{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "mkchf6PsO2vs", "outputId": "3c5b7a7b-8625-4ebd-8d53-22acb2e6fd68" }, "outputs": [], "source": [ "#pip install cobra" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "ub_5YicIO5US", "outputId": "4bec5d9b-f484-410c-f7f1-1d44b09b5682" }, "outputs": [], "source": [ "#pip install escher" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "id": "dHqKQRq3PBq4" }, "outputs": [], "source": [ "import cobra\n", "import escher" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 238 }, "id": "xSnvqrAxPHfw", "outputId": "7d2547a6-f7b4-44c5-98b9-86c42af99bd9" }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Adding exchange reaction EX_S with default bounds for boundary metabolite: S.\n", "Adding exchange reaction EX_biomass with default bounds for boundary metabolite: biomass.\n", "Adding exchange reaction EX_fuel1 with default bounds for boundary metabolite: fuel1.\n", "Adding exchange reaction EX_fuel2 with default bounds for boundary metabolite: fuel2.\n" ] }, { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Nametoy_model_xml
Memory address0x07fea90b94fd0
Number of metabolites17
Number of reactions22
Number of groups0
Objective expression1.0*R01 - 1.0*R01_reverse_59259
Compartmentsext, int
" ], "text/plain": [ "" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Loading a model\n", "model_path = 'toy_model.xml'\n", "model = cobra.io.read_sbml_model(model_path)\n", "\n", "model" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "yjTOtp9FQIwc", "outputId": "c17a90f0-752e-469e-97ae-360ce5b5a6d3" }, "outputs": [ { "data": { "text/plain": [ "{'EX_S': (-100, 0),\n", " 'EX_biomass': (0, 1000),\n", " 'EX_fuel1': (0, 1000),\n", " 'EX_fuel2': (0, 1000)}" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "environmental_conditions = {\n", " 'EX_S': (-100, 0),\n", " 'EX_biomass': (0, 1000),\n", " 'EX_fuel1': (0, 1000),\n", " 'EX_fuel2': (0, 1000),\n", "\n", "}\n", "environmental_conditions" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "id": "ZEr9bhxmz9Wd" }, "outputs": [], "source": [ "for reaction_id, bound in environmental_conditions.items():\n", " model.reactions.get_by_id(reaction_id).bounds = bound" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "id": "y12-JuGIS8Op" }, "outputs": [], "source": [ "model.objective='EX_biomass'" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 38 }, "id": "YMJIZUh3QMf7", "outputId": "18af01cc-f666-41f0-c437-6381c67634d5" }, "outputs": [ { "data": { "text/latex": [ "$\\displaystyle 1.0 \\cdot EX_{biomass} - 1.0 \\cdot EX_{biomass reverse 91cf2}$" ], "text/plain": [ "1.0*EX_biomass - 1.0*EX_biomass_reverse_91cf2" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model.objective.expression" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "65HRA5P8TAKw", "outputId": "875ea815-e335-4a82-a9f7-1c08af86faa9" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "EX_S : S <-- \n", "EX_biomass : biomass --> \n", "EX_fuel1 : fuel1 --> \n", "EX_fuel2 : fuel2 --> \n", "R01 : S --> M1\n", "R02 : M1 <=> M2\n", "R03 : M2 --> M3\n", "R04 : M3 <=> M4\n", "R05 : M4 <=> M5\n", "R06 : M3 --> M6\n", "R07 : M6 --> M7\n", "R08 : M7 --> 0.5 M5 + 0.5 M8\n", "R09 : M8 --> fuel1\n", "R10 : M1 <=> M9\n", "R11 : M9 --> M2\n", "R12 : M9 --> M10\n", "R13 : M9 --> M11\n", "R14 : M11 --> 0.7 M12 + 0.3 M13\n", "R15 : M13 --> fuel2\n", "R16 : M12 --> M5\n", "R17 : M5 --> biomass\n", "R18 : M3 --> 2.0 M8\n" ] } ], "source": [ "for i in range(0,len(model.reactions)):\n", " print(model.reactions[i].id,' : ', model.reactions[i].reaction)" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "X1-LHOLLQbw8", "outputId": "4a8cc89e-9e20-467b-9274-9a7ea9496939" }, "outputs": [ { "data": { "text/plain": [ "EX_S -100.0\n", "EX_biomass 100.0\n", "EX_fuel1 -0.0\n", "EX_fuel2 -0.0\n", "R01 100.0\n", "R02 100.0\n", "R03 100.0\n", "R04 100.0\n", "R05 100.0\n", "R06 0.0\n", "R07 0.0\n", "R08 0.0\n", "R09 0.0\n", "R10 0.0\n", "R11 0.0\n", "R12 0.0\n", "R13 0.0\n", "R14 0.0\n", "R15 0.0\n", "R16 0.0\n", "R17 100.0\n", "R18 0.0\n", "Name: fluxes, dtype: float64" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "solution = model.optimize()\n", "solution.fluxes" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "id": "lLw4gkj0TL3G" }, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": 11, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 1000 }, "id": "3wB6lIQMawti", "outputId": "24bdc788-8e29-4207-dc52-5ab851d90d86" }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "194ba233851c4ab9b9b8b6fa2a5267f3", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Builder(reaction_data={'EX_S': -100.0, 'EX_biomass': 100.0, 'EX_fuel1': -0.0, 'EX_fuel2': -0.0, 'R01': 100.0, …" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "builder = escher.Builder(map_json='toy_escher_map.json', model=model, reaction_data=solution.fluxes)\n", "#builder.save_html('map2')\n", "#from IPython.core.display import display, HTML\n", "#display(HTML('map2'))\n", "builder" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "ILggVurIax9p", "outputId": "08d3c6a5-95b9-4bb1-e203-8bc3c5e867c7" }, "outputs": [ { "data": { "text/plain": [ "EX_S -100.0\n", "EX_biomass -0.0\n", "EX_fuel1 200.0\n", "EX_fuel2 -0.0\n", "R01 100.0\n", "R02 100.0\n", "R03 100.0\n", "R04 0.0\n", "R05 0.0\n", "R06 0.0\n", "R07 0.0\n", "R08 0.0\n", "R09 200.0\n", "R10 0.0\n", "R11 0.0\n", "R12 0.0\n", "R13 0.0\n", "R14 0.0\n", "R15 0.0\n", "R16 0.0\n", "R17 0.0\n", "R18 100.0\n", "Name: fluxes, dtype: float64" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model.objective='EX_fuel1'\n", "solution = model.optimize()\n", "solution.fluxes" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 1000 }, "id": "8GAHi0l0ayYi", "outputId": "481141cc-0926-4dd2-909c-3f8c838fdf0c" }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "768d9dc7c302448c93ce3c60b02327fe", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Builder(reaction_data={'EX_S': -100.0, 'EX_biomass': -0.0, 'EX_fuel1': 200.0, 'EX_fuel2': -0.0, 'R01': 100.0, …" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "builder = escher.Builder(map_json='toy_escher_map.json', model=model, reaction_data=solution.fluxes)\n", "#builder.save_html('map2')\n", "#from IPython.core.display import display, HTML\n", "#display(HTML('map2'))\n", "builder" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "-5QTzw0_reIt", "outputId": "67c488ba-7397-4192-d457-d3eda1569005" }, "outputs": [ { "data": { "text/plain": [ "EX_S -100.0\n", "EX_biomass 100.0\n", "EX_fuel1 -0.0\n", "EX_fuel2 -0.0\n", "R01 100.0\n", "R02 100.0\n", "R03 100.0\n", "R04 100.0\n", "R05 100.0\n", "R06 0.0\n", "R07 0.0\n", "R08 0.0\n", "R09 0.0\n", "R10 0.0\n", "R11 0.0\n", "R12 0.0\n", "R13 0.0\n", "R14 0.0\n", "R15 0.0\n", "R16 0.0\n", "R17 100.0\n", "R18 0.0\n", "Name: fluxes, dtype: float64" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model.objective='EX_biomass'\n", "solution = model.optimize()\n", "solution.fluxes" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 739 }, "id": "E917rnQ3ays6", "outputId": "15b0c3c5-e1b6-4448-fae4-c4e3a6e83d65" }, "outputs": [ { "data": { "text/html": [ "
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minimummaximum
EX_S-100.0-100.0
EX_biomass100.0100.0
EX_fuel10.00.0
EX_fuel20.00.0
R01100.0100.0
R02-900.0100.0
R03100.0100.0
R04100.0100.0
R05100.0100.0
R060.00.0
R070.00.0
R080.00.0
R090.00.0
R100.01000.0
R110.01000.0
R120.00.0
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" ], "text/plain": [ " minimum maximum\n", "EX_S -100.0 -100.0\n", "EX_biomass 100.0 100.0\n", "EX_fuel1 0.0 0.0\n", "EX_fuel2 0.0 0.0\n", "R01 100.0 100.0\n", "R02 -900.0 100.0\n", "R03 100.0 100.0\n", "R04 100.0 100.0\n", "R05 100.0 100.0\n", "R06 0.0 0.0\n", "R07 0.0 0.0\n", "R08 0.0 0.0\n", "R09 0.0 0.0\n", "R10 0.0 1000.0\n", "R11 0.0 1000.0\n", "R12 0.0 0.0\n", "R13 0.0 0.0\n", "R14 0.0 0.0\n", "R15 0.0 0.0\n", "R16 0.0 0.0\n", "R17 100.0 100.0\n", "R18 0.0 0.0" ] }, "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from cobra.flux_analysis import flux_variability_analysis\n", "flux_variability_analysis(model)" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "id": "ekcssglglXLP" }, "outputs": [], "source": [ "environmental_conditions = {\n", " 'R11': (1000, 1000)\n", "}\n", "for reaction_id, bound in environmental_conditions.items():\n", " model.reactions.get_by_id(reaction_id).bounds = bound" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "3psb5oiNlXgj", "outputId": "1a82d2df-7447-47f2-be74-0e2e25b144e7" }, "outputs": [ { "data": { "text/plain": [ "EX_S -100.0\n", "EX_biomass 100.0\n", "EX_fuel1 -0.0\n", "EX_fuel2 -0.0\n", "R01 100.0\n", "R02 -900.0\n", "R03 100.0\n", "R04 100.0\n", "R05 100.0\n", "R06 0.0\n", "R07 0.0\n", "R08 0.0\n", "R09 0.0\n", "R10 1000.0\n", "R11 1000.0\n", "R12 0.0\n", "R13 0.0\n", "R14 0.0\n", "R15 0.0\n", "R16 0.0\n", "R17 100.0\n", "R18 0.0\n", "Name: fluxes, dtype: float64" ] }, "execution_count": 17, "metadata": {}, "output_type": "execute_result" } ], "source": [ "solution = model.optimize()\n", "solution.fluxes" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 1000 }, "id": "xraorRZ5TSKv", "outputId": "ab6a17f1-4119-4d53-f0f1-9b64eb8a641c" }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "0c625b3b668841a2bda3355709dacede", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Builder(reaction_data={'EX_S': -100.0, 'EX_biomass': 100.0, 'EX_fuel1': -0.0, 'EX_fuel2': -0.0, 'R01': 100.0, …" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "builder = escher.Builder(map_json='toy_escher_map.json', model=model, reaction_data=solution.fluxes)\n", "#builder.save_html('map2')\n", "#from IPython.core.display import display, HTML\n", "#display(HTML('map2'))\n", "builder" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "data": { "text/html": [ "

Objective

1.0 EX_fuel1 = 200.0

Uptake

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MetaboliteReactionFluxC-NumberC-Flux
SEX_S10000.00%

Secretion

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MetaboliteReactionFluxC-NumberC-Flux
fuel1EX_fuel1-20000.00%
" ], "text/plain": [ "" ] }, "execution_count": 28, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model.objective={model.reactions.EX_fuel1:1}\n", "solution = model.optimize()\n", "model.summary()" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "EX_S -100.0\n", "EX_biomass -0.0\n", "EX_fuel1 200.0\n", "EX_fuel2 -0.0\n", "R01 100.0\n", "R02 100.0\n", "R03 100.0\n", "R04 0.0\n", "R05 0.0\n", "R06 0.0\n", "R07 0.0\n", "R08 0.0\n", "R09 200.0\n", "R10 0.0\n", "R11 0.0\n", "R12 0.0\n", "R13 0.0\n", "R14 0.0\n", "R15 0.0\n", "R16 0.0\n", "R17 0.0\n", "R18 100.0\n", "Name: fluxes, dtype: float64" ] }, "execution_count": 29, "metadata": {}, "output_type": "execute_result" } ], "source": [ "solution.fluxes" ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [], "source": [ "model.objective={model.reactions.EX_biomass:1}" ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "id": "N2NQjVDeUzHn" }, "outputs": [], "source": [ "environmental_conditions = {\n", " 'R11': (0, 1000),\n", " 'R04': (0,0),\n", " 'R10': (0,0),\n", "}\n", "for reaction_id, bound in environmental_conditions.items():\n", " model.reactions.get_by_id(reaction_id).bounds = bound" ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "dKjcIhGadO63", "outputId": "fcdc6fe4-025d-4cca-a2f2-ec03d9188dd7" }, "outputs": [ { "data": { "text/plain": [ "EX_S -100.0\n", "EX_biomass 50.0\n", "EX_fuel1 50.0\n", "EX_fuel2 -0.0\n", "R01 100.0\n", "R02 100.0\n", "R03 100.0\n", "R04 0.0\n", "R05 0.0\n", "R06 100.0\n", "R07 100.0\n", "R08 100.0\n", "R09 50.0\n", "R10 0.0\n", "R11 0.0\n", "R12 0.0\n", "R13 0.0\n", "R14 0.0\n", "R15 0.0\n", "R16 0.0\n", "R17 50.0\n", "R18 0.0\n", "Name: fluxes, dtype: float64" ] }, "execution_count": 32, "metadata": {}, "output_type": "execute_result" } ], "source": [ "solution = model.optimize()\n", "solution.fluxes" ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 1000 }, "id": "1Yhz2EbYdPPP", "outputId": "a6139ec6-9568-49fb-f5d2-0470a346f84a" }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "2ae4d64f18134148b0667016c110dee9", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Builder(reaction_data={'EX_S': -100.0, 'EX_biomass': 50.0, 'EX_fuel1': 50.0, 'EX_fuel2': -0.0, 'R01': 100.0, '…" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "builder = escher.Builder(map_json='toy_escher_map.json', model=model, reaction_data=solution.fluxes)\n", "#builder.save_html('map2')\n", "#from IPython.core.display import display, HTML\n", "#display(HTML('map2'))\n", "builder" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "id": "T_ZO713GdPr3" }, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": { "id": "QD9_9xYxUzeC" }, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": { "id": "n9qmsvDKWaFK" }, "outputs": [], "source": [ "# Dessiner une map escher\n", "''' \n", "cobra.io.save_json_model(model,'toy_model.json')\n", "from escher import Builder\n", "b=Builder()\n", "b.model_json='toy_model.json'\n", "b.height=1600\n", "b.width=1600\n", "b.save_html('map')\n", "from IPython.core.display import display, HTML\n", "display(HTML('map'))\n", "'''" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "id": "KdGUXmxyg0OC" }, "outputs": [], "source": [ "\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "id": "5wpxRl0Ek8KB" }, "outputs": [], "source": [] } ], "metadata": { "colab": { "collapsed_sections": [], "provenance": [] }, "kernelspec": { "display_name": "Python 3 (ipykernel)", "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": "3.8.13" } }, "nbformat": 4, "nbformat_minor": 1 }