updated copasi process for schema and process notebook

biosimulators · Feb 27, 2024 · 19c0028 · 19c0028
1 parent 0f3d26e
commit 19c0028
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Showing 2 changed files with 114 additions and 22 deletions.
diff --git a/biosimulator_processes/processes/copasi_process.py b/biosimulator_processes/processes/copasi_process.py
@@ -75,12 +75,10 @@ def fetch_biomodel(term: str, index: int = 0):
 class CopasiProcess(Process):
     # TODO: Update this in constructor
     config_schema = {
-        'model_file': {
-            '_type': 'string',
-            '_default': ''
-        },
+        'model_file': 'string',
+        #
         'reactions': {
-            'name': {
+            'reaction_name': {
                 'scheme': 'string'
             },
         },

diff --git a/notebooks/copasi_process.ipynb b/notebooks/copasi_process.ipynb
@@ -2,10 +2,14 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 15,
    "id": "initial_id",
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "ExecuteTime": {
+     "end_time": "2024-02-27T15:36:56.096550Z",
+     "start_time": "2024-02-27T15:36:56.091278Z"
+    }
    },
    "outputs": [],
    "source": [
@@ -18,20 +22,45 @@
    "cell_type": "code",
    "outputs": [],
    "source": [
+    "from basico import *\n",
     "from process_bigraph import Composite, pf \n",
-    "from biosimulator_processes.copasi_process import CopasiProcess"
+    "from biosimulator_processes.processes.copasi_process import CopasiProcess"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-27T15:36:57.246146Z",
+     "start_time": "2024-02-27T15:36:57.239860Z"
+    }
+   },
+   "id": "c6c10dc5988e52d4",
+   "execution_count": 16
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### Example 1: Define a single process instance and a corresponding emitter"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "ac92611c7adf47e1"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "##### 1. Define the schema by which our Composite instance will be configured"
    ],
    "metadata": {
     "collapsed": false
    },
-   "id": "c6c10dc5988e52d4"
+   "id": "8608877d697af60c"
   },
   {
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "# 1. Define the sim state schema:\n",
-    "initial_sim_state = {\n",
+    "instance = {\n",
     "    'copasi': {\n",
     "        '_type': 'process',\n",
     "        'address': 'local:copasi',\n",
@@ -64,57 +93,103 @@
     "            'time': ['time_store'],\n",
     "        }\n",
     "    }\n",
-    "}\n",
-    "\n",
-    "\n",
-    "\n",
-    "\n",
-    "\n"
+    "}"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-27T15:44:23.766224Z",
+     "start_time": "2024-02-27T15:44:23.760968Z"
+    }
+   },
+   "id": "77636dbde3fa6b74",
+   "execution_count": 19
+  },
+  {
+   "cell_type": "markdown",
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "ab745a55ff67da50"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "##### 2. Instantiate the Process-Bigraph-Engine with the Composite class"
    ],
    "metadata": {
     "collapsed": false
    },
-   "id": "77636dbde3fa6b74"
+   "id": "e5199aee6d533761"
   },
   {
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "# 2. Make the composite:\n",
     "workflow = Composite({\n",
-    "    'state': initial_sim_state\n",
+    "    'state': instance\n",
     "})"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "4c2ef631b005be61"
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "##### 3. Run the Composite workflow with the Engine"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "6a402e48fbc30a5b"
+  },
   {
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "# 3. Run the composite workflow:\n",
     "workflow.run(10)"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "98676149a4ce822f"
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "##### 4. Gather and neatly-print the results."
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "d0ff3a2822a8fa2c"
+  },
   {
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "# 4. Gather and pretty print results\n",
     "results = workflow.gather_results()\n",
+    "\n",
     "print(f'RESULTS: {pf(results)}')"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "c15cee593ef000a7"
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "##### 5. Plot/Analyze the results with Plotly"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "b098a589f08ce138"
+  },
   {
    "cell_type": "code",
    "outputs": [],
@@ -125,6 +200,25 @@
     "collapsed": false
    },
    "id": "297504800772775e"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### Example 2: Define multiple processes in the same instance for a parameter scan"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "2afe93d975ed2aee"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "6157c1b8f1f67d05"
   }
  ],
  "metadata": {