From 93944fdc6f1f64e1f63988b8090b071e50d63140 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Fri, 1 Mar 2024 13:55:37 -0500 Subject: [PATCH] updated composer --- notebooks/builder_composer.ipynb | 139 ++++++++++++++++++++++++++----- 1 file changed, 117 insertions(+), 22 deletions(-) diff --git a/notebooks/builder_composer.ipynb b/notebooks/builder_composer.ipynb index 5d537efd1..ae47495aa 100644 --- a/notebooks/builder_composer.ipynb +++ b/notebooks/builder_composer.ipynb @@ -10,12 +10,18 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "id": "b385dca6-942d-472c-9963-13b8cb33843c", - "metadata": {}, + "metadata": { + "ExecuteTime": { + "end_time": "2024-03-01T18:50:04.271919Z", + "start_time": "2024-03-01T18:50:04.260886Z" + } + }, "outputs": [], "source": [ "from builder import Builder, Process\n", + "from process_bigraph import pp, pf \n", "from biosimulator_processes import CORE\n", "from biosimulator_processes.data_model import *\n", "from biosimulator_processes.biosimulator_builder import BiosimulatorBuilder" @@ -128,15 +134,23 @@ "cell_type": "code", "outputs": [ { - "data": { - "text/plain": "{'species_changes': {'species_name': 'SHP1',\n 'unit': None,\n 'initial_concentration': 5.0,\n 'initial_particle_number': None,\n 'initial_expression': None,\n 'expression': None},\n 'global_parameter_changes': None,\n 'reaction_changes': None}" - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" + "name": "stdout", + "output_type": "stream", + "text": [ + "{ 'global_parameter_changes': None,\n", + " 'reaction_changes': None,\n", + " 'species_changes': { 'expression': None,\n", + " 'initial_concentration': 5.0,\n", + " 'initial_expression': None,\n", + " 'initial_particle_number': None,\n", + " 'species_name': 'SHP1',\n", + " 'unit': None}}\n" + ] } ], "source": [ + "# 1. specify model changes\n", + "\n", "process_model_changes = ModelChanges(\n", " species_changes=SpeciesChanges(\n", " species_name='SHP1',\n", @@ -144,39 +158,120 @@ " )\n", ")\n", "\n", - "process_model_changes.model_dump()" + "\n", + "pp(process_model_changes.model_dump())" ], "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-03-01T18:46:50.284003Z", - "start_time": "2024-03-01T18:46:50.279111Z" + "end_time": "2024-03-01T18:51:15.399056Z", + "start_time": "2024-03-01T18:51:15.392102Z" } }, "id": "2b1c1bdd6864a771", - "execution_count": 13 + "execution_count": 23 }, { "cell_type": "code", - "execution_count": null, - "id": "b79dc6639a17e353", - "metadata": { - "collapsed": false - }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{ 'model_changes': { 'global_parameter_changes': None,\n", + " 'reaction_changes': None,\n", + " 'species_changes': { 'expression': None,\n", + " 'initial_concentration': 5.0,\n", + " 'initial_expression': None,\n", + " 'initial_particle_number': None,\n", + " 'species_name': 'SHP1',\n", + " 'unit': None}},\n", + " 'model_id': 'simple_copasi_process',\n", + " 'model_language': 'sbml',\n", + " 'model_name': 'Simple Composite Process',\n", + " 'model_source': {'value': 'BIOMD0000000861'}}\n" + ] + } + ], "source": [ + "# 2. define the model schema to be used by the composite process (one of the copasiprocess config parameters)\n", + "\n", "process_model = Model(\n", " model_id='simple_copasi_process',\n", " model_source='BIOMD0000000861',\n", " model_name='Simple Composite Process',\n", - " model_changes=\n", + " model_changes=process_model_changes\n", ")\n", "\n", + "\n", + "pp(process_model.model_dump())" + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-03-01T18:52:11.944029Z", + "start_time": "2024-03-01T18:52:11.940871Z" + } + }, + "id": "8d0566183a2d1c1f", + "execution_count": 25 + }, + { + "cell_type": "code", + "execution_count": 27, + "id": "b79dc6639a17e353", + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-03-01T18:53:12.797999Z", + "start_time": "2024-03-01T18:53:12.791670Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{ 'method': 'stochastic',\n", + " 'model': { 'model_changes': { 'global_parameter_changes': None,\n", + " 'reaction_changes': None,\n", + " 'species_changes': { 'expression': None,\n", + " 'initial_concentration': 5.0,\n", + " 'initial_expression': None,\n", + " 'initial_particle_number': None,\n", + " 'species_name': 'SHP1',\n", + " 'unit': None}},\n", + " 'model_id': 'simple_copasi_process',\n", + " 'model_language': 'sbml',\n", + " 'model_name': 'Simple Composite Process',\n", + " 'model_source': {'value': 'BIOMD0000000861'}}}\n" + ] + } + ], + "source": [ + "# 3. Define config schema to be used as 'config' parameter of Process constructor\n", + "\n", + "\n", "process_config = CopasiProcessConfigSchema(\n", - " \n", - ")" + " method='stochastic',\n", + " model=process_model\n", + ")\n", + "\n", + "\n", + "pp(process_config.model_dump())" ] }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "dir()" + ], + "metadata": { + "collapsed": false + }, + "id": "a8bc9415d6ac47ad" + }, { "cell_type": "code", "execution_count": null, @@ -185,7 +280,7 @@ "outputs": [], "source": [ "\n", - "b['copasi_A'].add_process(\n", + "b['simple_copasi'].add_process(\n", " name='CopasiProcess',\n", " kdeg=1.0, # kwargs fill parameters in the config\n", ")"