diff --git a/notebooks/copasi_process_composer.ipynb b/notebooks/copasi_process_composer.ipynb index 3f4a924f6..e15cef3e7 100644 --- a/notebooks/copasi_process_composer.ipynb +++ b/notebooks/copasi_process_composer.ipynb @@ -12,14 +12,9 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "initial_id", - "metadata": { - "ExecuteTime": { - "end_time": "2024-02-29T16:59:36.149145Z", - "start_time": "2024-02-29T16:59:36.144904Z" - } - }, + "metadata": {}, "outputs": [], "source": [ "import sys \n", @@ -29,27 +24,12 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "c6c10dc5988e52d4", "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-02-29T17:00:00.484873Z", - "start_time": "2024-02-29T16:59:55.278922Z" - } + "collapsed": false }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CobraProcess registered successfully.\n", - "CopasiProcess registered successfully.\n", - "SmoldynProcess registered successfully.\n", - "TelluriumProcess registered successfully.\n" - ] - } - ], + "outputs": [], "source": [ "import os \n", "from basico import *\n", @@ -374,223 +354,37 @@ "cell_type": "code", "outputs": [], "source": [ - "from biosimulator_processes.utils import generate_copasi_process_instance" - ], - "metadata": { - "collapsed": false - }, - "id": "56fe39f779b76c37", - "execution_count": null - }, - { - "cell_type": "code", - "outputs": [], - "source": [ - "PARAM SCAN FROM LOADED BIOMODEL HERE:\n", - "\n", - "\n" - ], - "metadata": { - "collapsed": false - }, - "id": "c7280f14074f4b17", - "execution_count": null - }, - { - "cell_type": "code", - "outputs": [], - "source": [ - "parameter_scan_instance = {\n", - " 'copasi_1': {\n", - " '_type': 'process',\n", - " 'address': 'local:copasi',\n", - " 'config': {\n", - " 'model': {\n", - " 'model_changes': {\n", - " 'reaction_changes': {\n", - " 'R1': 'A -> B'\n", - " }\n", - " }\n", - " }\n", - " },\n", - " 'inputs': {\n", - " 'floating_species': ['floating_species_store'],\n", - " 'model_parameters': ['model_parameters_store'],\n", - " 'time': ['time_store'],\n", - " 'reactions': ['reactions_store']\n", - " },\n", - " 'outputs': {\n", - " 'floating_species': ['floating_species_store'],\n", - " 'time': ['time_store'],\n", - " }\n", - " },\n", - " 'emitter': {\n", - " '_type': 'step',\n", - " 'address': 'local:ram-emitter',\n", - " 'config': {\n", - " 'emit': {\n", - " 'floating_species': 'tree[float]',\n", - " 'time': 'float',\n", - " },\n", - " },\n", - " 'inputs': {\n", - " 'floating_species': ['floating_species_store'],\n", - " 'time': ['time_store'],\n", - " }\n", - " }\n", - "}" - ], - "metadata": { - "collapsed": false - }, - "id": "3b8a27c7dd246d02", - "execution_count": null - }, - { - "cell_type": "code", - "outputs": [], - "source": [ - "from biosimulator_processes.utils import generate_composite_copasi_process_instance as copasi_instance" - ], - "metadata": { - "collapsed": false - }, - "id": "57712e54678bcb70", - "execution_count": null - }, - { - "cell_type": "code", - "outputs": [], - "source": [ - "model_config = {\n", - " 'model': {\n", - " 'model_changes': {\n", - " 'reaction_changes': {\n", - " 'R1': 'A -> B'\n", - " }\n", - " }\n", - " }\n", - "}\n", - "\n", + "from biosimulator_processes.utils import generate_copasi_parameter_scan_instance as param_scan\n", "\n", - "instance = copasi_instance(\n", - " instance_name='copasi_A',\n", - " config=model_config,\n", - " add_emitter=True\n", - ")" + "parameter_scan_instance = param_scan(num_iterations=100, entry_config={'biomodel_id': 'BIOMD0000000051'})" ], "metadata": { "collapsed": false }, - "id": "482579fdd5bb4350", + "id": "1ecc10e496abe9cb", "execution_count": null }, { "cell_type": "code", "outputs": [], - "source": [ - "instance" - ], + "source": [], "metadata": { "collapsed": false }, - "id": "9e11e97613ec9e16", + "id": "35ea2649d0f98801", "execution_count": null }, { "cell_type": "code", "outputs": [], - "source": [ - "from biosimulator_processes.utils import generate_copasi_parameter_scan_instance as param_scan" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-02-29T17:00:17.283305Z", - "start_time": "2024-02-29T17:00:17.280707Z" - } - }, - "id": "1ecc10e496abe9cb", - "execution_count": 3 - }, - { - "cell_type": "code", - "outputs": [], - "source": [ - "parameter_scan_instance = param_scan(num_iterations=100, entry_config={'biomodel_id': 'BIOMD0000000051'})" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-02-29T17:00:22.139870Z", - "start_time": "2024-02-29T17:00:22.131298Z" - } - }, - "id": "35ea2649d0f98801", - "execution_count": 4 - }, - { - "cell_type": "code", - "outputs": [ - { - "data": { - "text/plain": "{'copasi_0': {'copasi_0': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1.0}},\n 'parameter_changes': {'catp': {'initial_value': 1.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_1': {'copasi_1': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 3.0}},\n 'parameter_changes': {'catp': {'initial_value': 2.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_2': {'copasi_2': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 9.0}},\n 'parameter_changes': {'catp': {'initial_value': 1.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_3': {'copasi_3': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 27.0}},\n 'parameter_changes': {'catp': {'initial_value': 0.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_4': {'copasi_4': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 81.0}},\n 'parameter_changes': {'catp': {'initial_value': 1.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_5': {'copasi_5': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 243.0}},\n 'parameter_changes': {'catp': {'initial_value': -32.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_6': {'copasi_6': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 729.0}},\n 'parameter_changes': {'catp': {'initial_value': 729.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_7': {'copasi_7': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2187.0}},\n 'parameter_changes': {'catp': {'initial_value': -16384.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_8': {'copasi_8': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 6561.0}},\n 'parameter_changes': {'catp': {'initial_value': 390625.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_9': {'copasi_9': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 19683.0}},\n 'parameter_changes': {'catp': {'initial_value': -10077696.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_10': {'copasi_10': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 59049.0}},\n 'parameter_changes': {'catp': {'initial_value': 282475249.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_11': {'copasi_11': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 177147.0}},\n 'parameter_changes': {'catp': {'initial_value': -8589934592.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_12': {'copasi_12': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 531441.0}},\n 'parameter_changes': {'catp': {'initial_value': 282429536481.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_13': {'copasi_13': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1594323.0}},\n 'parameter_changes': {'catp': {'initial_value': -10000000000000.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_14': {'copasi_14': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 4782969.0}},\n 'parameter_changes': {'catp': {'initial_value': 379749833583241.0}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_15': {'copasi_15': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 14348907.0}},\n 'parameter_changes': {'catp': {'initial_value': -1.5407021574586368e+16}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_16': {'copasi_16': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 43046721.0}},\n 'parameter_changes': {'catp': {'initial_value': 6.654166091831799e+17}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_17': {'copasi_17': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 129140163.0}},\n 'parameter_changes': {'catp': {'initial_value': -3.0491346729331196e+19}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_18': {'copasi_18': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 387420489.0}},\n 'parameter_changes': {'catp': {'initial_value': 1.4778918800354003e+21}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_19': {'copasi_19': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1162261467.0}},\n 'parameter_changes': {'catp': {'initial_value': -7.555786372591432e+22}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_20': {'copasi_20': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 3486784401.0}},\n 'parameter_changes': {'catp': {'initial_value': 4.0642314066475725e+24}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_21': {'copasi_21': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 10460353203.0}},\n 'parameter_changes': {'catp': {'initial_value': -2.2946825189512942e+26}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_22': {'copasi_22': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 31381059609.0}},\n 'parameter_changes': {'catp': {'initial_value': 1.356998041817409e+28}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_23': {'copasi_23': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 94143178827.0}},\n 'parameter_changes': {'catp': {'initial_value': -8.388608e+29}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_24': {'copasi_24': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 282429536481.0}},\n 'parameter_changes': {'catp': {'initial_value': 5.410819837727259e+31}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_25': {'copasi_25': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 847288609443.0}},\n 'parameter_changes': {'catp': {'initial_value': -3.63552403817421e+33}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_26': {'copasi_26': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2541865828329.0}},\n 'parameter_changes': {'catp': {'initial_value': 2.5405265415414954e+35}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_27': {'copasi_27': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 7625597484987.0}},\n 'parameter_changes': {'catp': {'initial_value': -1.8437563379178328e+37}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_28': {'copasi_28': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': 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'parameter_changes': {'catp': {'initial_value': 5.7078987919450065e+118}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_67': {'copasi_67': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 9.270946314789783e+31}},\n 'parameter_changes': {'catp': {'initial_value': -1.0328999512347634e+121}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_68': {'copasi_68': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2.7812838944369352e+32}},\n 'parameter_changes': {'catp': {'initial_value': 1.8971787507474678e+123}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_69': {'copasi_69': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 8.343851683310805e+32}},\n 'parameter_changes': {'catp': {'initial_value': -3.536157110771666e+125}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_70': {'copasi_70': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2.5031555049932416e+33}},\n 'parameter_changes': {'catp': {'initial_value': 6.687074921915309e+127}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_71': {'copasi_71': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 7.509466514979725e+33}},\n 'parameter_changes': {'catp': {'initial_value': -1.282722764219853e+130}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_72': {'copasi_72': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2.252839954493917e+34}},\n 'parameter_changes': {'catp': {'initial_value': 2.4953676069084525e+132}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_73': {'copasi_73': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 6.758519863481753e+34}},\n 'parameter_changes': {'catp': {'initial_value': -4.922173535218487e+134}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_74': {'copasi_74': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2.0275559590445257e+35}},\n 'parameter_changes': {'catp': {'initial_value': 9.842780613983922e+136}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_75': {'copasi_75': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 6.0826678771335774e+35}},\n 'parameter_changes': {'catp': {'initial_value': -1.9949739648013772e+139}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_76': {'copasi_76': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1.8248003631400732e+36}},\n 'parameter_changes': {'catp': {'initial_value': 4.09767366999553e+141}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_77': {'copasi_77': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 5.474401089420219e+36}},\n 'parameter_changes': {'catp': {'initial_value': -8.527906287593991e+143}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_78': {'copasi_78': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1.6423203268260657e+37}},\n 'parameter_changes': {'catp': {'initial_value': 1.7979538686803107e+146}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_79': {'copasi_79': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 4.926960980478197e+37}},\n 'parameter_changes': {'catp': {'initial_value': -3.8394922047207187e+148}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_80': {'copasi_80': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1.4780882941434593e+38}},\n 'parameter_changes': {'catp': {'initial_value': 8.303439272767327e+150}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_81': {'copasi_81': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 4.434264882430378e+38}},\n 'parameter_changes': {'catp': {'initial_value': -1.8182886086129776e+153}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_82': {'copasi_82': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1.3302794647291133e+39}},\n 'parameter_changes': {'catp': {'initial_value': 4.031080637267739e+155}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_83': {'copasi_83': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 3.99083839418734e+39}},\n 'parameter_changes': {'catp': {'initial_value': -9.046256971665328e+157}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_84': {'copasi_84': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1.197251518256202e+40}},\n 'parameter_changes': {'catp': {'initial_value': 2.0546676624565614e+160}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_85': {'copasi_85': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 3.591754554768606e+40}},\n 'parameter_changes': {'catp': {'initial_value': -4.722559655150671e+162}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_86': {'copasi_86': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1.0775263664305817e+41}},\n 'parameter_changes': {'catp': {'initial_value': 1.098287256145076e+165}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_87': {'copasi_87': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 3.2325790992917455e+41}},\n 'parameter_changes': {'catp': {'initial_value': -2.5840319990130316e+167}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_88': {'copasi_88': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 9.697737297875236e+41}},\n 'parameter_changes': {'catp': {'initial_value': 6.149863307533675e+169}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_89': {'copasi_89': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2.909321189362571e+42}},\n 'parameter_changes': {'catp': {'initial_value': -1.4803423396265347e+172}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_90': {'copasi_90': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 8.727963568087712e+42}},\n 'parameter_changes': {'catp': {'initial_value': 3.603568116041181e+174}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_91': {'copasi_91': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2.6183890704263137e+43}},\n 'parameter_changes': {'catp': {'initial_value': -8.869990724142571e+176}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_92': {'copasi_92': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 7.855167211278941e+43}},\n 'parameter_changes': {'catp': {'initial_value': 2.2073978302726454e+179}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_93': {'copasi_93': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2.3565501633836824e+44}},\n 'parameter_changes': {'catp': {'initial_value': -5.55332867254366e+181}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_94': {'copasi_94': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 7.069650490151047e+44}},\n 'parameter_changes': {'catp': {'initial_value': 1.4121826718183249e+184}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_95': {'copasi_95': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 2.1208951470453142e+45}},\n 'parameter_changes': {'catp': {'initial_value': -3.629473232621766e+186}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_96': {'copasi_96': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 6.362685441135942e+45}},\n 'parameter_changes': {'catp': {'initial_value': 9.426773259036049e+188}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_97': {'copasi_97': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1.9088056323407826e+46}},\n 'parameter_changes': {'catp': {'initial_value': -2.4740119849691286e+191}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_98': {'copasi_98': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 5.726416897022348e+46}},\n 'parameter_changes': {'catp': {'initial_value': 6.560143180425513e+193}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'copasi_99': {'copasi_99': {'_type': 'process',\n 'address': 'local:copasi',\n 'config': {'model': {'model_changes': {'species_changes': {'Extracellular Glucose': {'initial_concentration': 1.7179250691067045e+47}},\n 'parameter_changes': {'catp': {'initial_value': -1.7573249332135053e+196}},\n 'reaction_changes': None}},\n 'biomodel_id': 'BIOMD0000000051'},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'model_parameters': ['model_parameters_store'],\n 'time': ['time_store'],\n 'reactions': ['reactions_store']},\n 'outputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}},\n 'emitter': {'_type': 'step',\n 'address': 'local:ram-emitter',\n 'config': {'emit': {'floating_species': 'tree[float]', 'time': 'float'}},\n 'inputs': {'floating_species': ['floating_species_store'],\n 'time': ['time_store']}}}" - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "parameter_scan_instance" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-02-29T17:00:24.990632Z", - "start_time": "2024-02-29T17:00:24.954228Z" - } - }, - "id": "b1c627f48370f410", - "execution_count": 5 - }, - { - "cell_type": "code", - "outputs": [ - { - "ename": "Exception", - "evalue": "config key biomodel_id not in config_schema for CopasiProcess", - "output_type": "error", - "traceback": [ - "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", - "\u001B[0;31mException\u001B[0m Traceback (most recent call last)", - "Cell \u001B[0;32mIn[7], line 1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m results \u001B[38;5;241m=\u001B[39m \u001B[43mplay_composition\u001B[49m\u001B[43m(\u001B[49m\u001B[43minstance\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mparameter_scan_instance\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mduration\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;241;43m10\u001B[39;49m\u001B[43m)\u001B[49m\n", - "File \u001B[0;32m~/Desktop/uchc_work/biosimulator-processes/notebooks/../biosimulator_processes/utils.py:31\u001B[0m, in \u001B[0;36mplay_composition\u001B[0;34m(instance, duration)\u001B[0m\n\u001B[1;32m 29\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21mplay_composition\u001B[39m(instance: \u001B[38;5;28mdict\u001B[39m, duration: \u001B[38;5;28mint\u001B[39m):\n\u001B[1;32m 30\u001B[0m \u001B[38;5;250m \u001B[39m\u001B[38;5;124;03m\"\"\"Configure and run a Composite workflow.\"\"\"\u001B[39;00m\n\u001B[0;32m---> 31\u001B[0m workflow \u001B[38;5;241m=\u001B[39m \u001B[43mComposite\u001B[49m\u001B[43m(\u001B[49m\u001B[43m{\u001B[49m\n\u001B[1;32m 32\u001B[0m \u001B[43m \u001B[49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[38;5;124;43mstate\u001B[39;49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[43m:\u001B[49m\u001B[43m \u001B[49m\u001B[43minstance\u001B[49m\n\u001B[1;32m 33\u001B[0m \u001B[43m \u001B[49m\u001B[43m}\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 34\u001B[0m workflow\u001B[38;5;241m.\u001B[39mrun(duration)\n\u001B[1;32m 35\u001B[0m results \u001B[38;5;241m=\u001B[39m workflow\u001B[38;5;241m.\u001B[39mgather_results()\n", - "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/composite.py:411\u001B[0m, in \u001B[0;36mComposite.__init__\u001B[0;34m(self, config, local_types)\u001B[0m\n\u001B[1;32m 408\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mglobal_time\u001B[39m\u001B[38;5;124m'\u001B[39m \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;129;01min\u001B[39;00m initial_state:\n\u001B[1;32m 409\u001B[0m initial_state[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mglobal_time\u001B[39m\u001B[38;5;124m'\u001B[39m] \u001B[38;5;241m=\u001B[39m \u001B[38;5;241m0.0\u001B[39m\n\u001B[0;32m--> 411\u001B[0m composition, state \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mcore\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mcomplete\u001B[49m\u001B[43m(\u001B[49m\n\u001B[1;32m 412\u001B[0m \u001B[43m \u001B[49m\u001B[43minitial_composition\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 413\u001B[0m \u001B[43m \u001B[49m\u001B[43minitial_state\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 415\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mcomposition \u001B[38;5;241m=\u001B[39m copy\u001B[38;5;241m.\u001B[39mdeepcopy(\n\u001B[1;32m 416\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mcore\u001B[38;5;241m.\u001B[39maccess(composition))\n\u001B[1;32m 418\u001B[0m \u001B[38;5;66;03m# TODO: add flag to self.core.access(copy=True)\u001B[39;00m\n", - "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/bigraph_schema/type_system.py:1251\u001B[0m, in \u001B[0;36mTypeSystem.complete\u001B[0;34m(self, initial_schema, initial_state)\u001B[0m\n\u001B[1;32m 1245\u001B[0m state \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mhydrate(\n\u001B[1;32m 1246\u001B[0m full_schema,\n\u001B[1;32m 1247\u001B[0m initial_state)\n\u001B[1;32m 1249\u001B[0m \u001B[38;5;66;03m# fill in the parts of the composition schema\u001B[39;00m\n\u001B[1;32m 1250\u001B[0m \u001B[38;5;66;03m# determined by the state\u001B[39;00m\n\u001B[0;32m-> 1251\u001B[0m schema, state \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43minfer_schema\u001B[49m\u001B[43m(\u001B[49m\n\u001B[1;32m 1252\u001B[0m \u001B[43m \u001B[49m\u001B[43mfull_schema\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 1253\u001B[0m \u001B[43m \u001B[49m\u001B[43mstate\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 1255\u001B[0m final_state \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mfill(schema, state)\n\u001B[1;32m 1257\u001B[0m \u001B[38;5;66;03m# TODO: add flag to types.access(copy=True)\u001B[39;00m\n", - "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/type_system.py:243\u001B[0m, in \u001B[0;36mProcessTypes.infer_schema\u001B[0;34m(self, schema, state, top_state, path)\u001B[0m\n\u001B[1;32m 240\u001B[0m inner_path \u001B[38;5;241m=\u001B[39m path \u001B[38;5;241m+\u001B[39m (key,)\n\u001B[1;32m 241\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m get_path(schema, inner_path) \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mor\u001B[39;00m get_path(state, inner_path) \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mor\u001B[39;00m (\n\u001B[1;32m 242\u001B[0m \u001B[38;5;28misinstance\u001B[39m(value, \u001B[38;5;28mdict\u001B[39m) \u001B[38;5;129;01mand\u001B[39;00m \u001B[38;5;124m'\u001B[39m\u001B[38;5;124m_type\u001B[39m\u001B[38;5;124m'\u001B[39m \u001B[38;5;129;01min\u001B[39;00m value):\n\u001B[0;32m--> 243\u001B[0m schema, top_state \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43minfer_schema\u001B[49m\u001B[43m(\u001B[49m\n\u001B[1;32m 244\u001B[0m \u001B[43m \u001B[49m\u001B[43mschema\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 245\u001B[0m \u001B[43m \u001B[49m\u001B[43mvalue\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 246\u001B[0m \u001B[43m \u001B[49m\u001B[43mtop_state\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mtop_state\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 247\u001B[0m \u001B[43m \u001B[49m\u001B[43mpath\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43minner_path\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 249\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(state, \u001B[38;5;28mstr\u001B[39m):\n\u001B[1;32m 250\u001B[0m \u001B[38;5;28;01mpass\u001B[39;00m\n", - "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/type_system.py:243\u001B[0m, in \u001B[0;36mProcessTypes.infer_schema\u001B[0;34m(self, schema, state, top_state, path)\u001B[0m\n\u001B[1;32m 240\u001B[0m inner_path \u001B[38;5;241m=\u001B[39m path \u001B[38;5;241m+\u001B[39m (key,)\n\u001B[1;32m 241\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m get_path(schema, inner_path) \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mor\u001B[39;00m get_path(state, inner_path) \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m \u001B[38;5;129;01mor\u001B[39;00m (\n\u001B[1;32m 242\u001B[0m \u001B[38;5;28misinstance\u001B[39m(value, \u001B[38;5;28mdict\u001B[39m) \u001B[38;5;129;01mand\u001B[39;00m \u001B[38;5;124m'\u001B[39m\u001B[38;5;124m_type\u001B[39m\u001B[38;5;124m'\u001B[39m \u001B[38;5;129;01min\u001B[39;00m value):\n\u001B[0;32m--> 243\u001B[0m schema, top_state \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43minfer_schema\u001B[49m\u001B[43m(\u001B[49m\n\u001B[1;32m 244\u001B[0m \u001B[43m \u001B[49m\u001B[43mschema\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 245\u001B[0m \u001B[43m \u001B[49m\u001B[43mvalue\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 246\u001B[0m \u001B[43m \u001B[49m\u001B[43mtop_state\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mtop_state\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 247\u001B[0m \u001B[43m \u001B[49m\u001B[43mpath\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43minner_path\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 249\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(state, \u001B[38;5;28mstr\u001B[39m):\n\u001B[1;32m 250\u001B[0m \u001B[38;5;28;01mpass\u001B[39;00m\n", - "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/type_system.py:195\u001B[0m, in \u001B[0;36mProcessTypes.infer_schema\u001B[0;34m(self, schema, state, top_state, path)\u001B[0m\n\u001B[1;32m 192\u001B[0m state_type \u001B[38;5;241m=\u001B[39m state[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m_type\u001B[39m\u001B[38;5;124m'\u001B[39m]\n\u001B[1;32m 193\u001B[0m state_schema \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39maccess(state_type)\n\u001B[0;32m--> 195\u001B[0m hydrated_state \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mdeserialize\u001B[49m\u001B[43m(\u001B[49m\u001B[43mstate_schema\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mstate\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 196\u001B[0m top_state \u001B[38;5;241m=\u001B[39m set_path(\n\u001B[1;32m 197\u001B[0m top_state,\n\u001B[1;32m 198\u001B[0m path,\n\u001B[1;32m 199\u001B[0m hydrated_state)\n\u001B[1;32m 201\u001B[0m schema \u001B[38;5;241m=\u001B[39m set_path(\n\u001B[1;32m 202\u001B[0m schema,\n\u001B[1;32m 203\u001B[0m path,\n\u001B[1;32m 204\u001B[0m {\u001B[38;5;124m'\u001B[39m\u001B[38;5;124m_type\u001B[39m\u001B[38;5;124m'\u001B[39m: state_type})\n", - "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/bigraph_schema/type_system.py:605\u001B[0m, in \u001B[0;36mTypeSystem.deserialize\u001B[0;34m(self, schema, encoded)\u001B[0m\n\u001B[1;32m 602\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m encoded \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;28;01mNone\u001B[39;00m:\n\u001B[1;32m 603\u001B[0m encoded \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mdefault(schema)\n\u001B[0;32m--> 605\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mdeserialize_function\u001B[49m\u001B[43m(\u001B[49m\n\u001B[1;32m 606\u001B[0m \u001B[43m \u001B[49m\u001B[43mencoded\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 607\u001B[0m \u001B[43m \u001B[49m\u001B[43mfound\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m 608\u001B[0m \u001B[43m \u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[43m)\u001B[49m\n\u001B[1;32m 610\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28misinstance\u001B[39m(encoded, \u001B[38;5;28mdict\u001B[39m):\n\u001B[1;32m 611\u001B[0m result \u001B[38;5;241m=\u001B[39m {}\n", - "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/type_system.py:86\u001B[0m, in \u001B[0;36mdeserialize_process\u001B[0;34m(encoded, schema, core)\u001B[0m\n\u001B[1;32m 81\u001B[0m interval \u001B[38;5;241m=\u001B[39m core\u001B[38;5;241m.\u001B[39mdeserialize(\n\u001B[1;32m 82\u001B[0m \u001B[38;5;124m'\u001B[39m\u001B[38;5;124minterval\u001B[39m\u001B[38;5;124m'\u001B[39m,\n\u001B[1;32m 83\u001B[0m encoded\u001B[38;5;241m.\u001B[39mget(\u001B[38;5;124m'\u001B[39m\u001B[38;5;124minterval\u001B[39m\u001B[38;5;124m'\u001B[39m))\n\u001B[1;32m 85\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;124m'\u001B[39m\u001B[38;5;124minstance\u001B[39m\u001B[38;5;124m'\u001B[39m \u001B[38;5;129;01min\u001B[39;00m deserialized:\n\u001B[0;32m---> 86\u001B[0m process \u001B[38;5;241m=\u001B[39m \u001B[43minstantiate\u001B[49m\u001B[43m(\u001B[49m\u001B[43mconfig\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 87\u001B[0m deserialized[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124minstance\u001B[39m\u001B[38;5;124m'\u001B[39m] \u001B[38;5;241m=\u001B[39m process\n\u001B[1;32m 89\u001B[0m deserialized[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mconfig\u001B[39m\u001B[38;5;124m'\u001B[39m] \u001B[38;5;241m=\u001B[39m config\n", - "File \u001B[0;32m~/Desktop/uchc_work/biosimulator-processes/notebooks/../biosimulator_processes/processes/copasi_process.py:121\u001B[0m, in \u001B[0;36mCopasiProcess.__init__\u001B[0;34m(self, config, core)\u001B[0m\n\u001B[1;32m 120\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21m__init__\u001B[39m(\u001B[38;5;28mself\u001B[39m, config\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mNone\u001B[39;00m, core\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mNone\u001B[39;00m):\n\u001B[0;32m--> 121\u001B[0m \u001B[38;5;28;43msuper\u001B[39;49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[38;5;21;43m__init__\u001B[39;49m\u001B[43m(\u001B[49m\u001B[43mconfig\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mcore\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 123\u001B[0m model_file \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mconfig\u001B[38;5;241m.\u001B[39mget(\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mmodel\u001B[39m\u001B[38;5;124m'\u001B[39m)\u001B[38;5;241m.\u001B[39mget(\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mmodel_source\u001B[39m\u001B[38;5;124m'\u001B[39m)\n\u001B[1;32m 124\u001B[0m sed_model_id \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mconfig\u001B[38;5;241m.\u001B[39mget(\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mmodel\u001B[39m\u001B[38;5;124m'\u001B[39m)\u001B[38;5;241m.\u001B[39mget(\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mmodel_id\u001B[39m\u001B[38;5;124m'\u001B[39m)\n", - "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/composite.py:105\u001B[0m, in \u001B[0;36mProcess.__init__\u001B[0;34m(self, config, local_types)\u001B[0m\n\u001B[1;32m 103\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m key \u001B[38;5;129;01min\u001B[39;00m config\u001B[38;5;241m.\u001B[39mkeys():\n\u001B[1;32m 104\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m key \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;129;01min\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mconfig_schema:\n\u001B[0;32m--> 105\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mException\u001B[39;00m(\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mconfig key \u001B[39m\u001B[38;5;132;01m{\u001B[39;00mkey\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m not in config_schema for \u001B[39m\u001B[38;5;132;01m{\u001B[39;00m\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m\u001B[38;5;18m__class__\u001B[39m\u001B[38;5;241m.\u001B[39m\u001B[38;5;18m__name__\u001B[39m\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m)\n\u001B[1;32m 107\u001B[0m \u001B[38;5;66;03m# fill in defaults for config\u001B[39;00m\n\u001B[1;32m 108\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mconfig \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mcore\u001B[38;5;241m.\u001B[39mfill(\n\u001B[1;32m 109\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mconfig_schema,\n\u001B[1;32m 110\u001B[0m config)\n", - "\u001B[0;31mException\u001B[0m: config key biomodel_id not in config_schema for CopasiProcess" - ] - } - ], "source": [ "results = play_composition(instance=parameter_scan_instance, duration=10)" ], "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-02-29T17:01:23.395584Z", - "start_time": "2024-02-29T17:01:23.095131Z" - } + "collapsed": false }, "id": "87cced9f87885d4e", - "execution_count": 7 + "execution_count": null }, { "cell_type": "code",