{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"id": "bad57316",
"metadata": {},
"source": [
"[](https://mybinder.org/v2/gh/combine-org/combine-notebooks/main?labpath=%2Fnotebooks%2Fomex.ipynb)\n",
"![\"Open](\"https://colab.research.google.com/assets/colab-badge.svg\")
"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "8c0154eb",
"metadata": {},
"source": [
"# Simple OMEX example"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "275bf1bb",
"metadata": {},
"source": [
"This notebook an example for creating a COMBINE archive. A COMBINE archive is a bundled package containing all the necessary documents and relevant information for a modeling and simulation project, ensuring that all components are conveniently stored together. The archive is encoded using the Open Modeling EXchange format (OMEX)."
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "5bb745f7",
"metadata": {},
"source": [
"## 1) Including libraries"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "1875d29c",
"metadata": {},
"source": [
"Note: Please change the `colab` flag to `True` if you are using Google Colab."
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "83f73430",
"metadata": {},
"outputs": [],
"source": [
"colab = False\n",
"if colab:\n",
" !pip install git+https://github.com/combine-org/combine-notebooks\n",
" !git clone https://github.com/combine-org/combine-notebooks\n",
" %cd /content/combine-notebooks/notebooks"
]
},
{
"cell_type": "code",
"execution_count": 38,
"id": "5e7c2a84",
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"from pathlib import Path\n",
"\n",
"from pymetadata.console import console\n",
"from pymetadata.omex import EntryFormat, ManifestEntry, Omex\n",
"\n",
"from combine_notebooks import RESULTS_DIR"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "2e806b7a",
"metadata": {},
"source": [
"## 2) Creating a COMBINE archieve"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "565b2c61",
"metadata": {},
"source": [
"Creating an empty archive and adding entry for SBML."
]
},
{
"cell_type": "code",
"execution_count": 39,
"id": "d1a747a8",
"metadata": {},
"outputs": [],
"source": [
"# Create OMEX archive of resources.\n",
"omex = Omex()"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "f7db9291",
"metadata": {},
"source": [
"Get the file location of our results files. These were generated by other notebooks in this repositiory. The files we will be adding to our OMEX file include:\n",
" - hello_world_sbml.xml - a simple SBML model\n",
" - hello_world_cellml.cellml - a simple CellML model\n",
" - hello_world_sbgn.png - a diagram showing a simple reacton that has been generated using SBGN\n",
" - hello_world_sbgn.sbgn - correponding SBGN used to generate the .png file\n",
" - hello_world_sedml.sedml - a simple simulation experiment described using SED-ML"
]
},
{
"cell_type": "code",
"execution_count": 40,
"id": "06cfde3a",
"metadata": {},
"outputs": [],
"source": [
"# Path to our results\n",
"results_dir = Path(RESULTS_DIR.stem)"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "518eca96",
"metadata": {},
"source": [
"First, lets add our simple SBML file into the COMBINE archieve."
]
},
{
"cell_type": "code",
"execution_count": 41,
"id": "83838073",
"metadata": {},
"outputs": [],
"source": [
"# Add entry for the SBML model\n",
"omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./sbml/hello_world_sbml.xml\",\n",
" format=EntryFormat.SBML_L3V2,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_sbml.xml\",\n",
")"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "3e5b1bd2",
"metadata": {},
"source": [
"Now we'll add our simple CellML model."
]
},
{
"cell_type": "code",
"execution_count": 42,
"id": "92c65b63",
"metadata": {},
"outputs": [],
"source": [
"# Add entry for the CellML model\n",
"omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./cellml/hello_world_cellml.cellml\",\n",
" format=EntryFormat.CELLML,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_cellml.cellml\",\n",
")"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "7b59fb69",
"metadata": {},
"source": [
"Next lets add entries for both our SBGN file and the png that it generated."
]
},
{
"cell_type": "code",
"execution_count": 43,
"id": "abfad069",
"metadata": {},
"outputs": [],
"source": [
"# Add entry for SBGN file\n",
"omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./sbgn/hello_world_sbgn.sbgn\",\n",
" format=EntryFormat.SBGN,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_sbgn.sbgn\",\n",
")\n",
"\n",
"# Add entry for corresponding png file generated from the SBGN\n",
"omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./sbgn/hello_world_sbgn.png\",\n",
" format=EntryFormat.PNG,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_sbgn.png\",\n",
")"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "fbf60539",
"metadata": {},
"source": [
"Finally, we will add a SED-ML file to the COMBINE archieve."
]
},
{
"cell_type": "code",
"execution_count": 44,
"id": "b8796964",
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"# Add entry for the SEDML simulation experiment\n",
"omex.add_entry(\n",
" entry=ManifestEntry(\n",
" location=\"./sedml/hello_world_sedml.sedml\",\n",
" format=EntryFormat.SEDML,\n",
" master=False,\n",
" ),\n",
" entry_path=results_dir / \"hello_world_sedml.sedml\"\n",
")"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "f55ed397",
"metadata": {},
"source": [
"## 3) Write and print the COMBINE archieve"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "8560c376",
"metadata": {},
"source": [
"And we're done creating the OMEX file. Now lets save it."
]
},
{
"cell_type": "code",
"execution_count": 45,
"id": "02f7c609",
"metadata": {},
"outputs": [],
"source": [
"RESULTS_DIR.mkdir(parents=True, exist_ok=True)\n",
"omex_path = RESULTS_DIR / \"combine_hello_world.omex\"\n",
"omex.to_omex(omex_path)"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "227ebc87",
"metadata": {},
"source": [
"We can also use the `console.print` function to display the comtent of the OMEX file."
]
},
{
"cell_type": "code",
"execution_count": 46,
"id": "09eda6c2",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"[ ManifestEntry(location='.', format='http://identifiers.org/combine.specifications:omex', master=False),\n",
" ManifestEntry(location='./manifest.xml', format='http://identifiers.org/combine.specifications:omex-manifest', \n",
"master=False),\n",
" ManifestEntry(location='./sbml/hello_world_sbml.xml', \n",
"format='http://identifiers.org/combine.specifications:sbml.level-3.version-2', master=False),\n",
" ManifestEntry(location='./cellml/hello_world_cellml.cellml', \n",
"format='http://identifiers.org/combine.specifications:cellml', master=False),\n",
" ManifestEntry(location='./sbgn/hello_world_sbgn.sbgn', \n",
"format='http://identifiers.org/combine.specifications:sbgn', master=False),\n",
" ManifestEntry(location='./sbgn/hello_world_sbgn.png', format='https://purl.org/NET/mediatypes/image/png', \n",
"master=False),\n",
" ManifestEntry(location='./sedml/hello_world_sedml.sedml', \n",
"format='http://identifiers.org/combine.specifications:sed-ml', master=False)]\n",
"\n"
],
"text/plain": [
"\u001b[1m[\u001b[0m \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'.'\u001b[0m, \u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:omex'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./manifest.xml'\u001b[0m, \u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:omex-manifest'\u001b[0m, \n",
"\u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./sbml/hello_world_sbml.xml'\u001b[0m, \n",
"\u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:sbml.level-3.version-2'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./cellml/hello_world_cellml.cellml'\u001b[0m, \n",
"\u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:cellml'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./sbgn/hello_world_sbgn.sbgn'\u001b[0m, \n",
"\u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:sbgn'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./sbgn/hello_world_sbgn.png'\u001b[0m, \u001b[33mformat\u001b[0m=\u001b[32m'https://purl.org/NET/mediatypes/image/png'\u001b[0m, \n",
"\u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m,\n",
" \u001b[1;35mManifestEntry\u001b[0m\u001b[1m(\u001b[0m\u001b[33mlocation\u001b[0m=\u001b[32m'./sedml/hello_world_sedml.sedml'\u001b[0m, \n",
"\u001b[33mformat\u001b[0m=\u001b[32m'http://identifiers.org/combine.specifications:sed-ml'\u001b[0m, \u001b[33mmaster\u001b[0m=\u001b[3;91mFalse\u001b[0m\u001b[1m)\u001b[0m\u001b[1m]\u001b[0m\n"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"console.print(omex)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.1"
}
},
"nbformat": 4,
"nbformat_minor": 5
}