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cshenrycshenry
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Initial commit of project notebooks for the team
1 parent ed3f386 commit e53ae56

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Diff for: ‎CommunityModeling/AimeeCommunityFBA.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"cobrakbase 0.2.7\n"
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]
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}
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],
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"source": [
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"import cobra\n",
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"from cobra import Model, Reaction, Metabolite\n",
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"import pandas as pd\n",
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"import cplex\n",
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"import optlang\n",
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"import math\n",
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"import json\n",
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"import sys\n",
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"import cProfile\n",
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"from optlang.symbolics import Zero, add\n",
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"import cobra.util.solver as sutil\n",
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"from cobra.flux_analysis.parsimonious import pfba\n",
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"from IPython.core.display import HTML\n",
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"import cobrakbase\n",
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"sys.path.append(\"/Users/chenry/code/ModelSEEDpy\")\n",
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"#import modelseedpy.fbapkg\n",
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"from modelseedpy import ElementUptakePkg, SimpleThermoPkg, ReactionUsePkg, BilevelPkg, CommKineticPkg,KBaseMediaPkg\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Warning:Community biomass reaction is being altered with input abundances\n"
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]
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},
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{
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"data": {
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"text/html": [
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"<div>\n",
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"<style scoped>\n",
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" .dataframe tbody tr th:only-of-type {\n",
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" vertical-align: middle;\n",
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" }\n",
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"\n",
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" .dataframe tbody tr th {\n",
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" vertical-align: top;\n",
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" }\n",
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"\n",
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" .dataframe thead tr th {\n",
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" text-align: left;\n",
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" }\n",
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"</style>\n",
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"<table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr>\n",
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" <th></th>\n",
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" <th colspan=\"2\" halign=\"left\">IN_FLUXES</th>\n",
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" <th colspan=\"2\" halign=\"left\">OUT_FLUXES</th>\n",
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" <th colspan=\"2\" halign=\"left\">OBJECTIVES</th>\n",
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" </tr>\n",
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" <tr>\n",
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" <th></th>\n",
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" <th>ID</th>\n",
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" <th>FLUX</th>\n",
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" <th>ID</th>\n",
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" <th>FLUX</th>\n",
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" <th>ID</th>\n",
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" <th>FLUX</th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th>0</th>\n",
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" <td>cpd00067_e0</td>\n",
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" <td>100.000000</td>\n",
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" <td>cpd00001_e0</td>\n",
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" <td>100.000000</td>\n",
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" <td>bio1</td>\n",
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" <td>3.653218</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>1</th>\n",
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" <td>cpd00209_e0</td>\n",
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" <td>100.000000</td>\n",
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" <td>cpd00075_e0</td>\n",
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" <td>100.000000</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>2</th>\n",
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" <td>cpd00033_e0</td>\n",
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" <td>11.465399</td>\n",
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" <td>cpd00009_e0</td>\n",
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" <td>79.464829</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3</th>\n",
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" <td>cpd00013_e0</td>\n",
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" <td>10.839234</td>\n",
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" <td>cpd00047_e0</td>\n",
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" <td>78.981183</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>4</th>\n",
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" <td>cpd00107_e0</td>\n",
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" <td>1.371377</td>\n",
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" <td>cpd11416_c0</td>\n",
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" <td>3.653218</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>\n",
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"</div>"
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],
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"text/plain": [
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"<cobra.core.summary.model_summary.ModelSummary at 0x7fdc6e499c90>"
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]
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},
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"execution_count": 2,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"kbase_api = cobrakbase.KBaseAPI()\n",
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"model = kbase_api.get_from_ws(\"Cjaponicus_Ecoli_Community\",92637)\n",
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"model.solver = 'optlang-cplex'\n",
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"\n",
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"#Applying uptake limit to total carbon uptake by model\n",
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"eup = ElementUptakePkg(model)\n",
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"eup.build_package({\"C\":60})\n",
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"#Applying constraints based on KBase media\n",
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"media = kbase_api.get_from_ws(\"GlucoseM9Media\",91858)\n",
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"kmp = KBaseMediaPkg(model)\n",
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"kmp.build_package(None)\n",
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"#Applying community model kinetic constraints\n",
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"ckp = CommKineticPkg(model)\n",
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"ckp.build_package(2100,{\"1\":0.9,\"2\":0.1})\n",
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"\n",
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"biomass_objective = model.problem.Objective(\n",
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" 1 * model.reactions.bio1.flux_expression,\n",
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" direction='max')\n",
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"model.objective = biomass_objective\n",
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"\n",
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"with open('/Users/chenry/code/ChrisJupyter/CommunityModeling/data/CommunityFBA.lp', 'w') as out:\n",
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" out.write(str(model.solver))\n",
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" \n",
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"sol=model.optimize()\n",
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"model.summary()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

Diff for: ‎CommunityModeling/AimeeCommunityModel.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [],
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"source": [
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"# import cobra\n",
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"from cobra import Model, Reaction, Metabolite\n",
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"import pandas as pd\n",
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"import cplex\n",
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"import optlang\n",
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"import math\n",
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"import json\n",
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"import sys\n",
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"from optlang.symbolics import Zero, add\n",
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"import cobra.util.solver as sutil\n",
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"from cobra.flux_analysis.parsimonious import pfba\n",
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"from IPython.core.display import HTML\n",
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"import cobrakbase\n",
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"#sys.path.append(\"/Users/chandhanavoleti/Documents/SULI/ModelSEEDpy/ModelSEEDpy\")\n",
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"sys.path.append(\"/Users/chenry/code/ModelSEEDpy\")\n",
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"#import modelseedpy.fbapkg\n",
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"from modelseedpy import MSPackageManager"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"source": [
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"kbase_api = cobrakbase.KBaseAPI()\n",
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"model = kbase_api.get_from_ws(\"Hot_Lake_seven.mdl\",93544)\n",
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"media = kbase_api.get_from_ws(\"HotLakeMedia\",40576)\n",
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"pkgmgr = MSPackageManager.get_pkg_mgr(model,1)\n",
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"pkgmgr.addpkgs([\"ElementUptakePkg\",\"KBaseMediaPkg\"])\n",
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"pkgmgr.getpkg(\"ElementUptakePkg\").build_package({\"C\":60})\n",
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"pkgmgr.getpkg(\"KBaseMediaPkg\").build_package(media)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"['BilevelPkg', 'CommKineticPkg', 'ElementUptakePkg', 'FlexibleBiomassPkg', 'FluxFittingPkg', 'FullThermoPkg', 'GapfillingPkg', 'KBaseMediaPkg', 'MetaboFBAPkg', 'ProblemReplicationPkg', 'ProteomeFittingPkg', 'ReactionUsePkg', 'RevBinPkg', 'SimpleThermoPkg', 'TotalFluxPkg']\n",
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"['ElementUptakePkg', 'KBaseMediaPkg']\n"
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]
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}
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],
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"source": [
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"print(pkgmgr.list_available_packages())\n",
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"print(pkgmgr.list_active_packages())"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"ename": "AttributeError",
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"evalue": "'NoneType' object has no attribute 'solver'",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
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"\u001b[0;32m<ipython-input-4-8fd2053ae1dc>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mkbase_api\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcobrakbase\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mKBaseAPI\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkbase_api\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_from_ws\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"CMM_iAH991V2_iML1515.kb\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m91858\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msolver\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'optlang-cplex'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;31m#Applying uptake limit to total carbon uptake by model\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;31mAttributeError\u001b[0m: 'NoneType' object has no attribute 'solver'"
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]
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}
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],
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"source": [
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"kbase_api = cobrakbase.KBaseAPI()\n",
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"model = kbase_api.get_from_ws(\"CMM_iAH991V2_iML1515.kb\",91858)\n",
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"model.solver = 'optlang-cplex'\n",
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"\n",
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"#Applying uptake limit to total carbon uptake by model\n",
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"eup = ElementUptakePkg(model)\n",
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"eup.build_package({\"C\":60})\n",
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"#Applying constraints based on KBase media\n",
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"media = kbase_api.get_from_ws(\"Btheta_Ecoli_minimal_media\",40576)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"model"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"model.reactions.EX_cpd00098_e0"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"kmp = KBaseMediaPkg(model)\n",
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"kmp.build_package(media)\n",
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"#Applying community model kinetic constraints\n",
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"ckp = CommKineticPkg(model)\n",
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"ckp.build_package(2100,{\"1\":0.5,\"2\":0.5})\n",
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"\n",
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"biomass_objective = model.problem.Objective(\n",
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" 1 * model.reactions.bio1.flux_expression,\n",
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" direction='max')\n",
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"model.objective = biomass_objective\n",
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"\n",
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"sol=model.optimize()\n",
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"model.summary()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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