reaction rules + +#writeModel({suffix=>"test",evaluate_expressions=>1}) +generate_network({overwrite=>1}) diff --git a/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules.bngl b/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules.bngl new file mode 100644 index 00000000..d2a68a7a --- /dev/null +++ b/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules.bngl @@ -0,0 +1,22 @@ +begin parameters + d 1 + kdeg_Ste2_PO4 1 +end parameters + +begin molecule types + CELL() + Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4) + Pheromone(Ste2_site) +end molecule types + +begin seed species + Pheromone(Ste2_site!1).Ste2(Pheromone_site!1,Gpa1_site,Sst2_site,Yck_site,S338_S339~PO4) 1 +end seed species + +begin reaction rules +# Ste2(S338_S339~PO4) -> CELL() kdeg_Ste2_PO4 DeleteMolecules + Ste2(S338_S339~PO4) -> CELL() 100 DeleteMolecules +end reaction rules + +writeModel({suffix=>"test",evaluate_expressions=>1}) +generate_network({overwrite=>1}) diff --git a/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.bngl b/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.bngl new file mode 100644 index 00000000..d2a68a7a --- /dev/null +++ b/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.bngl @@ -0,0 +1,22 @@ +begin parameters + d 1 + kdeg_Ste2_PO4 1 +end parameters + +begin molecule types + CELL() + Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4) + Pheromone(Ste2_site) +end molecule types + +begin seed species + Pheromone(Ste2_site!1).Ste2(Pheromone_site!1,Gpa1_site,Sst2_site,Yck_site,S338_S339~PO4) 1 +end seed species + +begin reaction rules +# Ste2(S338_S339~PO4) -> CELL() kdeg_Ste2_PO4 DeleteMolecules + Ste2(S338_S339~PO4) -> CELL() 100 DeleteMolecules +end reaction rules + +writeModel({suffix=>"test",evaluate_expressions=>1}) +generate_network({overwrite=>1}) diff --git a/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.net b/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.net new file mode 100644 index 00000000..e40367ea --- /dev/null +++ b/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.net @@ -0,0 +1,14 @@ +# Created by BioNetGen 2.9.0 +begin parameters + 1 d 1 # Constant + 2 kdeg_Ste2_PO4 1 # Constant + 3 _rateLaw1 100 # Constant +end parameters +begin species + 1 Pheromone(Ste2_site!1).Ste2(Gpa1_site,Pheromone_site!1,S338_S339~PO4,Sst2_site,Yck_site) 1 + 2 CELL() 0 + 3 Pheromone(Ste2_site) 0 +end species +begin reactions + 1 1 2,3 _rateLaw1 #_R1 +end reactions diff --git a/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules_test.bngl b/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules_test.bngl new file mode 100644 index 00000000..e175ec26 --- /dev/null +++ b/Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules_test.bngl @@ -0,0 +1,20 @@ +# Created by BioNetGen 2.9.0 + +begin model +begin parameters + d 1 + kdeg_Ste2_PO4 1 + _rateLaw1 100 +end parameters +begin molecule types + CELL() + Pheromone(Ste2_site) + Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4) +end molecule types +begin species + Pheromone(Ste2_site!1).Ste2(Gpa1_site,Pheromone_site!1,S338_S339~PO4,Sst2_site,Yck_site) 1 +end species +begin reaction rules + _R1: Ste2(S338_S339~PO4) -> CELL() _rateLaw1 DeleteMolecules +end reaction rules +end model diff --git a/Issues/nfsim_indrani/deleteMolecules_changed.bngl b/Issues/nfsim_indrani/deleteMolecules_changed.bngl new file mode 100644 index 00000000..3aeb823d --- /dev/null +++ b/Issues/nfsim_indrani/deleteMolecules_changed.bngl @@ -0,0 +1,25 @@ +begin model + +begin parameters + d 1 + kdeg_Ste2_PO4 1 + _rateLaw1 100 +end parameters + +begin molecule types + CELL() + Pheromone(Ste2_site) + Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4) +end molecule types + +begin species + Pheromone(Ste2_site!1).Ste2(Gpa1_site,Pheromone_site!1,S338_S339~PO4,Sst2_site,Yck_site) 1 +end species + +begin reaction rules + _R1: Ste2(S338_S339~PO4) -> CELL() _rateLaw1 DeleteMolecules +end reaction rules + +end model + +generate_network({overwrite=>1}) \ No newline at end of file diff --git a/Issues/nfsim_indrani/run_nf.ipynb b/Issues/nfsim_indrani/run_nf.ipynb new file mode 100644 index 00000000..20617645 --- /dev/null +++ b/Issues/nfsim_indrani/run_nf.ipynb @@ -0,0 +1,1196 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import bionetgen" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "BioNetGen version 2.9.0\n", + "Reading from file /Users/faeder/Library/CloudStorage/OneDrive-UniversityofPittsburgh/Code/bionetgen/Issues/nfsim_indrani/BioModel_ZAP70_SYK_v8_test1.bngl (level 0)\n", + "Read 45 parameters.\n", + "Read 7 molecule types.\n", + "Read 8 species.\n", + "Read 13 observable(s).\n", + "Read 0 functions.\n", + "Read 179 reaction rule(s).\n", + "ACTION: simulate_nf( )\n", + "Wrote model in xml format to ./BioModel_ZAP70_SYK_v8_test1.xml.\n", + "Running NFsim on Jamess-MBP-3\n", + "full command: /Users/faeder/opt/anaconda3/lib/python3.9/site-packages/bionetgen/bng-mac/bin/NFsim -xml ./BioModel_ZAP70_SYK_v8_test1.xml -o ./BioModel_ZAP70_SYK_v8_test1.gdat -sim 270 -oSteps 1000 -seed 1 -cb -ss ./BioModel_ZAP70_SYK_v8_test1.species\n", + "[simulation PID is: 37761]\n", + "starting NFsim v1.14.1...\n", + "\n", + "Seeding random number generator with: 1\n", + "reading xml file (./BioModel_ZAP70_SYK_v8_test1.xml)\n", + "[------\n", + "Warning! You have a binding rxn (bound_ZAP_dephosphorylation_SHP) that allows a moleculeType to bind another of the same type.\n", + "Make sure that is correct, because this can potentially make long polymers or large aggregates.\n", + "\n", + "\n", + "Warning! You have a binding rxn (free_ZAP_dephosphorylation_SHP) that allows a moleculeType to bind another of the same type.\n", + "Make sure that is correct, because this can potentially make long polymers or large aggregates.\n", + "\n", + "\n", + "Warning! You have a binding rxn (pSYK_transphosphorylation_uSYK) that allows a moleculeType to bind another of the same type.\n", + "Make sure that is correct, because this can potentially make long polymers or large aggregates.\n", + "\n", + "\n", + "Warning! You have a binding rxn (free_SYK_dephosphorylation_SHP) that allows a moleculeType to bind another of the same type.\n", + "Make sure that is correct, because this can potentially make long polymers or large aggregates.\n", + "\n", + "\n", + "Warning! You have a binding rxn (bound_SYK_dephosphorylation_SHP) that allows a moleculeType to bind another of the same type.\n", + "Make sure that is correct, because this can potentially make long polymers or large aggregates.\n", + "\n", + "-]\n", + "preparing simulation...\n", + "\n", + "\n", + "\n", + "Equilibrating for :0s. Please wait.\n", + "\n", + "simulating system for: 2.700000e+02 second(s).\n", + "\n", + "Sim time: 0.000000e+00\tCPU time (total): 1.280000e-04s\t events (step): 0\n", + "Sim time: 2.700000e-01\tCPU time (total): 1.266900e-02s\t events (step): 1861\n", + "Sim time: 5.400000e-01\tCPU time (total): 4.125900e-02s\t events (step): 774\n", + "Sim time: 8.100000e-01\tCPU time (total): 7.720800e-02s\t events (step): 919\n", + "Sim time: 1.080000e+00\tCPU time (total): 1.101340e-01s\t events (step): 743\n", + "Sim time: 1.350000e+00\tCPU time (total): 1.399100e-01s\t events (step): 700\n", + "Sim time: 1.620000e+00\tCPU time (total): 1.672990e-01s\t events (step): 664\n", + "Sim time: 1.890000e+00\tCPU time (total): 1.990210e-01s\t events (step): 757\n", + "Sim time: 2.160000e+00\tCPU time (total): 2.292430e-01s\t events (step): 675\n", + "Sim time: 2.430000e+00\tCPU time (total): 2.620840e-01s\t events (step): 710\n", + "Sim time: 2.700000e+00\tCPU time (total): 2.919230e-01s\t events 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2.689200e+02\tCPU time (total): 4.962736e+00s\t events (step): 16\n", + "Sim time: 2.691900e+02\tCPU time (total): 4.962767e+00s\t events (step): 8\n", + "Sim time: 2.694600e+02\tCPU time (total): 4.962808e+00s\t events (step): 9\n", + "Sim time: 2.697300e+02\tCPU time (total): 4.962837e+00s\t events (step): 8\n", + "Sim time: 2.697300e+02\tCPU time (total): 4.962864e+00s\t events (step): 12\n", + "\n", + "You just simulated 118658 reactions in 4.962887e+00s\n", + "( 2.390907e+04 reactions/sec, 4.182514e-05 CPU seconds/event )\n", + "Null events: 0 (4.182514e-05 CPU seconds/non-null event )\n", + "\n", + "\n", + "saving list of final molecular species...\n", + "\n", + "done. Total CPU time: 5.57231s\n", + "\n", + "SpeciesLabel max molecule threshold set to 20.\n", + "WARNING: Species with more than 20 molecules will be labeled with the Quasi method.\n", + "readNFspecies::Reading from file ./BioModel_ZAP70_SYK_v8_test1.species\n", + "Read 7 unique species of 7 total.\n", + "SpeciesLabel max molecule threshold set to 0.\n", + "(all species will be labeled with the Auto method)\n", + "CPU TIME: simulate_nf 5.63 s.\n", + "Finished processing file /Users/faeder/Library/CloudStorage/OneDrive-UniversityofPittsburgh/Code/bionetgen/Issues/nfsim_indrani/BioModel_ZAP70_SYK_v8_test1.bngl.\n", + "CPU TIME: total 5.93 s.\n" + ] + } + ], + "source": [ + "res= bionetgen.run(\"BioModel_ZAP70_SYK_v8_test1.bngl\")" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "import matplotlib.pyplot as plt\n", + "\n", + "r= res[0]\n", + "names= ['PZAP_total']# r.dtype.names\n", + "for name in names:\n", + " if name != \"time\":\n", + " plt.plot(r['time'], r[name], label = name)\n", + "plt.xlabel(\"time\")\n", + "plt.ylabel(\"species (counts)\")\n", + "_ = plt.legend(frameon = False)" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [], + "source": [ + "#res2= bionetgen.core.tools.BNGResult(direct_path='BioModel_ZAP70_SYK_v8_test1/2024_02_02__10_05_13/BioModel_ZAP70_SYK_v8_test1.gdat')\n", + "res2= bionetgen.core.tools.BNGResult(direct_path='BioModel_ZAP70_SYK_v8_test1.gdat')\n", + "r2= res2[0]\n", + "r3= bionetgen.core.tools.BNGResult(direct_path='BioModel_ZAP70_SYK_v8_test2.gdat')[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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6H3/8MR07diQ7OxtnZ2f++OMPjhw5wrZt29Ba079/fzZs2ED16tVZvHgxf/75Jw4ODowdO5b58+dz++2388orr7Bjxw7c3d259dZbadmyJWAZKmLatGmX/Xdu0KABS5cuvfnX8Rqk6JeRosJCDp5ZiNnbnv4tnzc6zmWUUnx2+2d8uusTFh5ZTOzm/0nRF39TpUoVduzYwcaNG1m7di1DhgxhypQpjBw58rJ1lyxZwuzZsykoKCA+Pp79+/dfLPqDBg0CoHXr1heHM/63oY0/+OADfvjhBwBOnz7NkSNH/lb0N23axMCBA3Fzc7u4/40bN9K/f3+CgoIuDgXdunVrTpw48a9DL1+qY8eOPP300wwbNoxBgwbh7+/PH3/8wR9//HGxcGdnZ3PkyBH27NnDjh07iIiwfHfm/Pnz1KhRg8jISLp27Ur16pbhz4cMGcLhw4cBGDZsGMOGDbuRl6BESNEvI3u2/so8TxMN7WrRp91Qo+NckbeLN2NaPsriw0vY7XScVq8GcbzZY7ToNxZn1ypGxxOX+pcr8tJkZ2dH165d6dq1K82bN2fevHmXFf3jx48zffp0tm/fjqenJyNHjrw4WiZwsXvIzs6Ogmt0I65bt45Vq1axZcsWXF1d6dq169/2dS0XjnXheOfPn6eoqOiqQy9fauLEifTt25fly5fTsWNHfv/9d7TWPP/88zzyyN+7Zz/88ENGjBhxccC3C3788cer7t+oK33p0y8DW+e/xrlND3PeZOLRiKf4x8ik5YqPiw/d63RjQbVqHHTJoe3+ydhNDWDXH98YHU0Y7NChQxw5cuTi8+joaOrWtczRULVq1Yt93pmZmbi5ueHu7k5iYiIrVqy45r6vNrRxRkYGnp6euLq6cvDgQbZu3XrZtp06deLHH38kJyeHc+fO8cMPP9CpU6fL1rvg34ZevtTRo0dp3rw5EyZMICIigoMHD9KzZ0/mzp1LdnY2YBnlMykpiW7durF06VKSkpIASE1N5eTJk7Rt25b169eTkpKC2Wy+eEywXOlfacjm0iz4IFf6ZaLdkXeZ6uWBA3Z0qn+r0XGu6fXOb3Js+Qled/bhzdiqBJw7iN/ml8jpcId8a9eGZWdnM378eNLT07G3t6dBgwYXP1gdM2YMvXr1wtfXl7Vr19KyZUuaNGlCnTp16Nix4zX3fbWhjXv16sWsWbMuzkPbrl27y7Zt1aoVI0eOpE2bNoBlQpeWLVty4sSJqx7vakMvX2rGjBmsXbsWk8lEcHAwvXv3xsnJiQMHDtC+fXvA0uX1zTff0KxZM95880169OhBUVERDg4OfPzxx7Rr145XX32V9u3b4+HhcbGr6Xpd+JA5Ozsbf39/5syZc9X5Cq6XDMNQyhJjj3JuXhuG+QcS6hvOp7d/anSk67I5bjOPrLL8CTs98L/0XPsEWwIeof2D7xiczHbJMAziSmQYhnIm7q+NfOLhTq4q4slWTxod57p18OvAQ80fAuDd5AVEunUi7OQXbP/xIwrMl89gJISoGKTol7LME5tZ6+rKwPp30tS7Yl2l/afVf5jVfRZnzp3h8+AaxNn7EhE9iaS3QjibcOraOxBClDtS9EvZkZwo8kyKOxr2NzrKTeng24Fm3s3Ymrydw/dOJrLJRHx1Ij6zmsuHu0JUQFL0S9HuNYvY6ZKJd5ETLaobO+TCzVJKMbfnXNwc3Fh28hfa3vs8W3xHABD85xOcP5dlcEIhxI2Qol9KEs4lMO7EZDa5utCzfv+rzn5VEbg5uDG0yVC2nNlC4rlE2o/5gB0R/8NRFXJkW/mdAFoIcbmKW4nKuadWjCXdzvJ4SOj9xoYpAXc2uBOA0X+MJrcgl8adBpOMJ2rrR8YGE0LcECn6pcBcZOZgdgx3ZOWyuPt86nnUMzpSsQVUC+DOBndyMvMkT657ki1pURwIGETzvF2cOXHI6HiijMjQysVzI0MrR0dH0759+4v/vRcvXlwiGa5Z9JVSc5VSSUqpvy5pm6aUOqiU2qOU+kEp5XHJsueVUjFKqUNKqZ6XtPeytsUopSaWSPpy6ucfp1CgNL46gGZ+oUbHKTETIiYwqOEg/oz7k6fXPc2metUo0ooz37+ALioyOp4oZTK0ctlydXXlq6++Yt++ffz22288+eSTpKenF3u/13Ol/yXQ6x9tK4EQrXUocBh4HkAp1Qy4Fwi2bjNTKWWnlLIDPgZ6A82A+6zrVkpnTlu+dh7R7QWDk5QsVwdXJrWdxKCGlgGzlp5exvoqrQnPXMW2794zOJ0obTK0ctkOrdyoUSMaNrSMxuvr60uNGjVITk6+7u2v5prDMGitNyilAv/R9sclT7cCd1kfDwAWaa3zgONKqRigjXVZjNb6GIBSapF13f3Fi1/+5Oflkq4ScNRVCW/S1eg4Jc7RzpHXOrzG8GbDGbxsMKvbtKXOhjTa7nudrXmZtB36CsokvYalbeq2qRxMvbxQFUcTryZMaDPhqstlaGXjhlbetm0b+fn51K9f/wZf1cuVxNg7DwIXOpv8sLwJXBBrbQM4/Y/2tlfamVJqDDAGuDj+RkVyZMcaDjjZU9exNnYmO6PjlJr6HvXpXrc7a86so2OLYTTY+TrtYmbA6zPYUvdR2o+aanREUcJkaGVjhlaOj4/ngQceYN68eZhK4IKqWEVfKTUJKADmFzuJldZ6NjAbLGPvlNR+y0rCvl/Y4+zE6Po9jI5S6saFjWNT3Ca+UJHUGLAE85bvaJ74E+1PzmLntP2oFkNo2aPi37lUHv3bFXlpkqGVy3Zo5czMTPr27cvkyZOvONjczbjptw2l1EigHzBM/38HXBxQ55LV/K1tV2uvdLLTLHcztPK74lhHlUqgeyATIiYQkx7Dh4kLafPYLPIe30kmbrQ6t4GWmx/nYNRqo2OKEiJDK5ft0Mr5+fkMHDiQ4cOHc9ddd12W72bd1JW+UqoX8BzQRWt96Uf2y4AFSql3AV+gIbANUEBDpVQQlmJ/L1A+ZxIphvSzCeSaEgAvGng0MDpOmRjYcCBZ+VlMi5rGq5tf5fWOr5M6djtRW38mZMeL1Pl5KEfsvqVhy85GRxXFJEMrl+3QykuWLGHDhg2kpKTw5ZdfApZbPm90eOZ/uubQykqphUBXwAdIBF7BcreOE5BiXW2r1vpR6/qTsPTzFwBPaq1XWNv7ADMAO2Cu1nrytcJVtKGVo1cv4pf9E1nm4UPk/dvL9WQpJUlrzfObnufXY7/yeY/PaVvb8nHNkV0bcFs2Gl+dRKTPYNqM/Vw+5C0GGVpZXEmJD62stb5Pa11ba+2gtfbXWs/RWjfQWtfRWodZfx69ZP3JWuv6WuvGFwq+tX251rqRddk1C35FlBW3l5VurrT0aWkzBR8s4/OMCxuHQvHUuqfIMVv++GvYsjPmexYB0Pbsd0R+MsbImEII5Bu5JWplxh+k2tkxrPkDRkcpc/5V/fmk+ydk5Wfx2KrHeDvybTLyMqjbtDX5zycC0C75W2J2bzI4qRC2TYp+CSkw5xPtnEX9wqp09rfN/uuOfh15NvxZjmccZ8HBBYz+fTRaaxydnIkbvpkkvHD98UHM+ZffHieuT3me6U6UvZv59yBFv4Rs/esPjjs6EOEWYnQUQw0PHs76IesJrBbIobRD/HzsZwD86gVzptPb+OpEdn80TIZtuAnOzs6kpKRI4ReApeCnpKTg7Ox8Q9vJHLklwFxkps3X4RRQxOctp9M2tHgTF1cG+YX5DF42mJTcFJYPXI6Hswe6qIjI2eNolzCfyKYv0HaIMfeaV1Rms5nY2Ngbuk9dVG7Ozs74+/vj4ODwt/Z/+yC3JL6Ra/OiEqIooIieWZo2IbcbHadccLRz5N2u73LXz3fx6Z5PmdBmAspkos3DH7J7egwt90/lUFQEjcNvMzpqheHg4EBQUJDRMUQFJ907JSAqfjsmremnIuSWxEs09GzIwAYDWXRwEetPrwfAZGdH4ENfc9bkjfsvDxN37IDBKYWwLVKhSsCu2G3UM5tx9W1pdJRyZ1zLcfi4+jBuzTiik6IBcPeuybkBc3HXmbjPu5W4Y/uMDSmEDZGiX0xaaw5lHCI4Lx+veq2MjlPu+Lj4MK/XPAAeWPEAW+MtX6NvGNaJhHt+wUQRid9J374QZUWKfjFFJ0eTqXMJynMmKLhkBkSqbHyr+DKz20wAHl35KEk5lvFJgoLbstenN02yt3E24fS/7UIIUUKk6BfTt4e+pUqhpr5DKHb28rn41XTy78TrHV6nUBcyeNlgMvIyAKjd8ykcKKBoVmd2/Pq5wSmFqPyk6BfTgbP7CMvLxdm70k4EVmIGNhzI+7e+T3peOrcsuoWNsRvxbRDC3vbvkmOqQui256R/X4hSJkW/GNJy0ziaeZzgvHxcajc2Ok6FcFvAbbza/lUAxq4ey9RtUwnrORyXB3/EjD3539xHRmrxp4QTQlyZFP1i2Ht2LxpNh/O5eNWR0Q+v1+BGg1l510pCfUJZdGgR41aPw7m6D8e6f4Z/YSyxswZRYM43OqYQlZIU/WLYmbgTgKC8AmrVbWJwmoqlllstvunzDQ83f5iNcRuZsHECzW65g501BhKcv4ftC14zOqIQlZIU/ZuUX5jPksNLaJ+TT6J9Ixwcna69kfgbpRRPtHqCIY2H8Gfcn4z5YwzVh05it3MEIcfmkJIYa3REISodKfo36UjaEbLys7grK4P0+v2NjlOhvdD2BcaGjWVfyj7Grx2P6x1v4kABCXPuk24eIUqYFP2bdCzjGAANzGZcajU0OE3FZlImHmvxGFM7T+VU1il+yd3C3lavE5y/h6jPnzA6nhCVihT9m7Q1fituyokAcwFe/o2MjlMpdPLrRGf/zsz9ay7Hm/iw1WcQ7RIXErXsE6OjCVFpXLPoK6XmKqWSlFJ/XdLmpZRaqZQ6Yv3taW1XSqkPlFIxSqk9SqlWl2wzwrr+EaXUiNI5nbJhLjKz9vRaQgs8UVpRM0Bu1ywJSikmRkykhmsN3tj6BtEd23DYvhH1d77FyUPRRscTolK4niv9L4Fe/2ibCKzWWjcEVlufA/QGGlp/xgCfgOVNAsuE6m2BNsArF94oKqIdiTvIys+ibWYup+zq4uh0Y5MYiKurU60Oq+5axe11b+fjPTOZFtoMs8ql7sIu7Fj+hdHxhKjwrmdi9A1A6j+aBwDzrI/nAXde0v6VttgKeCilagM9gZVa61StdRqwksvfSCqMjbEbcTQ50jPjJGeryf35JU0pxdROU7m/6f1Epu1iTKNWHFfeNNw2iYNRq42OJ0SFdrN9+jW11vHWxwlATetjP+DSkbNirW1Xa7+MUmqMUipKKRWVnFw+v5m5+cxmQtyb4K8zKKodZnScSsnBzoEJbSbwXMRzHM0/w6etepOLE4E/D5Ex+IUohmJ/kKst8y2W2JyLWuvZWutwrXV49erVS2q3JSbhXAIx6TE0LrD0TnnUb2Nwosrt/mb3M6D+AH5N3cCZIV/jrMzE/vo2RYWFRkcTokK62aKfaO22wfo7ydoeB9S5ZD1/a9vV2iucPcl7AGh4+jiZuFE3uK3BiSq/oU2HAjDt2Cds8R5A25SfSH2jHgcj/zA4mRAVz80W/WXAhTtwRgA/XdI+3HoXTzsgw9oN9DvQQynlaf0At4e1rcI5nnEcgNbphzhStS3OLm4GJ6r8mnk3Y3iz4ew5u4cpdTJY0+QZfEinyYq7ZRx+IW7Q9dyyuRDYAjRWSsUqpUYDU4DblVJHgO7W5wDLgWNADPAZMBZAa50KvAFst/68bm2rcI5lHKOGkw/1dDLmGs2NjmMz/hv+X15q9xLHMo4R06wWe2+13MkT/8VwzPl5BqcTouK45qwfWuv7rrKo2xXW1cDjV9nPXGDuDaUrh45nHKe62QEAv/Z3G5zGdiiluKfxPaw5vYaFBxcycvDvRO24nfDMlRx6pzPuw7+hVoB8M1qIa5Fv5N4Ac6GZmPQY6pzL5Swe+NcLNjqSzRnebDhnz5/li7++oPWTS4gKn0Yd83G85rQjcsk7RscTotyTon8DdifvxlxkpnVWEqfdQlAm+c9X1trXbk+vwF58FP0Rvxz/lfB+Y0gfuYEDrq1ou38ykR+NkkHahPgXUrVuwMa4jdgre/rnJJBXq7XRcWySUoq3Or1FqxqtmLRpEh/t+ojagY0JeWYFW2sNo+3Z79m+4FWjYwpRbknRvwGHUg/ha+eFq9Z4NLrF6Dg2y8HkwIfdPqRPvT58uudT1pxeg529Pe0enclul7a0PTaTbTPuIyc7w+ioQpQ7UvRvwKG0Q/jlQr62IzC0o9FxbFo1x2q80fENgtyDeGvrW8RmWSZcCXzoa7bVvJvWaSuIf68LZ44fNDipEOWLFP3rlHgukbPnzxKcmcRh5+Zyf3454GByYGKbiaTnpTNs+TDisuNw965Ju7Gfsa/r51QvTMTny45s//Fjo6MKUW5I0b9O2xK2AdDzfDxZPi0NTiMu6ODbga96f0Vqbiq9vuvFljNbAAi99S6yR67jiFMwrXZN4vDOdcYGFaKckKJ/nU5mnkRpqJ9vxtGvhdFxxCWCfYKZ1mUaNV1rMnb1WFadXAWAb2Bj6o77ifM4Y/r1adKS46+xJyEqPyn61yk2OxbvQhMOQMuew42OI/6hV2Av5vWeRyPPRrz454uczrQMz1Clmicxnd4joOAkx798GF1UZHBSIYwlRf86xWXF4WfOZ7t7D0x2dkbHEVfgV8WPGV1nYFImHln1CDnmHADCut/HzhoDaXVuI9s+HiUjdAqbJkX/Op3KPEm9glwKq8u3cMuz2lVqc3/T+zmddZru33ZnyrYpFBYV0ubRT9nm2Y+2KT+y46ePjI4phGGk6F+HjLwMUvPSCDAX4N6wvdFxxDU81uIx5vacS2iNUOYfmM+iQ4sw2dkRMf5rYlUtXA8uNTqiEIaRon8d9p3dB0DTXDNBzeX+/PJOKUVErQg+uu0jbvG7hSnbpjD/wHyUycTpwLsIzt9D1LJPyM5MMzqqEGVOiv51iDtnme9FE4CzaxWD04jrZW+y5/1b3+e2OrcxZdsU3o58m6YDnyKNqoTvnIj53eYknI4xOqYQZUqK/nWIz4pHaQ2erYyOIm6Qo50j07tOp13tdiw4uIBxm54kddgytjV/FWedR+KCx8hISTQ6phBlRor+dTiecACfwkKcaocaHUXcBAeTA590/4QnWj7B7uTd/Hf/G7h2uZ3djZ+gxfltmD9sI5OtC5shRf86HMs4Sj1zAe51mhkdRdwke5M9D4c+zLQu04jNimX8mvG0vncih/svwwEzRV8P4vy5LKNjClHqpOhfQ0ZeBqfMiTTLy8ejZl2j44hi6hXYi6mdp3L2/FkWH1xMo1ZdONF5BnX0GXb/+J7R8YQodVL0r2Hv2b0UUMQtObl41fAzOo4oAZ38OxHqE8rU7VN5fcvrNO00gN0ubWhz+F32bvjJ6HhClKpiFX2l1FNKqX1Kqb+UUguVUs5KqSClVKRSKkYptVgp5Whd18n6PMa6PLBEzqCUncw8CYCn2QV7B0eD04iS4GBy4IteX9C3Xl++PfwtE/98Hv9HvyFR+eC5dgLH9283OqIQpeami75Syg94AgjXWocAdsC9wFTgPa11AyANGG3dZDSQZm1/z7peubcrLgrPwkJSPDsbHUWUIEc7R6Z0msL4luNZfWo1Y9aPZW/7Z/AoSqfO4h7sXvut0RGFKBXF7d6xB1yUUvaAKxAP3AZc+MrjPOBO6+MB1udYl3dTSqliHr9Uaa2JjN9Ku/O5VG19r9FxRCkYEzqGmd1mEp8dz6TkufzabypnlTeN1z3GyYM7jY4nRIm76aKvtY4DpgOnsBT7DGAHkK61LrCuFgtc6Aj3A05bty2wru/9z/0qpcYopaKUUlHJyck3G69ExGbHkl6UTXhuHrXqy+2alVVHv4582/9b3J3ceXP/dOZ3e5AkOxdcFg2We/hFpVOc7h1PLFfvQYAv4Ab0Km4grfVsrXW41jq8evXqxd1dsZzOsgzP62N2wKu6r6FZROnyq+LHt3d8S8/Annx5bCGDg2rwag07ds65V0blFJVKcbp3ugPHtdbJWmsz8D3QEfCwdvcA+ANx1sdxQB0A63J3IKUYxy91F+ZdLXJojDLJjU6VnaezJ9M6T+PzHp9za91ubHFz48cqp9j/zm0kxR03Op4QJaI4lewU0E4p5Wrtm+8G7AfWAndZ1xkBXLgHbpn1Odbla7TWuhjHL3Un009grzUuHjKcsq1QStG2dlve6fwOD4WOYY2bK4mmQ6R8OdToaEKUiOL06Udi+UB2J7DXuq/ZwATgaaVUDJY++znWTeYA3tb2p4GJxchdJo4mHsCvoADnWvJNXFs0MmQkjT0b82St6mx0jSVyxr2cTThldCwhiqVYfRZa61e01k201iFa6we01nla62Na6zZa6wZa67u11nnWdXOtzxtYlx8rmVMoPWeyTuFvLsArsLnRUYQB3Bzc+Kr3V/Su25sPvTz4wWEbiZ/1lSGZRYUmHdX/Ismchm9BIb71pejbKlcHV6Z2mcq4sHH8WsWNZ2oXsHX2YHJzso2OJsRNkaJ/Fam5qZxTZqoVuODk7Gp0HGEgpRSPtHiEybdM5qyDM697JbD0y+FGxxLipkjRv4o9yXsAqKVrGJxElBf96/fn2zu/x0G58a7rYSZ9+xAxaTIJi6hYpOhfRXTiLuy0prZLA6OjiHIkyD2IBQN/okmeHctyIhm4bCCTt06mnN+IJsRFUvSv4q+EPdQzm3H2bmR0FFHO1PTw5bX2nzA/NoGueV4sOrSIOX/NufaGQpQDUvSvIjbzJAHmAlxrNTY6iiiHGoZ2IMdrMDPORBNm8uf9ne/T/8f+rDi+wuhoQvwrKfpXUKSLSDKn4l9QQI16IUbHEeVU8NC3SMGLuUc3c3dWNfLzzvPchueYvWe20dGEuCop+leQnJOMmUK8zA7U8A0yOo4op6q6e1Htub3sqDWM55MP8N3+HdQtrMKHuz6UK35RbknRv4LTmZaB1nBuJmPuiH/l7FqFdo/OJP2RnRyu0p4lpw/QIN+RCRsm8NqW19ifst/oiEL8jVS0K4hJPgSAd7WGBicRFUV130BaPvsre+qOZeGZo0QU+rD08FKG/jqUn2JkCkZRfkjRv4LjyYcwaU2NqoFGRxEVTKv7XuaIYxhzTu3gf/b9CfYO5n9R/yPxnIzLL8oHKfpXcDLjOLULCqniKROhixvj6ORM8HOr2e3Shh5HPmJQkjt5hXk8ufZJzIVmo+MJIUX/SuKyTxNQYKZ6PZktS9w4k50dTZ/8mahqtzP45HyGZdXir5S/eGLtE1L4heGk6P+D1pqkonRqmhU1/eoZHUdUUI5OzrT6z2J2uXbg8YR1dDwHm+I2MWHjBPIL842OJ2yYFP1/SM9LJ0cV4lFYRe7cEcVisrOj3sNfs73Bk0xPTGZCShorT67k8dWPU1BUcO0dCFEKpKr9w6E0y507PuqyOduFuGHunj60u/81MkeuIyLHj2fPprM1fiv3L7+f9Nx0o+MJGyRF/x92JuxAaY2/c32jo4hKxDeoCdUe+IqI8748m5LGvpR9jFjcn4TseKOjCRsjRf8ftsVuoWG+mSqeMrqmKFm16zamwXMbaFznKd5KyOAYafRb2pvfTvxGjjnH6HjCRhSr6CulPJRSS5VSB5VSB5RS7ZVSXkqplUqpI9bfntZ1lVLqA6VUjFJqj1KqVcmcQsk6lXGCBmYz1erKnTui5Dk4OtH27mfoPm4fL6R44lWQx7Prn6XL4i48s+4ZEs4lUFhUaHRMUYkV90r/feA3rXUToAVwAMuE56u11g2B1fz/BOi9gYbWnzHAJ8U8donLMeeQXJiBR4E9DVp2NTqOqMRc3Kpyx0M/MSXFj48TkmiT58G60+u4fent3LLoFqZum0p2vkzJKEreTRd9pZQ70BmYA6C1ztdapwMDgHnW1eYBd1ofDwC+0hZbAQ+lVO2bPX5p+PnozwA4OtbHwdHJ4DSisqtSzZPQp5fj5NaHj09v47Vkbx5tNJqIWhF8c+AbJm6cSF5hntExRSVTnCv9ICAZ+EIptUsp9blSyg2oqbW+8OlUAlDT+tgPOH3J9rHWtr9RSo1RSkUppaKSk5OLEe/GHU60DI7VoWrbMj2usF32Do60GTuHrY3+S5+MbYz+7U2GZzdlYpuJrI9dz6MrHyUzP9PomKISKU7RtwdaAZ9orVsC5/j/rhwAtGUOuRuaR05rPVtrHa61Dq9evXox4t24mIS9NMjPx71BuzI9rrBtymSi3dCXiBnwE0edmhC+cyL1Nu/i7VveJjo5mkE/DWJn4k6jY4pKojhFPxaI1VpHWp8vxfImkHih28b6O8m6PA6oc8n2/ta2ciM+N4EAcwF1mrYxOoqwQY1adaHhM6vY7tGb9qc/w++7j3nOZygFRQWMWz2OqIQomYtXFNtNF32tdQJwWil1YT7BbsB+YBkwwto2ArgwruwyYLj1Lp52QMYl3UCGK9JFnNXZ1DCbqOruZXQcYaMcnZwJf2IBW4LG0eLcFu6LfJPXjp/HuVAx6vdRtFvQjvkH5hsdU1Rgxb17ZzwwXym1BwgD3gKmALcrpY4A3a3PAZYDx4AY4DNgbDGPXaKScpIwK03VoqpGRxE2TplMtB8xmawnDrG15r2E5sbxw/F9jErT+CkPpmybwlNrnyIjL8PoqKICsi/OxlrraCD8Cou6XWFdDTxenOOVpqNnDwNQ1VmmRxTlg7t3Tdo99ilFhYVELfuYe/d8yKMZkfzPoyZLWMWupF3c2eBOHg59GDcHN6PjigpCvpFrtX33cgACGvQ2OIkQf2eys6PNwCfwmbiXPfWfZNC5GryTdBbPjFTm/DWHdgva8fKfL8vtneK6SNG3OpNxDHutadGil9FRhLgiRydn2t3/Ks0mrsen/kQWxZ1hSqIjt/p35YeYH3hk5SNye6e4Jin6Vkn5ifiaC/H28TU6ihD/SplMRAz6D/s7/I++OTEMPWzmnc7vsDt5NyNWjCDhXILREUU5Vqw+/crkrM6keqGDjKEvKoyWPUcQeWQ97RIXcuarNTxRuzWzTMfo+V1PWtdsTUffjoT4hNDIsxGezp5GxxXlhBR9q7MmM/VlDH1RwYQ99BFblwZQ9dQaRp1ZTrCDN3ObdyE5L4MZO2cA4GLvwhsd36BnYE9jw4pyQYo+kJR6hnN2Cg+7mtdeWYhyxMnZlXb3vwq8yq7f5xG6+Rne3fErR7t9hsetrTiSdoQ5e+fw3/X/JfFcIg80ewCllNGxhYGkLwM4cNTypeLqVesanESIm9ey5wjSH9pKqsmTWmv+Q/yqH+ji25mZ3Wfi4+LDtKhpjF8znlOZp4yOKgwkRR84mfAXAHVqNDU4iRDFU6tOA3LumE2ecqLN7pfYN70X5rQM/rjrD/rV68fmM5sZvmI4b0W+ReK5RKPjCgNI0QeS0o4C0DgwwuAkQhRfo1Zd8HvpAJHNJtHk/E48Pwkl6vNneLTGEBb2WUAtt1osPbyUocuHcij1kNFxRRmTog+knT+D0pr6tZsYHUWIEqFMJtre8xxxQ34numoX2p+ZR92FXeCTEUwOeIKFfRcCMHzFcDbEbjA4rShLUvSBzKI03IsUDnYORkcRokQFNYug9X9/4thdf7C14TPUKDhDre8G4pqSy4I+C6hbrS7j14xn8cHFRkcVZUSKPpClcvAskpmyROVVL6Qt7Ya9TN6Da8hXDnh805PkD+5hotdQbvG7hTcj36Tbkm48u/5Z4rLL1YjnooTZfNEvMOeTZleIh0lG1xSVX62AhqQOWsJBj0745MXR4o+RDD1cwGP1RhJaPZR1p9cx9NehrD+93uioopTYfNFPPH2UJHs7vJxrGB1FiDJRP7QDEU99S5WntxNd7VY6Ji5i9Kq3eaRKXxb1W0R+YT7j1ozj4T8eZn/KfqPjihJm80X/1NFtZJtM1PasZ3QUIcpUlWqetH7mBxIejOKccsHr14fhVCKr7l7FXY3uYmv8Vh5f/TinM09fe2eiwrD5on86wTL3aKOA1gYnEcIYtQIakjpwEXYUUve7vpyO3sLLbV9i6R1LOWc+R58f+vDejveMjilKiM0X/bhzxwBo4d/K4CRCGKdBi47EdX2PdFWNJr8OZu87t1NwIIYFt82jZY2WzNs3jyNpR4yOKUqAzRf9+KKzOBZBQNUAo6MIYajQroPh0Y1Eeg+g6fldBK8cSsCsjgw4pbBTdgxaNojxq8eTY84xOqoohmIXfaWUnVJql1LqF+vzIKVUpFIqRim1WCnlaG13sj6PsS4PLO6xS0KCKRvfQgfsTTL2nBA+tQJoO/4rkkZsZEebd4lxasbAMz+x7PhJOlCHdbHrGLdmHOm56UZHFTepJK70/wMcuOT5VOA9rXUDIA0YbW0fDaRZ29+zrme4JPtCaiC3awpxKb96wbTuM5pmL2zizAObSHEM49Pjf/JaUga74rdz90+D2Z6wnYKiAqOjihtUrKKvlPIH+gKfW58r4DZgqXWVecCd1scDrM+xLu+mDB7jNS0tiUR7Ez4OPkbGEKJc828QQsizvxPV+h3q6WZ8cSaRwux4Hvz9QXosuZ29yXuNjihuQHGv9GcAzwFF1ufeQLrW+sLbfyzgZ33sB5wGsC7PsK7/N0qpMUqpKKVUVHJycjHj/buDx7dRoBS1qkh/vhD/xmRnR/gdjxD23G9437OaF/PaMiE5E/vsRIb/Ooypy/7LyfQTRscU1+Gmi75Sqh+QpLXeUYJ50FrP1lqHa63Dq1evXpK7vszReMsVSoCPDLQmxPWq06A5t439gg69lvD6WQ9a5ObyTdrv9PvpDob9MpRPdn/C8YzjRscUV1GcTy87Av2VUn0AZ6Aa8D7goZSyt17N+wMXBvKIA+oAsUope8AdSCnG8Ystzvptw5B67Y2MIUSFVC+kLfVCNhOcmcryBY9zOn8zywuimZmyl5nRMwmyq8HotuPpGnAr7k7uRscVVjd9pa+1fl5r7a+1DgTuBdZorYcBa4G7rKuNAH6yPl5mfY51+Rqttb7Z45eEszmncNCahv4hRsYQokKrWs2Lux/+ho7u9zM5/xbeSvXnnnQzGfnxvLj5JXot7s4n2z+WSVvKidK4T3ECsEgp9SawC5hjbZ8DfK2UigFSsbxRGCqVLKoXmDApm/+6ghDFYrKzo/2IyRef9ysqosdPH5N0+BO+8Mpk5v5ZzNw/i7pF1ehboztDuz2Fu7OHcYFtmDL4YvtfhYeH66ioqFLb/4DPQqiqXflmzLZSO4YQtiw/L5d9679jz7FlxOftZa2b5oyD5VpzdJORPNn2GYMTVk5KqR1a6/ArLbPZbyQVFhSQaK8JLJB79IUoLY5OzrTsMYyWDAPgkfQkvv/qAZa6nuSr/V/gtuUHmvsOoM3gpzHZ2Rmc1jbYbL/G7l0rOWcyUd29gdFRhLAZnh41eHDcCp71GUO1IhMfeGYwO3U23/8vmM2fP0VergzxUNps9kr/+KlIAOoHyGToQpQlZTJx251P0878KAsPLGDmro/Z7lKAv3kFfWZtpbVHZ2q0vIMGLW4xOmqlZLNX+kkZRwFoEtDS4CRC2CZXB1dGhz7E+vs28lK7l8izd2e2ZzYvFi5j3sYHmD8tlF2blxkds9Kx2aKfkXsGgADPQGODCGHjqjhW4Z7G97B6xFbe7vQ2Pt7B/Fi1ClNqaF7YP4Gl09sT9cts8vNyjY5aKdhu0S9Kw0GDl7OX0VGEEIBSin71+rHkzqWsH7KeyRGvk2vnyhs+WRw6/BrmtwLY+vXL6KKia+9MXJXNFv0ku/PUKnTG4DHfhBBX4OXsRf9mA/nl/g10rtOVKd5e9AuozYc5i3h59u3s3LmS8ny7eXlmkx/k5mRnEOsA/naXjfcmhChH3BzceP+2D1hwYAF7knez79hGfjQl8ePep6kSDfXxpqVTQ7r596Rus454Vq9tdORyzyaL/qlDO0iytyPMVf6BCFHemZSJ+5vdD9wPXWD1zu9Zt3s+6ecPssclid0FKSw6tpnb9ubR0b4jNWq2pkWPUbi4yXdwrsQ2i/5fv1KgFA2C5HZNISqabq0G0a3VIAAKzGZ+jF7ImhN/8JvazXK1E8+07dT5ZiZFdl74uwQQFtybjkFdqFutrnTnYqNFPzMzBqpBYI2GRkcRQhSDvYMDd0UM566I4ew7u4/dibvYcGA5iWkHUUWp/FaQxW+798Hu6QQ51GaQbx96tLob32p+1955JWWTRT/VHA9AYLVAY4MIIUpMsE8wwT7BDA2+HwBzfh7Rm5dxcvs7JDokMs+9iP+dnMP/Ts4hsKgKrb3b8HjX56lerZbBycuWTRb9BPsM7LUTAdVkxiwhKisHRyciut5NRNe7yUhNJnzPag4e/pXEnF1scUvlu7Q1/Pj9akKpRWv7IILdGtMktA/+9ZsZHb1U2dwom7k52Yz6phX5jrX5buT6Et23EKJiyEhN5rvfJxOZ9gc7XBR5Jsvd63XzCxiS409d9zBqhfYjoGk4zi5uBqe9cTLK5iXiTxzghIMDbZxtt09PCFvn7lWdB++bwcjCQlLSEtmetJ0FB75hd/ZB3nFMwLFoBcM3Lmb0T7lsCRxFswH/xd2rdKdvLSs2V/RPnYom22SirqeMrimErTPZ2VHdx5c+PgPo3bQ/sVmxHEo7xJK9C/jctJ0fqngSen4pz838DAezPXtqDqDlg+/j5OxqdPSbZnNF//RZy2ToTfxbG5xECFGeKKWoU60OdarVoVtAN5YcWsKW+C2sPbWWXa6edM4u4j8p33Hmnd+Jqz+aWiHdCApuh519xSqjFSttCUjKPg4u0Mwv1OgoQohySinFkCZDGNJkCPtT9vPGljdYpv5iWVVLt7BL/hIeWDuHW382UWBfj7x6vfFt2YM6DVsYnPzabrroK6XqAF8BNQENzNZav6+U8gIWA4HACeAerXWasnwr4n2gD5ADjNRa7yxe/BuXWpCMSYNfNf+yPrQQogJq5t2Mhf0WEp0Uzb6UfRQVFbH20HJmm/5itie4FybRPOVT2v38Pr2y8ohza0dhve4EthtAdd9Ao+Nf5qbv3lFK1QZqa613KqWqAjuAO4GRQKrWeopSaiLgqbWeoJTqA4zHUvTbAu9rrdv+2zFK4+6dsTODOeTsyOoHd5XofoUQtmV7wnZi0mOITowmMm4zKeZ0qhfYMTQjhcACMx3P55JCTeKajqZWix7UadC8zKaELJW7d7TW8UC89XGWUuoA4AcMALpaV5sHrAMmWNu/0pZ3ma1KKQ+lVG3rfspEYUEBSfYFVMenrA4phKikImpFEFErgvua3IfWmi1ntjAtahrv2xcC4KztaZNTwMAT71L/0NvkFjiQaFeblCoNMFfxBXsX3JvdRtM2PVCmshvwuET69JVSgUBLIBKoeUkhT8DS/QOWN4TTl2wWa20rs6KfcDqG0w72tHesee2VhRDiOiml6ODXgR/8fiDxXCIHUg8w/8B8opL3sMGtOi440D+3Bt1TMwjN2Ih9RiGOqgBOfcqujbeQ59cej0btadzq1lJ/Ayh20VdKVQG+A57UWmdeOqCR1lorpW6o/0gpNQYYAxAQULLfmD1+Ioockwl/j/olul8hhLigpltNarrVpGudrmTkZRCdFM2MnTNYnB7DisBqDGn8Io08GxHi2pjTv31G62OzcDy8CQ5D4i/enPRsh1PoQJq071sqt4YWq+grpRywFPz5Wuvvrc2JF7ptrP3+Sdb2OKDOJZv7W9v+Rms9G5gNlj794uT7pxMJ0QA08gsryd0KIcQVuTu506VOFzr7d2Z/yn5e3/o6n+39DABPJ0/8ffyJaDqJENdGuEXvoOrp9YSnLse0/leObgqi3qSdJX7lX5y7dxQwBzigtX73kkXLgBHAFOvvny5pH6eUWoTlg9yMsuzPB0jMigEnCA1sU5aHFULYOKUUwT7BLO63mIy8DDaf2cxvx38jLS+NuQe+BMDV3pWg5kEEuo6hQZYTzez9qF8KXT3FudLvCDwA7FVKRVvbXsBS7JcopUYDJ4F7rMuWY7lzJwbLLZujinHsm5JiTsDOEfyr1bn2ykIIUQrcndzpHdSb3kG9AUjKSWJ7wna2J2zneMZx1sav59eCHJr7NKdt0cPYmUr2jp/i3L2zCbjajATdrrC+Bh6/2eOVhHSVhXeRI/Ymm/tOmhCinKrhWoO+9frSt15fAM6Zz7Hq5Coc7RxLvOCDDX0j15yfR5pdAd5K5sUVQpRfbg5uDGgwoNT2X3Y3hxos4eRBzjjYUd1JbtcUQtgumyn6sUciSbWzw99bpkgUQtgumyn6Z85sB6BZoEyGLoSwXTZT9NNzzwBQ1zPI4CRCCGEc2yn6hSkA+FWRGbOEELbLZop+kikL5yKFt4vcvSOEsF02UfQzUpM55FxAA1N1TMomTlkIIa7IJipg3NFoTjo4EFhVBloTQtg2myj6J85EU6AU9XyaGh1FCCEMZRNFPzbZMktWcxloTQhh42yi6CflHAagUQ250hdC2LZKX/Tz83I57JhJ3UI3vJy9jI4jhBCGqvRF/9jeP4l3sMPfra7RUYQQwnCVvuifPbCeJDs76vmGGh1FCCEMV+mLfkryFoqUIsSvpdFRhBDCcJW66OuiIs4VHQOgiVcTg9MIIYTxKnXRP7R9FXGOBThgR0C1AKPjCCGE4Sp10c/+81P+dHGhqUcTmSJRCCEwoOgrpXoppQ4ppWKUUhNL6zi6qIiC83s46uhA30b9S+swQghRoZRp0VdK2QEfA72BZsB9SqlmpXGs2KN7iayShwJur3t7aRxCCCEqnLLu82gDxGitjwEopRYBA4D9JXmQ0/FHeHzdvcS6V6Ojd1uqu1Yvyd0LIUSFVdbdO37A6Uuex1rbLlJKjVFKRSmlopKTk2/qIHb2jvjoarQx1ePVWyfffFohhKhkyt2nm1rr2cBsgPDwcH0z+/CtXpe5YyJLNJcQQlQGZX2lHwfUueS5v7VNCCFEGSjror8daKiUClJKOQL3AsvKOIMQQtisMu3e0VoXKKXGAb8DdsBcrfW+sswghBC2rMz79LXWy4HlZX1cIYQQlfwbuUIIIf5Oir4QQtgQKfpCCGFDpOgLIYQNUVrf1PefyoRSKhk4WYxd+ABnSyhOeSTnV/FV9nOU8zNGXa31FcefKddFv7iUUlFa63Cjc5QWOb+Kr7Kfo5xf+SPdO0IIYUOk6AshhA2p7EV/ttEBSpmcX8VX2c9Rzq+cqdR9+kIIIf6usl/pCyGEuIQUfSGEsCGVsuiX1eTrZU0pdUIptVcpFa2UirK2eSmlViqljlh/exqd83oppeYqpZKUUn9d0nbF81EWH1hf0z1KqVbGJb8+Vzm/V5VScdbXMFop1eeSZc9bz++QUqqnMamvn1KqjlJqrVJqv1Jqn1LqP9b2yvQaXu0cK+7rqLWuVD9Yhmw+CtQDHIHdQDOjc5XQuZ0AfP7R9g4w0fp4IjDV6Jw3cD6dgVbAX9c6H6APsAJQQDsg0uj8N3l+rwL/vcK6zaz/Vp2AIOu/YTujz+Ea51cbaGV9XBU4bD2PyvQaXu0cK+zrWBmv9C9Ovq61zgcuTL5eWQ0A5lkfzwPuNC7KjdFabwBS/9F8tfMZAHylLbYCHkqp2mUS9CZd5fyuZgCwSGudp7U+DsRg+bdcbmmt47XWO62Ps4ADWOa8rkyv4dXO8WrK/etYGYv+NSdfr8A08IdSaodSaoy1rabWOt76OAGoaUy0EnO186lMr+s4a/fG3Eu64yr0+SmlAoGWQCSV9DX8xzlCBX0dK2PRr8xu0Vq3AnoDjyulOl+6UFv+vqw09+BWtvOx+gSoD4QB8cD/DE1TApRSVYDvgCe11pmXLqssr+EVzrHCvo6VsehX2snXtdZx1t9JwA9Y/mxMvPAnsvV3knEJS8TVzqdSvK5a60StdaHWugj4jP//079Cnp9SygFLMZyvtf7e2lypXsMrnWNFfh0rY9GvlJOvK6XclFJVLzwGegB/YTm3EdbVRgA/GZOwxFztfJYBw613gLQDMi7pQqgw/tGHPRDLawiW87tXKeWklAoCGgLbyjrfjVBKKWAOcEBr/e4liyrNa3i1c6zQr6PRnySXxg+WuwQOY/nkfJLReUronOphuStgN7DvwnkB3sBq4AiwCvAyOusNnNNCLH8am7H0fY6+2vlguePjY+truhcINzr/TZ7f19b8e7AUiNqXrD/Jen6HgN5G57+O87sFS9fNHiDa+tOnkr2GVzvHCvs6yjAMQghhQypj944QQoirkKIvhBA2RIq+EELYECn6QghhQ6ToCyGEDZGiL4QQNkSKvhBC2JD/Ay8l2rDM/JkHAAAAAElFTkSuQmCC", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "# Compare results\n", + "name= 'PZAP_total' \n", + "plt.plot(r['time'], r[name], label = 'PyBNG seed=1')\n", + "plt.plot(r2['time'], r2[name], label = 'Standalone seed=1')\n", + "plt.plot(r3['time'], r3[name], label = 'Standalone seed=2')\n", + "_=plt.legend()\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "base", + "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": "3.9.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/Issues/nfsim_indrani/run_pybng.ipynb b/Issues/nfsim_indrani/run_pybng.ipynb new file mode 100644 index 00000000..3fd682ba --- /dev/null +++ b/Issues/nfsim_indrani/run_pybng.ipynb @@ -0,0 +1,86 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import bionetgen" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "begin reaction rules\n", + " dZeta: Zeta() -> dead() kdl DeleteMolecules\n", + "end reaction rules\n", + "\n" + ] + } + ], + "source": [ + "#mname=\"deleteMolecules\"\n", + "#mname=\"test_deleteMolecules\"\n", + "mname= \"test_deleteMolecules_simple\"\n", + "model= bionetgen.bngmodel(mname+\".bngl\")\n", + "#with open(mname+\"_pybng.bngl\", \"w\") as f:\n", + "# f.write(str(model)) # writes the changed model to new_model file\n", + "print(model.rules)\n", + "#ret = bionetgen.run(\"Model_ZAP70_SYK.bngl\", out=\"HPC\",suppress=False)" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "DeleteMolecules\n" + ] + } + ], + "source": [ + "print(model.rules[model.rules[0]].rule_mod.type)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "base", + "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": "3.9.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/Issues/nfsim_indrani/run_pybng.py b/Issues/nfsim_indrani/run_pybng.py new file mode 100644 index 00000000..0802faad --- /dev/null +++ b/Issues/nfsim_indrani/run_pybng.py @@ -0,0 +1,8 @@ +import bionetgen + +#mname="deleteMolecules" +mname="test_deleteMolecules" +model= bionetgen.bngmodel(mname+".bngl") +#with open(mname+"_pybng.bngl", "w") as f: +# f.write(str(model)) # writes the changed model to new_model file +print(model.rules) \ No newline at end of file diff --git a/Issues/nfsim_indrani/test_deleteMolecules.bngl b/Issues/nfsim_indrani/test_deleteMolecules.bngl new file mode 100644 index 00000000..8b6d0fc4 --- /dev/null +++ b/Issues/nfsim_indrani/test_deleteMolecules.bngl @@ -0,0 +1,31 @@ +begin model + + + +begin parameters + kdl 0.03 #CBL degrades ZAP/SYK +end parameters + +begin molecule types + A(State~UZAP~PZAP~SHP~uSYK~pSYK,CBL) + Zeta(receptor,ITAM1~U~PP,ITAM2~U~PP,ITAM3~U~PP,ITAM4~U~PP,ITAM5~U~PP,ITAM6~U~PP) + CBL(site) + dead() +end molecule types + +begin seed species + A(State~UZAP,CBL) 1 + Zeta(receptor,ITAM1~U,ITAM2~U,ITAM3~U,ITAM4~U,ITAM5~U,ITAM6~U) 1 + CBL(site) 1 +end seed species + +begin reaction rules + CBL_degrade_ITAM1: Zeta(ITAM1!1).A(State!1,CBL!3).CBL(site!3) -> dead() kdl DeleteMolecules +end reaction rules + +end model + +writeModel({suffix=>"changed",evaluate_expressions=>1,overwrite=>1}) +writeXML() +#simulate_nf({t_end=>270,n_steps=>1000}) + diff --git a/Issues/nfsim_indrani/test_deleteMolecules.xml b/Issues/nfsim_indrani/test_deleteMolecules.xml new file mode 100644 index 00000000..270d78f2 --- /dev/null +++ b/Issues/nfsim_indrani/test_deleteMolecules.xml @@ -0,0 +1,171 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Issues/nfsim_indrani/test_deleteMolecules_changed.bngl b/Issues/nfsim_indrani/test_deleteMolecules_changed.bngl new file mode 100644 index 00000000..fcb8d541 --- /dev/null +++ b/Issues/nfsim_indrani/test_deleteMolecules_changed.bngl @@ -0,0 +1,21 @@ +# Created by BioNetGen 2.9.0 + +begin model +begin parameters + kdl 0.03 +end parameters +begin molecule types + A(State~UZAP~PZAP~SHP~uSYK~pSYK,CBL) + CBL(site) + Zeta(receptor,ITAM1~U~PP,ITAM2~U~PP,ITAM3~U~PP,ITAM4~U~PP,ITAM5~U~PP,ITAM6~U~PP) + dead() +end molecule types +begin species + A(CBL,State~UZAP) 1 + Zeta(ITAM1~U,ITAM2~U,ITAM3~U,ITAM4~U,ITAM5~U,ITAM6~U,receptor) 1 + CBL(site) 1 +end species +begin reaction rules + CBL_degrade_ITAM1: Zeta(ITAM1!1).A(State!1,CBL!2).CBL(site!2) -> dead() kdl DeleteMolecules +end reaction rules +end model diff --git a/Issues/nfsim_indrani/test_deleteMolecules_simple.bngl b/Issues/nfsim_indrani/test_deleteMolecules_simple.bngl new file mode 100644 index 00000000..49be500a --- /dev/null +++ b/Issues/nfsim_indrani/test_deleteMolecules_simple.bngl @@ -0,0 +1,31 @@ +begin model + + + +begin parameters + kdl 0.03 #CBL degrades ZAP/SYK +end parameters + +begin molecule types + A(State~UZAP~PZAP~SHP~uSYK~pSYK,CBL) + Zeta(receptor,ITAM1~U~PP,ITAM2~U~PP,ITAM3~U~PP,ITAM4~U~PP,ITAM5~U~PP,ITAM6~U~PP) + CBL(site) + dead() +end molecule types + +begin seed species + A(State~UZAP,CBL) 1 + Zeta(receptor,ITAM1~U,ITAM2~U,ITAM3~U,ITAM4~U,ITAM5~U,ITAM6~U) 1 + CBL(site) 1 +end seed species + +begin reaction rules + dZeta: Zeta() -> dead() kdl DeleteMolecules +end reaction rules + +end model + +writeModel({suffix=>"changed",evaluate_expressions=>1,overwrite=>1}) +writeXML() +#simulate_nf({t_end=>270,n_steps=>1000}) + diff --git a/Issues/nfsim_indrani/test_totalRate.bngl b/Issues/nfsim_indrani/test_totalRate.bngl new file mode 100644 index 00000000..2014adda --- /dev/null +++ b/Issues/nfsim_indrani/test_totalRate.bngl @@ -0,0 +1,31 @@ +begin model + + + +begin parameters + kdl 0.03 #CBL degrades ZAP/SYK +end parameters + +begin molecule types + A(State~UZAP~PZAP~SHP~uSYK~pSYK,CBL) + Zeta(receptor,ITAM1~U~PP,ITAM2~U~PP,ITAM3~U~PP,ITAM4~U~PP,ITAM5~U~PP,ITAM6~U~PP) + CBL(site) + dead() +end molecule types + +begin seed species + A(State~UZAP,CBL) 1 + Zeta(receptor,ITAM1~U,ITAM2~U,ITAM3~U,ITAM4~U,ITAM5~U,ITAM6~U) 1 + CBL(site) 1 +end seed species + +begin reaction rules + CBL_degrade_ITAM1: Zeta(ITAM1!1).A(State!1,CBL!3).CBL(site!3) -> dead() kdl TotalRate +end reaction rules + +end model + +writeModel({suffix=>"changed",evaluate_expressions=>1,overwrite=>1}) +writeXML() +#simulate_nf({t_end=>270,n_steps=>1000}) + diff --git a/Issues/nfsim_indrani/test_totalRate.xml b/Issues/nfsim_indrani/test_totalRate.xml new file mode 100644 index 00000000..da81a13d --- /dev/null +++ b/Issues/nfsim_indrani/test_totalRate.xml @@ -0,0 +1,174 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + kdl + + + + diff --git a/Issues/nfsim_indrani/test_totalRate_changed.bngl b/Issues/nfsim_indrani/test_totalRate_changed.bngl new file mode 100644 index 00000000..906cab9e --- /dev/null +++ b/Issues/nfsim_indrani/test_totalRate_changed.bngl @@ -0,0 +1,24 @@ +# Created by BioNetGen 2.9.0 + +begin model +begin parameters + kdl 0.03 +end parameters +begin molecule types + A(State~UZAP~PZAP~SHP~uSYK~pSYK,CBL) + CBL(site) + Zeta(receptor,ITAM1~U~PP,ITAM2~U~PP,ITAM3~U~PP,ITAM4~U~PP,ITAM5~U~PP,ITAM6~U~PP) + dead() +end molecule types +begin functions + _rateLaw1() = kdl +end functions +begin species + A(CBL,State~UZAP) 1 + Zeta(ITAM1~U,ITAM2~U,ITAM3~U,ITAM4~U,ITAM5~U,ITAM6~U,receptor) 1 + CBL(site) 1 +end species +begin reaction rules + CBL_degrade_ITAM1: Zeta(ITAM1!1).A(State!1,CBL!2).CBL(site!2) -> dead() _rateLaw1() TotalRate +end reaction rules +end model diff --git a/Issues/paramchange_rama/param_change.ipynb b/Issues/paramchange_rama/param_change.ipynb new file mode 100644 index 00000000..d47533b9 --- /dev/null +++ b/Issues/paramchange_rama/param_change.ipynb @@ -0,0 +1,160 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "import matplotlib.pyplot as plt\n", + "import bionetgen\n", + "import roadrunner" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# A simple BioNetGen model\n", + "mname=\"simple\"\n", + "mstring='''\n", + "begin model\n", + "begin parameters\n", + " k1 10\n", + " k2 1\n", + "end parameters\n", + "begin species\n", + " A() 0\n", + "end species\n", + "begin observables\n", + " Molecules A A()\n", + "end observables\n", + "begin reaction rules\n", + " 0 <-> A() k1, k2\n", + "end reaction rules\n", + "end model\n", + "'''\n", + "with open(mname+\".bngl\", \"w\") as f:\n", + " f.write(mstring) \n", + "f.close()" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "# Load model from BNGL\n", + "\n", + "model = bionetgen.bngmodel( mname + \".bngl\") \n", + "# Parameter change needs to occur before simulator object is created\n", + "model.parameters.k1=100 # Original value is 10\n", + "sim = model.setup_simulator() # sim is a libroadrunner simulator object\n", + "res= sim.simulate(0,10,1000,selections=['Time']+['A'])\n", + "plt.plot(res['time'],res['A'],label='A')\n", + "plt.title('Simulator k1 value is '+ f'{sim.k1}')\n", + "_= plt.legend()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "# Load model from BNGL\n", + "mname=\"simple\"\n", + "model = bionetgen.bngmodel( mname + \".bngl\") \n", + "sim = model.setup_simulator() # sim is a libroadrunner simulator object\n", + "# Changing the value of the parameter in the bngmodel object has no effect on the simulator\n", + "model.parameters.k1=100\n", + "res= sim.simulate(0,10,1000,selections=['Time']+['A'])\n", + "plt.plot(res['time'],res['A'],label='A')\n", + "plt.title('Simulator k1 value is '+ f'{sim.k1}')\n", + "_= plt.legend()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "# Load model from BNGL\n", + "mname=\"simple\"\n", + "model = bionetgen.bngmodel( mname + \".bngl\") \n", + "sim = model.setup_simulator() # sim is a libroadrunner simulator object\n", + "# Parameters of the sim object can be changed directly\n", + "sim.k1= 100 \n", + "res= sim.simulate(0,10,1000,selections=['Time']+['A'])\n", + "plt.plot(res['time'],res['A'],label='A')\n", + "plt.title('Simulator k1 value is '+ f'{sim.k1}')\n", + "_= plt.legend()\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "base", + "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": "3.9.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/Issues/paramchange_rama/simple.bngl b/Issues/paramchange_rama/simple.bngl new file mode 100644 index 00000000..ed675be8 --- /dev/null +++ b/Issues/paramchange_rama/simple.bngl @@ -0,0 +1,16 @@ + +begin model +begin parameters + k1 10 + k2 1 +end parameters +begin species + A() 0 +end species +begin observables + Molecules A A() +end observables +begin reaction rules + 0 <-> A() k1, k2 +end reaction rules +end model diff --git a/Issues/paramchange_rama/simple/2024_02_13__09_14_02/simple.bngl b/Issues/paramchange_rama/simple/2024_02_13__09_14_02/simple.bngl new file mode 100644 index 00000000..c92958de --- /dev/null +++ b/Issues/paramchange_rama/simple/2024_02_13__09_14_02/simple.bngl @@ -0,0 +1,22 @@ +begin model + +begin parameters + k1 10 + k2 1 +end parameters + +begin species + A() 0 +end species + +begin observables + Molecules A A() +end observables + +begin reaction rules + 0 <-> A() k1, k2 +end reaction rules + +end model + +simulate({method=>"ode",t_end=>5,n_steps=>200}) \ No newline at end of file diff --git a/Issues/paramchange_rama/simple_sbml.xml b/Issues/paramchange_rama/simple_sbml.xml new file mode 100644 index 00000000..03d22bfb --- /dev/null +++ b/Issues/paramchange_rama/simple_sbml.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + S1 + + + + + + + + + + + + + + k1 + + + + + + + + + + + + + k2 + S1 + + + + + + +