{
"cells": [
{
"cell_type": "markdown",
"id": "1982c8ef-670b-4418-b346-00dfba8d0f76",
"metadata": {},
"source": [
"# Getting started"
]
},
{
"cell_type": "markdown",
"id": "fea21fff-173c-40f9-8919-ccb8b501bf4e",
"metadata": {},
"source": [
"## Reconstruct with coralME\n",
"\n",
"Here we show an example to reconstruct a dME-model of *B. subtilis*."
]
},
{
"cell_type": "markdown",
"id": "cc93ed2c-c978-45fa-ae0e-731c7f10e7dd",
"metadata": {},
"source": [
"### Import packages"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "968eedc7-c1ce-4b5a-ae06-1daf3f39a109",
"metadata": {},
"outputs": [],
"source": [
"from coralme.builder.main import MEBuilder\n",
"from importlib.resources import files"
]
},
{
"cell_type": "markdown",
"id": "be6449ec-ddc0-42b3-b49d-cf5e6b8ef12d",
"metadata": {},
"source": [
"### Define path to inputs"
]
},
{
"cell_type": "markdown",
"id": "7172b5e8-6fc5-4a88-a6cd-69a12d3b5ee9",
"metadata": {},
"source": [
"Define the paths to inputs and desired outputs. For more information about these files see [Description of inputs](BasicInputs.ipynb)."
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "2e0e9e63-c7f1-4a69-8478-7ffe71c6bf07",
"metadata": {},
"outputs": [],
"source": [
"input = {\n",
" # Inputs\n",
" \"m-model-path\": \"./helper_files/inputs/m_model.json\", # Path to model file\n",
" \"genbank-path\": \"./helper_files/inputs/genome.gb\", # Path to genome genbank file\n",
"\n",
" # Outputs\n",
" \"df_gene_cplxs_mods_rxns\": \"./helper_files/building_data/OSM.xlsx\", # Desired output path of OSM\n",
" \"out_directory\": \"./helper_files/\", # Output directory\n",
" \"log_directory\": \"./helper_files/\", # Log directory\n",
" \"locus_tag\": \"old_locus_tag\", # What IDs were used in the M-model? e.g. locus_tag, old_locus_tag\n",
" \"ME-Model-ID\" : \"EXAMPLE-BACILLUS-ME\" # Name of the ME-model\n",
"}"
]
},
{
"cell_type": "markdown",
"id": "5ec56049-90aa-40c6-bb71-10b52740e415",
"metadata": {},
"source": [
"Load organism setup. For now we can use the minimal setup with biological numbers from E. coli."
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "3c40401d-8820-4405-88a3-847f97907c10",
"metadata": {},
"outputs": [],
"source": [
"organism = str(files(\"coralme\") / \"iJL1678b\") + \"-ME/minimal-organism.json\""
]
},
{
"cell_type": "markdown",
"id": "38fdfacb-e080-4d08-abe1-f563e963c394",
"metadata": {},
"source": [
"### Create builder"
]
},
{
"cell_type": "markdown",
"id": "44c364d3-92aa-4b43-8571-a55d7e42bf0e",
"metadata": {},
"source": [
"For more information about this class see [Architecture of coralME](coralMEArchitecture.ipynb)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "f04001c0-8b9b-41fa-9a17-55ca6006af41",
"metadata": {
"ExecuteTime": {
"end_time": "2022-12-12T06:30:28.060280Z",
"start_time": "2022-12-12T06:30:01.706785Z"
},
"scrolled": true,
"tags": []
},
"outputs": [],
"source": [
"builder = MEBuilder(*[organism], **input)"
]
},
{
"cell_type": "markdown",
"id": "91ed12aa-2dbc-4808-9f5c-38486450860d",
"metadata": {},
"source": [
"### Generate files"
]
},
{
"cell_type": "markdown",
"id": "c93557b6-b8bb-4a45-8e88-3470520413d8",
"metadata": {},
"source": [
"This corresponds to _Synchronyze_ and _Complement_ steps in [Architecture of coralME](coralMEArchitecture.ipynb)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "17b488c8-822e-4598-a72e-33367294b3b2",
"metadata": {
"scrolled": true,
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Initiating file processing...\n",
"~ Processing files for EXAMPLE-BACILLUS-ME...\n",
"Set parameter Username\n",
"Academic license - for non-commercial use only - expires 2025-09-03\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Checking M-model metabolites... : 100.0%|██████████| 990/ 990 [00:00<00:00]\n",
"Checking M-model genes... : 100.0%|██████████| 844/ 844 [00:00<00:00]\n",
"Checking M-model reactions... : 100.0%|██████████| 1250/ 1250 [00:00<00:00]\n",
"Syncing optional genes file... : 0.0%| | 0/ 0 [00:00"
]
},
{
"cell_type": "markdown",
"id": "529527be-a1fa-4750-b0db-a625961985c7",
"metadata": {},
"source": [
"## Curate manually"
]
},
{
"cell_type": "markdown",
"id": "539e4555-603c-4226-ac26-8d928a506cc4",
"metadata": {},
"source": [
"1. __Copy__ all of the generated _reference files_ in building_data/reference_files and replace accordingly in building_data/\n",
"\n",
"2. __Go one by one__ through the files in building_data/ curating as needed! Important flags are risen in curation_notes.json to further guide you through curation.\n",
"\n",
"3. Everytime you make a change, __run the model through the troubleshooter!__ It will show you remaining gaps to look at, and the new curation notes might show new warnings.\n",
"\n",
"4. __Keep iterating!__ You will have finished when no gaps are present, and all remaining warnings in curation notes are irrelevant."
]
}
],
"metadata": {
"kernelspec": {
"display_name": "coralme-dev",
"language": "python",
"name": "coralme-dev"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
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