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Merge branch 'main' of https://github.com/cshenry/ModelSEEDpy into main
# Conflicts: # modelseedpy/core/mseditorapi.py
2 parents 7c1d107 + 74ee6e4 commit 3d3f67f

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‎examples/build_metabolic_model.ipynb

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"outputs": [],
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"source": [
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"import modelseedpy\n",
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"from modelseedpy.core.msgenome import MSGenome\n",
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"from modelseedpy.core.msbuilder import build_metabolic_model"
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"from modelseedpy import MSBuilder, MSGenome"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"model = build_metabolic_model('ecoli.core', genome, core_template, allow_all_non_grp_reactions=True)"
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"model = MSBuilder.build_metabolic_model('ecoli.core', genome, core_template, allow_all_non_grp_reactions=True)"
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]
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{
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" <td>ecoli.core</td>\n",
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" </tr><tr>\n",
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" <td><strong>Memory address</strong></td>\n",
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" <td>0x07feb71fa6510</td>\n",
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" <td>0x07faf31a00190</td>\n",
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" </tr><tr>\n",
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" <td><strong>Number of metabolites</strong></td>\n",
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" <td>190</td>\n",
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" <td>0</td>\n",
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" </tr><tr>\n",
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" <td><strong>Objective expression</strong></td>\n",
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" <td>0</td>\n",
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" <td>1.0*bio1 - 1.0*bio1_reverse_b18f7</td>\n",
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" </tr><tr>\n",
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" <td><strong>Compartments</strong></td>\n",
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" <td>c0, e0</td>\n",
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" </tr>\n",
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" </table>"
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],
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"text/plain": [
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"<Model ecoli.core at 0x7feb71fa6510>"
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"<Model ecoli.core at 0x7faf31a00190>"
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]
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{
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"cell_type": "markdown",
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"source": [
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"### TODO: add biomass/exchanges"
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]
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"outputs": [],
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"source": []
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{
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"</table>"
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],
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"text/plain": [
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"<cobra.summary.model_summary.ModelSummary at 0x7feb84437490>"
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"<cobra.summary.model_summary.ModelSummary at 0x7faf4344bd90>"
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]
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},
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"execution_count": 9,
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"output_type": "execute_result"
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},
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{
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"cell_type": "code",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/html": [
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"<h3>Objective</h3><p>1.0 bio1 = 0.1229368143626848</p><h4>Uptake</h4><table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th>Metabolite</th>\n",
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" <th>Reaction</th>\n",
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" <th>Flux</th>\n",
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" <th>C-Number</th>\n",
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" <th>C-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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" <td>cpd00007_e0</td>\n",
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" <td>EX_cpd00007_e0</td>\n",
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" <td>1.371</td>\n",
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" <td>0</td>\n",
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" <td>0.00%</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td>cpd00009_e0</td>\n",
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" <td>EX_cpd00009_e0</td>\n",
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" <td>0.5182</td>\n",
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" <td>0</td>\n",
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" <td>0.00%</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td>cpd00027_e0</td>\n",
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" <td>EX_cpd00027_e0</td>\n",
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" <td>1</td>\n",
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" <td>6</td>\n",
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" <td>100.00%</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table><h4>Secretion</h4><table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th>Metabolite</th>\n",
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" <th>Reaction</th>\n",
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" <th>Flux</th>\n",
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" <th>C-Number</th>\n",
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" <th>C-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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" <td>cpd00001_e0</td>\n",
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" <td>EX_cpd00001_e0</td>\n",
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" <td>-2.812</td>\n",
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" <td>0</td>\n",
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" <td>0.00%</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td>cpd00011_e0</td>\n",
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" <td>EX_cpd00011_e0</td>\n",
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" <td>-0.5044</td>\n",
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" <td>1</td>\n",
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" <td>100.00%</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td>cpd00067_e0</td>\n",
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" <td>EX_cpd00067_e0</td>\n",
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" <td>-1.749</td>\n",
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" <td>0</td>\n",
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" <td>0.00%</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td>cpd11416_c0</td>\n",
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" <td>SK_cpd11416_c0</td>\n",
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" <td>-0.1229</td>\n",
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" <td>0</td>\n",
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" <td>0.00%</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>"
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],
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"text/plain": [
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"<cobra.summary.model_summary.ModelSummary at 0x7faf31083d10>"
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]
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},
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"execution_count": 17,
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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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"model.objective = 'bio1'\n",
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"model.medium = {\n",
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" 'EX_cpd00067_e0': 1000,\n",
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" 'EX_cpd00027_e0': 1,\n",
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" 'EX_cpd00007_e0': 1000,\n",
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" 'EX_cpd00001_e0': 1000,\n",
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" 'EX_cpd00009_e0': 1000,\n",
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" \n",
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"}\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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{
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" <td>GCF_000005845.2.RAST.mdl</td>\n",
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" </tr><tr>\n",
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" <td><strong>Memory address</strong></td>\n",
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" <td>0x07feb922dea90</td>\n",
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" <td>0x07fa6819dee50</td>\n",
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" </tr><tr>\n",
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" <td><strong>Number of metabolites</strong></td>\n",
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" <td>190</td>\n",
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" </table>"
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"<FBAModel GCF_000005845.2.RAST.mdl at 0x7feb922dea90>"
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"<FBAModel GCF_000005845.2.RAST.mdl at 0x7fa6819dee50>"
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"set()"
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