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added data_demo.ipynb and combined_fvsolver_data.ipynb notebooks
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-32
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‎examples/combined_fvsolver_data.ipynb‎

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‎examples/data_demo.ipynb‎

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‎examples/fvsolver_demo.ipynb‎

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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T23:01:54.750649Z",
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"start_time": "2025-01-23T23:01:53.532205Z"
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"end_time": "2025-01-24T00:16:36.920764Z",
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"start_time": "2025-01-24T00:16:36.911105Z"
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}
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},
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"cell_type": "code",
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"outputs": [],
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"execution_count": 2,
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"source": [
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"import tempfile\n",
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"import os\n",
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"import requests\n",
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"import tarfile\n",
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"import shutil\n",
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"import tempfile\n",
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"from pathlib import Path\n",
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"\n",
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"temp_dir = tempfile.mkdtemp(prefix='pyvcell_test_data_')\n",
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"filename = os.path.join(temp_dir, 'SimID_946368938_simdata.tgz')\n",
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"url = 'https://github.com/virtualcell/pyvcell/blob/main/tests/test_data/SimID_946368938_simdata.tgz?raw=true'\n",
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"response = requests.get(url)\n",
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"test_data_dir = Path(os.getcwd()) / \"solver_input\"\n",
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"\n",
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"with open(filename, 'wb') as f:\n",
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" f.write(response.content)\n",
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"\n",
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"with tarfile.open(filename, 'r:gz') as tar:\n",
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" tar.extractall(temp_dir)\n",
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"print(f\"Files extracted to {temp_dir}\")"
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],
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"id": "5e183b4a68315dfe",
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Files extracted to /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/pyvcell_test_data_i35r8_br\n"
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]
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}
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"# move all files from test_data_dir to temp_dir\n",
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"for file in test_data_dir.iterdir():\n",
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" shutil.copy(file, temp_dir)\n"
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],
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"execution_count": 1
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"id": "5e183b4a68315dfe"
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},
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{
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"cell_type": "code",
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T23:19:41.486252Z",
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"start_time": "2025-01-23T23:19:40.386826Z"
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"end_time": "2025-01-24T00:16:42.160301Z",
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"start_time": "2025-01-24T00:16:40.970873Z"
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}
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},
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"id": "902c6d3a8dc70af",
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]
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}
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],
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"execution_count": 4
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"execution_count": 3
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},
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{
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"cell_type": "code",
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"id": "ed266f9194abb748",
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T23:22:08.523252Z",
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"start_time": "2025-01-23T23:22:08.520883Z"
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"end_time": "2025-01-24T00:18:02.630310Z",
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"start_time": "2025-01-24T00:18:02.627900Z"
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}
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},
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"source": [
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]
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}
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],
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"execution_count": 7
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"execution_count": 5
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}
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],
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"metadata": {

‎examples/solver_input/SimID_946368938_0_.functions‎

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##---------------------------------------------
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## /Users/schaff/.vcell/simdata/temp/SimID_946368938_0_.functions
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##---------------------------------------------
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Nucleus_cytosol_membrane::J_flux0; (2.0 * (RanC_cyt - RanC_nuc)); ; Membrane_VariableType; false
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cytosol::J_r0; (RanC_cyt - (1000.0 * C_cyt * Ran_cyt)); ; Volume_VariableType; false
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cytosol_ec_membrane::s2; 0.0; ; Membrane_Region_VariableType; false
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cytosol::Size_cyt; vcRegionVolume('cytosol'); ; Volume_Region_VariableType; false
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ec::Size_EC; vcRegionVolume('ec'); ; Volume_Region_VariableType; false
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Nucleus_cytosol_membrane::Size_nm; vcRegionArea('Nucleus_cytosol_membrane'); ; Membrane_Region_VariableType; false
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Nucleus::Size_nuc; vcRegionVolume('Nucleus'); ; Volume_Region_VariableType; false
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cytosol_ec_membrane::Size_pm; vcRegionArea('cytosol_ec_membrane'); ; Membrane_Region_VariableType; false
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cytosol_ec_membrane::sobj_cytosol1_ec0_size; vcRegionArea('cytosol_ec_membrane'); ; Membrane_Region_VariableType; false
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Nucleus_cytosol_membrane::sobj_Nucleus2_cytosol1_size; vcRegionArea('Nucleus_cytosol_membrane'); ; Membrane_Region_VariableType; false
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cytosol::vobj_cytosol1_size; vcRegionVolume('cytosol'); ; Volume_Region_VariableType; false
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ec::vobj_ec0_size; vcRegionVolume('ec'); ; Volume_Region_VariableType; false
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Nucleus::vobj_Nucleus2_size; vcRegionVolume('Nucleus'); ; Volume_Region_VariableType; false
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‎examples/solver_input/SimID_946368938_0_.fvinput‎

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# Simulation Parameters
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SIMULATION_PARAM_BEGIN
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SOLVER SUNDIALS_PDE_SOLVER 1.0E-7 1.0E-9 0.1
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BASE_FILE_NAME /Users/schaff/.vcell/simdata/temp/SimID_946368938_0_
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ENDING_TIME 1.0
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TIME_STEP 0.25
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KEEP_EVERY 1
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SIMULATION_PARAM_END
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# Model description: FEATURE name handle boundary_conditions
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MODEL_BEGIN
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FEATURE ec 0 flux flux flux flux flux flux
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FEATURE cytosol 1 flux flux flux flux flux flux
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FEATURE Nucleus 2 flux flux flux flux flux flux
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MEMBRANE cytosol_ec_membrane cytosol ec flux flux flux flux flux flux
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MEMBRANE Nucleus_cytosol_membrane Nucleus cytosol flux flux flux flux flux flux
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MODEL_END
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# Mesh file
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MESH_BEGIN
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VCG_FILE /Users/schaff/.vcell/simdata/temp/SimID_946368938_0_.vcg
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MESH_END
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# Variables : type name domain time_dependent_flag advection_flag grad_flag solve_whole_mesh_flag solve_regions
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VARIABLE_BEGIN
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VOLUME_PDE C_cyt cytosol false false false false cytosol
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VOLUME_PDE Ran_cyt cytosol false false false false cytosol
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VOLUME_PDE RanC_cyt cytosol false false false false cytosol
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VOLUME_PDE RanC_nuc Nucleus false false false false Nucleus
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VARIABLE_END
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# Post Processing Block
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POST_PROCESSING_BLOCK_BEGIN
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PROJECTION_DATA_GENERATOR fluor null z sum (602.214179 * RanC_cyt);
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POST_PROCESSING_BLOCK_END
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COMPARTMENT_BEGIN ec
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EQUATION_BEGIN C_cyt
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INITIAL 0.0;
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RATE 0.0;
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DIFFUSION 0.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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EQUATION_BEGIN Ran_cyt
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INITIAL 0.0;
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RATE 0.0;
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DIFFUSION 0.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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EQUATION_BEGIN RanC_cyt
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INITIAL 0.0;
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RATE 0.0;
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DIFFUSION 0.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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EQUATION_BEGIN RanC_nuc
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INITIAL 0.0;
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RATE 0.0;
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DIFFUSION 0.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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COMPARTMENT_END
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COMPARTMENT_BEGIN cytosol
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EQUATION_BEGIN RanC_cyt
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INITIAL 0.0;
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RATE - (RanC_cyt - (1000.0 * C_cyt * Ran_cyt));
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DIFFUSION 10.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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EQUATION_BEGIN Ran_cyt
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INITIAL 0.0;
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RATE (RanC_cyt - (1000.0 * C_cyt * Ran_cyt));
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DIFFUSION 10.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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EQUATION_BEGIN C_cyt
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INITIAL 0.0;
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RATE (RanC_cyt - (1000.0 * C_cyt * Ran_cyt));
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DIFFUSION 10.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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EQUATION_BEGIN RanC_nuc
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INITIAL 0.0;
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RATE 0.0;
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DIFFUSION 0.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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COMPARTMENT_END
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COMPARTMENT_BEGIN Nucleus
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EQUATION_BEGIN RanC_nuc
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INITIAL 4.5E-4;
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RATE 0.0;
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DIFFUSION 10.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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EQUATION_BEGIN C_cyt
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INITIAL 0.0;
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RATE 0.0;
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DIFFUSION 0.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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EQUATION_BEGIN Ran_cyt
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INITIAL 0.0;
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RATE 0.0;
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DIFFUSION 0.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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EQUATION_BEGIN RanC_cyt
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INITIAL 0.0;
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RATE 0.0;
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DIFFUSION 0.0;
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VELOCITY_X 0.0;
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VELOCITY_Y 0.0;
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VELOCITY_Z 0.0;
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BOUNDARY_XM 0.0;
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BOUNDARY_XP 0.0;
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BOUNDARY_YM 0.0;
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BOUNDARY_YP 0.0;
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BOUNDARY_ZM 0.0;
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BOUNDARY_ZP 0.0;
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EQUATION_END
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COMPARTMENT_END
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MEMBRANE_BEGIN cytosol_ec_membrane cytosol ec
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JUMP_CONDITION_BEGIN RanC_cyt
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FLUX cytosol 0.0;
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JUMP_CONDITION_END
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JUMP_CONDITION_BEGIN Ran_cyt
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FLUX cytosol 0.0;
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JUMP_CONDITION_END
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JUMP_CONDITION_BEGIN C_cyt
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FLUX cytosol 0.0;
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JUMP_CONDITION_END
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MEMBRANE_END
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MEMBRANE_BEGIN Nucleus_cytosol_membrane Nucleus cytosol
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JUMP_CONDITION_BEGIN RanC_nuc
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FLUX Nucleus (2.0 * (RanC_cyt_cytosol_membrane - RanC_nuc_Nucleus_membrane));
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JUMP_CONDITION_END
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JUMP_CONDITION_BEGIN RanC_cyt
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FLUX cytosol - (2.0 * (RanC_cyt_cytosol_membrane - RanC_nuc_Nucleus_membrane));
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JUMP_CONDITION_END
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JUMP_CONDITION_BEGIN Ran_cyt
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FLUX cytosol 0.0;
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JUMP_CONDITION_END
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JUMP_CONDITION_BEGIN C_cyt
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FLUX cytosol 0.0;
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JUMP_CONDITION_END
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MEMBRANE_END
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