{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Predict expression modulation targets\n", "\n", "Cameo provides algorithms to search for genes or reactions that can be over- or down-regulated in order to achieve a given biological objective." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from cameo import models" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Load the E. coli core model." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "model = models.bigg.e_coli_core" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Flux Scanning based on Enforced Objective Flux" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "from cameo.strain_design.deterministic.flux_variability_based import FSEOF" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "fseof = FSEOF(model)" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "Model: e_coli_core
\n", "Enforced objective: EX_succ_e
\n", "Primary objective: Maximize\n", "-1.0*BIOMASS_Ecoli_core_w_GAM_reverse_712e5 + 1.0*BIOMASS_Ecoli_core_w_GAM
\n", "
\n", "Reaction fluxes

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FRD70.0000000.0000000.0000001.4532353.1753024.8973696.5867037.7551419.12784210.852285
GAPD16.43113216.83873717.17361817.42198917.67035917.91873018.19843118.97672319.54778419.761991
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THD20.0000000.0000000.0000000.0000000.0000000.0000000.1196742.1438482.9168071.535161
TPI7.7569418.0364998.2425158.3610488.4795828.5981158.7477939.3931029.8307879.910940
EX_succ_e1.4745752.9491504.4237255.8983007.3728758.84745010.32202511.79660013.27117514.745750
\n", "
\n" ], "text/plain": [ "" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fseof.run(target=model.reactions.EX_succ_e)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Differential flux variability analysis\n", "\n", "Compares flux ranges of a reference model to a set of models that have been parametrized to lie on a grid of evenly spaced points in the *n*-dimensional production envelope (*n* being the number of reaction bounds to be varied)." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "from cameo.flux_analysis.analysis import phenotypic_phase_plane\n", "from cameo.strain_design.deterministic import DifferentialFVA" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Succinate production" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The production envelope looks like this." ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "" ], "text/vnd.plotly.v1+html": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.plotly.v1+json": { "data": [ { "fill": "toself", "fillcolor": "#B3E2CD", "hoverinfo": "none", "marker": { "line": { "color": "#B3E2CD" }, "opacity": 0.3 }, "mode": "line", "name": "WT", "opacity": 0.3, "type": "scatter", "x": [ 0, 0.04599586878781212, 0.09199173757562425, 0.13798760636343638, 0.1839834751512485, 0.2299793439390606, 0.27597521272687275, 0.32197108151468484, 0.367966950302497, 0.41396281909030913, 0.4599586878781212, 0.5059545566659334, 0.5519504254537455, 0.5979462942415577, 0.6439421630293697, 0.6899380318171818, 0.735933900604994, 0.7819297693928061, 0.8279256381806183, 0.8739215069684304, 0.8739215069684304, 0.8279256381806183, 0.7819297693928061, 0.735933900604994, 0.6899380318171818, 0.6439421630293697, 0.5979462942415577, 0.5519504254537455, 0.5059545566659334, 0.4599586878781212, 0.41396281909030913, 0.367966950302497, 0.32197108151468484, 0.27597521272687275, 0.2299793439390606, 0.1839834751512485, 0.13798760636343638, 0.09199173757562425, 0.04599586878781212, 0, 0, 0 ], "y": [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.8811810012837018, 1.7623620025673965, 2.64354300385109, 3.5247240051347886, 4.396864526652468, 5.265895211723508, 6.134925896794553, 7.003956581865594, 7.872987266936641, 8.742017952007677, 9.611048637078724, 10.474279162179371, 11.322755999193262, 12.171232836207146, 13.017389427255482, 13.859083737108278, 14.700778046961073, 15.542472356813862, 16.38416666666667, 0, 16.38416666666667 ] } ], "layout": { "height": 400, "title": "Phenotypic Phase Plane (flux)", "width": 700, "xaxis": { "title": "BIOMASS_Ecoli_core_w_GAM [h^-1]" }, "yaxis": { "title": "DM_succ_e: succ_e --> [mmol gDW^-1 h^-1]" } } }, "text/html": [ "
" ], "text/vnd.plotly.v1+html": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "production_envelope = phenotypic_phase_plane(model, \n", " variables=[model.reactions.BIOMASS_Ecoli_core_w_GAM],\n", " objective=model.metabolites.succ_e)\n", "production_envelope.plot(height=400)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Set up a model that represents a reference state (in this case a model with a constrained growth rate)." ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "model.reactions.EX_o2_e.lower_bound = 0\n", "reference_model = model.copy()\n", "biomass_rxn = reference_model.reactions.BIOMASS_Ecoli_core_w_GAM\n", "biomass_rxn.lower_bound = 0.\n", "target = reference_model.metabolites.succ_e" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Set up the differential flux variability analysis strain design method." ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [], "source": [ "diffFVA = DifferentialFVA(design_space_model=model,\n", " reference_model=reference_model,\n", " objective=target,\n", " variables=[biomass_rxn],\n", " normalize_ranges_by=biomass_rxn,\n", " points=10)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Run differential flux variability analysis (only on the surface of the production envelope)" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "scrolled": false }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "419491eab5bf46d688035f15f058463e", "version_major": 2, "version_minor": 0 }, "text/html": [ "

Failed to display Jupyter Widget of type HBox.

\n", "

\n", " If you're reading this message in Jupyter Notebook or JupyterLab, it may mean\n", " that the widgets JavaScript is still loading. If this message persists, it\n", " likely means that the widgets JavaScript library is either not installed or\n", " not enabled. See the Jupyter\n", " Widgets Documentation for setup instructions.\n", "

\n", "

\n", " If you're reading this message in another notebook frontend (for example, a static\n", " rendering on GitHub or NBViewer),\n", " it may mean that your frontend doesn't currently support widgets.\n", "

\n" ], "text/plain": [ "HBox()" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "result = diffFVA.run(surface_only=True)" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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lower_boundupper_boundgapsnormalized_gapsbiomassproductionKOflux_reversalsuddenly_essentialfree_fluxreactionexcluded
reaction
ACALD0.0000000.000000-2.339592e+00NaN0.00000013.905778TrueFalseFalseFalseACALDFalse
ACALDt0.0000000.0000000.000000e+00NaN0.00000013.905778FalseFalseFalseFalseACALDtFalse
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FBA10.00000010.0000001.579059e-01NaN0.00000013.905778FalseFalseFalseFalseFBAFalse
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FORt20.0000000.0000000.000000e+00NaN0.00000013.905778FalseFalseTrueFalseFORt2False
FRD713.4764441000.0000000.000000e+00NaN0.00000013.905778FalseFalseFalseFalseFRD7False
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.......................................
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NH4t1.0259161.0259160.000000e+002.9946830.1881452.123333FalseFalseFalseFalseNH4tFalse
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PPC2.6624812.6624810.000000e+007.5578770.1881452.123333FalseFalseFalseFalsePPCFalse
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THD23.2259503.2259500.000000e+004.8692040.1881452.123333FalseFalseFalseFalseTHD2False
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684 rows × 12 columns

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" ], "text/plain": [ " lower_bound upper_bound gaps \\\n", "reaction \n", "ACALD 0.000000 0.000000 -2.339592e+00 \n", "ACALDt 0.000000 0.000000 0.000000e+00 \n", "ACKr -5.664889 -5.664889 0.000000e+00 \n", "ACONTa 0.429333 0.429333 0.000000e+00 \n", "ACONTb 0.429333 0.429333 0.000000e+00 \n", "ACt2r -5.664889 -5.664889 0.000000e+00 \n", "ADK1 3.476444 3.476444 0.000000e+00 \n", "AKGDH 0.000000 0.000000 0.000000e+00 \n", "AKGt2r 0.000000 0.000000 0.000000e+00 \n", "ALCD2x 0.000000 0.000000 -2.339592e+00 \n", "ATPM 8.390000 8.390000 -3.552714e-15 \n", "ATPS4r -0.322000 -0.322000 0.000000e+00 \n", "BIOMASS_Ecoli_core_w_GAM 0.000000 0.000000 -1.587472e-01 \n", "CO2t 6.952889 6.952889 1.891755e+00 \n", "CS 0.429333 0.429333 0.000000e+00 \n", "CYTBD 0.000000 0.000000 0.000000e+00 \n", "DM_succ_e 13.905778 13.905778 9.128278e+00 \n", "D_LACt2 0.000000 0.000000 0.000000e+00 \n", "ENO 20.000000 20.000000 6.594835e-01 \n", "ETOHt2r 0.000000 0.000000 -2.339592e+00 \n", "FBA 10.000000 10.000000 1.579059e-01 \n", "FBP 0.000000 0.000000 0.000000e+00 \n", "FORt 0.000000 0.000000 0.000000e+00 \n", "FORt2 0.000000 0.000000 0.000000e+00 \n", "FRD7 13.476444 1000.000000 0.000000e+00 \n", "FRUpts2 0.000000 0.000000 0.000000e+00 \n", "FUM -13.476444 -13.476444 8.698944e+00 \n", "FUMt2_2 0.000000 0.000000 0.000000e+00 \n", "G6PDH2r 0.000000 0.000000 0.000000e+00 \n", "GAPD 20.000000 20.000000 4.219977e-01 \n", "... ... ... ... \n", "ME2 0.000000 0.000000 0.000000e+00 \n", "NADH16 2.123333 2.123333 0.000000e+00 \n", "NADTRHD 0.000000 0.000000 0.000000e+00 \n", "NH4t 1.025916 1.025916 0.000000e+00 \n", "O2t 0.000000 0.000000 0.000000e+00 \n", "PDH 0.000000 0.000000 0.000000e+00 \n", "PFK 9.812852 9.812852 0.000000e+00 \n", "PFL 15.925266 15.925266 0.000000e+00 \n", "PGI 9.961430 9.961430 0.000000e+00 \n", "PGK -19.499855 -19.499855 0.000000e+00 \n", "PGL 0.000000 0.000000 0.000000e+00 \n", "PGM -19.218390 -19.218390 0.000000e+00 \n", "PIt2r 0.692128 0.692128 0.000000e+00 \n", "PPC 2.662481 2.662481 0.000000e+00 \n", "PPCK 0.000000 0.000000 0.000000e+00 \n", "PPS 0.000000 0.000000 0.000000e+00 \n", "PTAr 8.669854 8.669854 0.000000e+00 \n", "PYK 6.458243 6.458243 0.000000e+00 \n", "PYRt2 0.000000 0.000000 0.000000e+00 \n", "RPE -0.135239 -0.135239 0.000000e+00 \n", "RPI -0.135239 -0.135239 0.000000e+00 \n", "SUCCt2_2 0.000000 0.000000 0.000000e+00 \n", "SUCCt3 2.123333 2.123333 0.000000e+00 \n", "SUCDi 0.000000 997.876667 0.000000e+00 \n", "SUCOAS 0.000000 0.000000 0.000000e+00 \n", "TALA -0.033659 -0.033659 0.000000e+00 \n", "THD2 3.225950 3.225950 0.000000e+00 \n", "TKT1 -0.033659 -0.033659 0.000000e+00 \n", "TKT2 -0.101579 -0.101579 0.000000e+00 \n", "TPI 9.812852 9.812852 0.000000e+00 \n", "\n", " normalized_gaps biomass production KO \\\n", "reaction \n", "ACALD NaN 0.000000 13.905778 True \n", "ACALDt NaN 0.000000 13.905778 False \n", "ACKr NaN 0.000000 13.905778 False \n", "ACONTa NaN 0.000000 13.905778 False \n", "ACONTb NaN 0.000000 13.905778 False \n", "ACt2r NaN 0.000000 13.905778 False \n", "ADK1 NaN 0.000000 13.905778 False \n", "AKGDH NaN 0.000000 13.905778 False \n", "AKGt2r NaN 0.000000 13.905778 False \n", "ALCD2x NaN 0.000000 13.905778 True \n", "ATPM NaN 0.000000 13.905778 False \n", "ATPS4r NaN 0.000000 13.905778 False \n", "BIOMASS_Ecoli_core_w_GAM NaN 0.000000 13.905778 True \n", "CO2t NaN 0.000000 13.905778 False \n", "CS NaN 0.000000 13.905778 False \n", "CYTBD NaN 0.000000 13.905778 False \n", "DM_succ_e NaN 0.000000 13.905778 False \n", "D_LACt2 NaN 0.000000 13.905778 False \n", "ENO NaN 0.000000 13.905778 False \n", "ETOHt2r NaN 0.000000 13.905778 True \n", "FBA NaN 0.000000 13.905778 False \n", "FBP NaN 0.000000 13.905778 False \n", "FORt NaN 0.000000 13.905778 False \n", "FORt2 NaN 0.000000 13.905778 False \n", "FRD7 NaN 0.000000 13.905778 False \n", "FRUpts2 NaN 0.000000 13.905778 False \n", "FUM NaN 0.000000 13.905778 False \n", "FUMt2_2 NaN 0.000000 13.905778 False \n", "G6PDH2r NaN 0.000000 13.905778 False \n", "GAPD NaN 0.000000 13.905778 False \n", "... ... ... ... ... \n", "ME2 0.000000 0.188145 2.123333 False \n", "NADH16 6.508131 0.188145 2.123333 False \n", "NADTRHD 0.000000 0.188145 2.123333 False \n", "NH4t 2.994683 0.188145 2.123333 False \n", "O2t 0.000000 0.188145 2.123333 False \n", "PDH 0.000000 0.188145 2.123333 False \n", "PFK 37.536245 0.188145 2.123333 False \n", "PFL 66.290142 0.188145 2.123333 False \n", "PGI 42.978083 0.188145 2.123333 False \n", "PGK 84.064777 0.188145 2.123333 False \n", "PGL 0.000000 0.188145 2.123333 False \n", "PGM 82.806263 0.188145 2.123333 False \n", "PIt2r 2.900056 0.188145 2.123333 False \n", "PPC 7.557877 0.188145 2.123333 False \n", "PPCK 0.000000 0.188145 2.123333 False \n", "PPS 0.000000 0.188145 2.123333 False \n", "PTAr 37.203051 0.188145 2.123333 False \n", "PYK 20.745204 0.188145 2.123333 False \n", "PYRt2 0.000000 0.188145 2.123333 False \n", "RPE -0.566657 0.188145 2.123333 False \n", "RPI 0.000000 0.188145 2.123333 False \n", "SUCCt2_2 0.000000 0.188145 2.123333 False \n", "SUCCt3 4.915631 0.188145 2.123333 False \n", "SUCDi 0.000000 0.188145 2.123333 False \n", "SUCOAS 0.000000 0.188145 2.123333 False \n", "TALA -0.141033 0.188145 2.123333 False \n", "THD2 4.869204 0.188145 2.123333 False \n", "TKT1 -0.141033 0.188145 2.123333 False \n", "TKT2 -0.425623 0.188145 2.123333 False \n", "TPI 42.313745 0.188145 2.123333 False \n", "\n", " flux_reversal suddenly_essential free_flux \\\n", "reaction \n", "ACALD False False False \n", "ACALDt False False False \n", "ACKr False False False \n", "ACONTa False False False \n", "ACONTb False False False \n", "ACt2r False False False \n", "ADK1 False False False \n", "AKGDH False True False \n", "AKGt2r False False False \n", "ALCD2x False False False \n", "ATPM False False False \n", "ATPS4r False False False \n", "BIOMASS_Ecoli_core_w_GAM False True False \n", "CO2t False False False \n", "CS False False False \n", "CYTBD False True False \n", "DM_succ_e False False False \n", "D_LACt2 False False False \n", "ENO False False False \n", "ETOHt2r False False False \n", "FBA False False False \n", "FBP False True False \n", "FORt False False False \n", "FORt2 False True False \n", "FRD7 False False False \n", "FRUpts2 False True False \n", "FUM False False False \n", "FUMt2_2 False True False \n", "G6PDH2r False True False \n", "GAPD False False False \n", "... ... ... ... \n", "ME2 False True False \n", "NADH16 False False False \n", "NADTRHD False True False \n", "NH4t False False False \n", "O2t False True False \n", "PDH False True False \n", "PFK False False False \n", "PFL False False False \n", "PGI False False False \n", "PGK False False False \n", "PGL False True False \n", "PGM False False False \n", "PIt2r False False False \n", "PPC False False False \n", "PPCK False True False \n", "PPS False True False \n", "PTAr False False False \n", "PYK False False False \n", "PYRt2 False False False \n", "RPE False False False \n", "RPI False False False \n", "SUCCt2_2 False True False \n", "SUCCt3 False False False \n", "SUCDi False False False \n", "SUCOAS False False False \n", "TALA False False False \n", "THD2 False False False \n", "TKT1 False False False \n", "TKT2 False False False \n", "TPI False False False \n", "\n", " reaction excluded \n", "reaction \n", "ACALD ACALD False \n", "ACALDt ACALDt False \n", "ACKr ACKr False \n", "ACONTa ACONTa False \n", "ACONTb ACONTb False \n", "ACt2r ACt2r False \n", "ADK1 ADK1 False \n", "AKGDH AKGDH False \n", "AKGt2r AKGt2r False \n", "ALCD2x ALCD2x False \n", "ATPM ATPM False \n", "ATPS4r ATPS4r False \n", "BIOMASS_Ecoli_core_w_GAM BIOMASS_Ecoli_core_w_GAM True \n", "CO2t CO2t False \n", "CS CS False \n", "CYTBD CYTBD False \n", "DM_succ_e DM_succ_e True \n", "D_LACt2 D_LACt2 False \n", "ENO ENO False \n", "ETOHt2r ETOHt2r False \n", "FBA FBA False \n", "FBP FBP False \n", "FORt FORt False \n", "FORt2 FORt2 False \n", "FRD7 FRD7 False \n", "FRUpts2 FRUpts2 False \n", "FUM FUM False \n", "FUMt2_2 FUMt2_2 False \n", "G6PDH2r G6PDH2r False \n", "GAPD GAPD False \n", "... ... ... \n", "ME2 ME2 False \n", "NADH16 NADH16 False \n", "NADTRHD NADTRHD False \n", "NH4t NH4t False \n", "O2t O2t False \n", "PDH PDH False \n", "PFK PFK False \n", "PFL PFL False \n", "PGI PGI False \n", "PGK PGK False \n", "PGL PGL False \n", "PGM PGM False \n", "PIt2r PIt2r False \n", "PPC PPC False \n", "PPCK PPCK False \n", "PPS PPS False \n", "PTAr PTAr False \n", "PYK PYK False \n", "PYRt2 PYRt2 False \n", "RPE RPE False \n", "RPI RPI False \n", "SUCCt2_2 SUCCt2_2 False \n", "SUCCt3 SUCCt3 False \n", "SUCDi SUCDi False \n", "SUCOAS SUCOAS False \n", "TALA TALA False \n", "THD2 THD2 False \n", "TKT1 TKT1 False \n", "TKT2 TKT2 False \n", "TPI TPI False \n", "\n", "[684 rows x 12 columns]" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "result.solutions" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "data": { 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