{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This notebook shows how to use `biolqm` to upload a model and compute its fixpoints."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from colomoto_jupyter import tabulate\n",
"import biolqm"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You can upload a model in any format supported by `bioLQM` (see https://github.com/colomoto/bioLQM#how-to-use-it), including GINsim (`.zginml` or `.ginml` files) and SBML-qual (`.sbml` files)."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
""
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"lqm = biolqm.upload()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The following cell code computes the fixpoints, and use `tabulate` to display the resulting table."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"fps = biolqm.fixpoints(lqm)\n",
"tabulate(fps)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python3",
"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": "3.6.6"
}
},
"nbformat": 4,
"nbformat_minor": 2
}