diff --git a/notebooks/copasi_process_composer.ipynb b/notebooks/copasi_process_composer.ipynb
index 307830958..8dd0495bb 100644
--- a/notebooks/copasi_process_composer.ipynb
+++ b/notebooks/copasi_process_composer.ipynb
@@ -17,8 +17,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-03-04T18:12:46.780098Z",
- "start_time": "2024-03-04T18:12:46.776381Z"
+ "end_time": "2024-03-04T18:16:40.552145Z",
+ "start_time": "2024-03-04T18:16:40.547337Z"
}
},
"outputs": [],
@@ -51,8 +51,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-03-04T18:13:02.776479Z",
- "start_time": "2024-03-04T18:12:47.630719Z"
+ "end_time": "2024-03-04T18:16:44.740326Z",
+ "start_time": "2024-03-04T18:16:40.740803Z"
}
},
"id": "65385e04f4f5dd1a",
@@ -70,10 +70,14 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 3,
"id": "cc709690e20090cf",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:44.743127Z",
+ "start_time": "2024-03-04T18:16:44.741263Z"
+ }
},
"outputs": [],
"source": [
@@ -102,12 +106,25 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 4,
"id": "edf123175ec3408c",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:45.946766Z",
+ "start_time": "2024-03-04T18:16:45.942700Z"
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "True"
+ },
+ "execution_count": 4,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
"model_filepath = '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'\n",
"\n",
@@ -116,10 +133,14 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 5,
"id": "40ab6f70ac3f4996",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:46.356620Z",
+ "start_time": "2024-03-04T18:16:46.354301Z"
+ }
},
"outputs": [],
"source": [
@@ -130,12 +151,31 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 6,
"id": "d02a547b85138f96",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:46.739805Z",
+ "start_time": "2024-03-04T18:16:46.737224Z"
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{ 'global_parameter_changes': [],\n",
+ " 'reaction_changes': [],\n",
+ " 'species_changes': [ { 'expression': '',\n",
+ " 'initial_concentration': 9.261000000000001,\n",
+ " 'initial_expression': '',\n",
+ " 'initial_particle_number': None,\n",
+ " 'name': 'ADP',\n",
+ " 'unit': ''}]}\n"
+ ]
+ }
+ ],
"source": [
"# 1. specify model changes (we know the model specs as we are providing the file. TODO: allow users to introspect the model before change)\n",
"process_model_changes = ModelChanges(\n",
@@ -148,12 +188,36 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 7,
"id": "1b6c269646357d7d",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:47.333078Z",
+ "start_time": "2024-03-04T18:16:47.329862Z"
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{ 'model_changes': { 'global_parameter_changes': [],\n",
+ " 'reaction_changes': [],\n",
+ " 'species_changes': [ { 'expression': '',\n",
+ " 'initial_concentration': 9.261000000000001,\n",
+ " 'initial_expression': '',\n",
+ " 'initial_particle_number': None,\n",
+ " 'name': 'ADP',\n",
+ " 'unit': ''}]},\n",
+ " 'model_id': 'copasi_process_from_file',\n",
+ " 'model_language': 'sbml',\n",
+ " 'model_name': 'Simple Composite Process from File',\n",
+ " 'model_source': { 'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n",
+ " 'model_units': None}\n"
+ ]
+ }
+ ],
"source": [
"# 2. define the model schema to be used by the composite process (one of the copasiprocess config parameters)\n",
"\n",
@@ -170,12 +234,38 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 8,
"id": "5d434956e65b1a42",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:47.811Z",
+ "start_time": "2024-03-04T18:16:47.807927Z"
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{ 'method': 'stochastic',\n",
+ " 'model': { 'model_changes': { 'global_parameter_changes': [],\n",
+ " 'reaction_changes': [],\n",
+ " 'species_changes': [ { 'expression': '',\n",
+ " 'initial_concentration': 9.261000000000001,\n",
+ " 'initial_expression': '',\n",
+ " 'initial_particle_number': None,\n",
+ " 'name': 'ADP',\n",
+ " 'unit': ''}]},\n",
+ " 'model_id': 'copasi_process_from_file',\n",
+ " 'model_language': 'sbml',\n",
+ " 'model_name': 'Simple Composite Process from File',\n",
+ " 'model_source': { 'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n",
+ " 'model_units': None},\n",
+ " 'process_name': 'simple_copasi_from_file'}\n"
+ ]
+ }
+ ],
"source": [
"# 3. Define config schema to be used as 'config' parameter of Process constructor\n",
"process_config_from_file = CopasiProcessConfigSchema(\n",
@@ -190,22 +280,39 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 9,
"id": "de88e95d8f616779",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:48.288307Z",
+ "start_time": "2024-03-04T18:16:48.285654Z"
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "{'model_id': 'copasi_process_from_file',\n 'model_source': {'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n 'model_language': 'sbml',\n 'model_name': 'Simple Composite Process from File',\n 'model_changes': {'species_changes': [{'name': 'ADP',\n 'unit': '',\n 'initial_concentration': 9.261000000000001,\n 'initial_particle_number': None,\n 'initial_expression': '',\n 'expression': ''}],\n 'global_parameter_changes': [],\n 'reaction_changes': []},\n 'model_units': None}"
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
"process_config_from_file.model"
]
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 10,
"id": "52d81ea2ea688d47",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:48.904487Z",
+ "start_time": "2024-03-04T18:16:48.722041Z"
+ }
},
"outputs": [],
"source": [
@@ -231,10 +338,14 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 11,
"id": "f499f96a817d9faf",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:50.115960Z",
+ "start_time": "2024-03-04T18:16:50.114064Z"
+ }
},
"outputs": [],
"source": [
@@ -250,10 +361,14 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 12,
"id": "c24594c6e8229e20",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:50.523673Z",
+ "start_time": "2024-03-04T18:16:50.520712Z"
+ }
},
"outputs": [],
"source": [
@@ -264,10 +379,14 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 13,
"id": "454db50d61220bc5",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:50.988474Z",
+ "start_time": "2024-03-04T18:16:50.986417Z"
+ }
},
"outputs": [],
"source": [
@@ -294,10 +413,14 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 14,
"id": "bd6781fe4a749c29",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:51.753456Z",
+ "start_time": "2024-03-04T18:16:51.751025Z"
+ }
},
"outputs": [],
"source": [
@@ -308,24 +431,73 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 15,
"id": "e414174a2d6d331b",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:52.897856Z",
+ "start_time": "2024-03-04T18:16:52.894173Z"
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{ 'global_parameter_changes': [],\n",
+ " 'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n",
+ " 'value': 21312.2},\n",
+ " { 'parameter_name': 'EpoRJAK2',\n",
+ " 'value': 21312.2}],\n",
+ " 'reaction_name': 'reaction_1',\n",
+ " 'reaction_scheme': None},\n",
+ " { 'parameter_changes': [],\n",
+ " 'reaction_name': 'reaction_11',\n",
+ " 'reaction_scheme': 'A + B -> C'}],\n",
+ " 'species_changes': []}\n"
+ ]
+ }
+ ],
"source": [
"pp(biomodel_process_changes.model_dump())"
]
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 16,
"id": "9de88bc52fb9a164",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:53.574506Z",
+ "start_time": "2024-03-04T18:16:53.571474Z"
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{ 'model_changes': { 'global_parameter_changes': [],\n",
+ " 'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n",
+ " 'value': 21312.2},\n",
+ " { 'parameter_name': 'EpoRJAK2',\n",
+ " 'value': 21312.2}],\n",
+ " 'reaction_name': 'reaction_1',\n",
+ " 'reaction_scheme': None},\n",
+ " { 'parameter_changes': [],\n",
+ " 'reaction_name': 'reaction_11',\n",
+ " 'reaction_scheme': 'A + B -> C'}],\n",
+ " 'species_changes': []},\n",
+ " 'model_id': 'BIOMD0000000861',\n",
+ " 'model_language': 'sbml',\n",
+ " 'model_name': 'composite_from_biomodel',\n",
+ " 'model_source': {'value': 'BIOMD0000000861'},\n",
+ " 'model_units': None}\n"
+ ]
+ }
+ ],
"source": [
"biomodel_id = 'BIOMD0000000861'\n",
"\n",
@@ -342,12 +514,45 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 17,
"id": "25ba11c1e1e75f94",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:54.320763Z",
+ "start_time": "2024-03-04T18:16:54.318201Z"
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{ 'method': 'directMethod',\n",
+ " 'model': { 'model_changes': { 'global_parameter_changes': [],\n",
+ " 'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n",
+ " 'value': 21312.2},\n",
+ " { 'parameter_name': 'EpoRJAK2',\n",
+ " 'value': 21312.2}],\n",
+ " 'reaction_name': 'reaction_1',\n",
+ " 'reaction_scheme': None},\n",
+ " { 'parameter_changes': [],\n",
+ " 'reaction_name': 'reaction_11',\n",
+ " 'reaction_scheme': 'A '\n",
+ " '+ '\n",
+ " 'B '\n",
+ " '-> '\n",
+ " 'C'}],\n",
+ " 'species_changes': []},\n",
+ " 'model_id': 'BIOMD0000000861',\n",
+ " 'model_language': 'sbml',\n",
+ " 'model_name': 'composite_from_biomodel',\n",
+ " 'model_source': {'value': 'BIOMD0000000861'},\n",
+ " 'model_units': None},\n",
+ " 'process_name': 'copasi_process_from_biomodel'}\n"
+ ]
+ }
+ ],
"source": [
"biomodel_process_config = CopasiProcessConfigSchema(\n",
" process_name='copasi_process_from_biomodel',\n",
@@ -371,10 +576,14 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 18,
"id": "4c3f073b10e2dcc0",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:16:59.244410Z",
+ "start_time": "2024-03-04T18:16:56.934443Z"
+ }
},
"outputs": [],
"source": [
@@ -397,12 +606,26 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 19,
"id": "c5e03e6714faf9f4",
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:17:00.597043Z",
+ "start_time": "2024-03-04T18:17:00.378837Z"
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "image/svg+xml": "\n\n\n\n\n",
+ "text/plain": ""
+ },
+ "execution_count": 19,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
"b.visualize()"
]
@@ -419,17 +642,30 @@
},
{
"cell_type": "code",
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "Builder({ 'copasi_process_from_biomodel': { '_type': 'process',\n 'address': 'local:CopasiProcess',\n 'config': { 'method': 'directMethod',\n 'model': { 'model_changes': { 'global_parameter_changes': [ ],\n 'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n 'value': 21312.2},\n { 'parameter_name': 'EpoRJAK2',\n 'value': 21312.2}],\n 'reaction_name': 'reaction_1',\n 'reaction_scheme': None},\n { 'parameter_changes': [ ],\n 'reaction_name': 'reaction_11',\n 'reaction_scheme': 'A '\n '+ '\n 'B '\n '-> '\n 'C'}],\n 'species_changes': [ ]},\n 'model_id': 'BIOMD0000000861',\n 'model_language': 'sbml',\n 'model_name': 'composite_from_biomodel',\n 'model_source': { 'value': 'BIOMD0000000861'},\n 'model_units': None}},\n 'inputs': { 'floating_species': [ 'floating_species_store'],\n 'model_parameters': [ 'model_parameters_store'],\n 'reactions': [ 'reactions_store'],\n 'time': ['time_store']},\n 'instance': ,\n 'interval': 1.0,\n 'outputs': { 'floating_species': [ 'floating_species_store'],\n 'time': ['time_store']}},\n 'simple_copasi_from_file': { '_type': 'process',\n 'address': 'local:CopasiProcess',\n 'config': { 'method': 'stochastic',\n 'model': { 'model_changes': { 'global_parameter_changes': [ ],\n 'reaction_changes': [ ],\n 'species_changes': [ { 'expression': '',\n 'initial_concentration': 9.261000000000001,\n 'initial_expression': '',\n 'initial_particle_number': None,\n 'unit': ''}]},\n 'model_id': 'copasi_process_from_file',\n 'model_language': 'sbml',\n 'model_name': 'Simple '\n 'Composite '\n 'Process '\n 'from File',\n 'model_source': { 'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n 'model_units': None}},\n 'inputs': { 'floating_species': [ 'floating_species_store'],\n 'model_parameters': [ 'model_parameters_store'],\n 'reactions': ['reactions_store'],\n 'time': ['time_store']},\n 'instance': ,\n 'interval': 1.0,\n 'outputs': { 'floating_species': [ 'floating_species_store'],\n 'time': ['time_store']}}})"
+ },
+ "execution_count": 20,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
"b.connect_all(append_to_store_name='_store')\n",
"\n",
"b"
],
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-04T18:17:08.884244Z",
+ "start_time": "2024-03-04T18:17:08.876800Z"
+ }
},
"id": "d9bef3f51b50fbd5",
- "execution_count": null
+ "execution_count": 20
},
{
"cell_type": "code",