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"cells": [
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"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",
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" window._bokeh_onload_callbacks = [];\n",
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" }\n",
"\n",
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],
"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": {
"collapsed": true
},
"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
\n",
"
\n", " | 1 | \n", "2 | \n", "3 | \n", "4 | \n", "5 | \n", "6 | \n", "7 | \n", "8 | \n", "9 | \n", "10 | \n", "
---|---|---|---|---|---|---|---|---|---|---|
ADK1 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.410338 | \n", "1.527283 | \n", "
ENO | \n", "15.238892 | \n", "15.761645 | \n", "16.212407 | \n", "16.577535 | \n", "16.942662 | \n", "17.307790 | \n", "17.704415 | \n", "18.602292 | \n", "19.293292 | \n", "19.628048 | \n", "
FBA | \n", "7.756941 | \n", "8.036499 | \n", "8.242515 | \n", "8.361048 | \n", "8.479582 | \n", "8.598115 | \n", "8.747793 | \n", "9.393102 | \n", "9.830787 | \n", "9.910940 | \n", "
FRD7 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "1.453235 | \n", "3.175302 | \n", "4.897369 | \n", "6.586703 | \n", "7.755141 | \n", "9.127842 | \n", "10.852285 | \n", "
GAPD | \n", "16.431132 | \n", "16.838737 | \n", "17.173618 | \n", "17.421989 | \n", "17.670359 | \n", "17.918730 | \n", "18.198431 | \n", "18.976723 | \n", "19.547784 | \n", "19.761991 | \n", "
ICL | \n", "0.000000 | \n", "0.000000 | \n", "0.386057 | \n", "1.231342 | \n", "2.076627 | \n", "2.921912 | \n", "3.735322 | \n", "4.041459 | \n", "4.143333 | \n", "3.893465 | \n", "
MALS | \n", "0.000000 | \n", "0.000000 | \n", "0.386057 | \n", "1.231342 | \n", "2.076627 | \n", "2.921912 | \n", "3.735322 | \n", "4.041459 | \n", "4.143333 | \n", "3.893465 | \n", "
PDH | \n", "8.809270 | \n", "8.336008 | \n", "8.179868 | \n", "8.400957 | \n", "8.622045 | \n", "8.843134 | \n", "9.064539 | \n", "9.290984 | \n", "9.107760 | \n", "8.219084 | \n", "
PFK | \n", "7.756941 | \n", "8.036499 | \n", "8.242515 | \n", "8.361048 | \n", "8.479582 | \n", "8.598115 | \n", "8.747793 | \n", "9.393102 | \n", "9.830787 | \n", "9.910940 | \n", "
PGI | \n", "5.485630 | \n", "6.110399 | \n", "6.513173 | \n", "6.651876 | \n", "6.790579 | \n", "6.929282 | \n", "7.161108 | \n", "8.874882 | \n", "9.965126 | \n", "9.981645 | \n", "
PGK | \n", "-16.431132 | \n", "-16.838737 | \n", "-17.173618 | \n", "-17.421989 | \n", "-17.670359 | \n", "-17.918730 | \n", "-18.198431 | \n", "-18.976723 | \n", "-19.547784 | \n", "-19.761991 | \n", "
PGM | \n", "-15.238892 | \n", "-15.761645 | \n", "-16.212407 | \n", "-16.577535 | \n", "-16.942662 | \n", "-17.307790 | \n", "-17.704415 | \n", "-18.602292 | \n", "-19.293292 | \n", "-19.628048 | \n", "
PPC | \n", "3.758320 | \n", "5.012330 | \n", "5.878875 | \n", "6.284516 | \n", "6.690157 | \n", "7.095799 | \n", "7.532996 | \n", "8.472367 | \n", "9.615323 | \n", "11.108854 | \n", "
PPS | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.410338 | \n", "1.527283 | \n", "
SUCCt3 | \n", "1.474575 | \n", "2.949150 | \n", "4.423725 | \n", "5.898300 | \n", "7.372875 | \n", "8.847450 | \n", "10.322025 | \n", "11.796600 | \n", "13.271175 | \n", "14.745750 | \n", "
THD2 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.119674 | \n", "2.143848 | \n", "2.916807 | \n", "1.535161 | \n", "
TPI | \n", "7.756941 | \n", "8.036499 | \n", "8.242515 | \n", "8.361048 | \n", "8.479582 | \n", "8.598115 | \n", "8.747793 | \n", "9.393102 | \n", "9.830787 | \n", "9.910940 | \n", "
EX_succ_e | \n", "1.474575 | \n", "2.949150 | \n", "4.423725 | \n", "5.898300 | \n", "7.372875 | \n", "8.847450 | \n", "10.322025 | \n", "11.796600 | \n", "13.271175 | \n", "14.745750 | \n", "
\n", " | lower_bound | \n", "upper_bound | \n", "gaps | \n", "normalized_gaps | \n", "biomass | \n", "production | \n", "KO | \n", "flux_reversal | \n", "suddenly_essential | \n", "free_flux | \n", "reaction | \n", "excluded | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
reaction | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
ACALD | \n", "0.000000 | \n", "0.000000 | \n", "-2.339592e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "True | \n", "False | \n", "False | \n", "False | \n", "ACALD | \n", "False | \n", "
ACALDt | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ACALDt | \n", "False | \n", "
ACKr | \n", "-5.664889 | \n", "-5.664889 | \n", "0.000000e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ACKr | \n", "False | \n", "
ACONTa | \n", "0.429333 | \n", "0.429333 | \n", "0.000000e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ACONTa | \n", "False | \n", "
ACONTb | \n", "0.429333 | \n", "0.429333 | \n", "0.000000e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ACONTb | \n", "False | \n", "
ACt2r | \n", "-5.664889 | \n", "-5.664889 | \n", "0.000000e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ACt2r | \n", "False | \n", "
ADK1 | \n", "3.476444 | \n", "3.476444 | \n", "0.000000e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ADK1 | \n", "False | \n", "
AKGDH | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "AKGDH | \n", "False | \n", "
AKGt2r | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "AKGt2r | \n", "False | \n", "
ALCD2x | \n", "0.000000 | \n", "0.000000 | \n", "-2.339592e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "True | \n", "False | \n", "False | \n", "False | \n", "ALCD2x | \n", "False | \n", "
ATPM | \n", "8.390000 | \n", "8.390000 | \n", "-3.552714e-15 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ATPM | \n", "False | \n", "
ATPS4r | \n", "-0.322000 | \n", "-0.322000 | \n", "0.000000e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ATPS4r | \n", "False | \n", "
BIOMASS_Ecoli_core_w_GAM | \n", "0.000000 | \n", "0.000000 | \n", "-1.587472e-01 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "True | \n", "False | \n", "True | \n", "False | \n", "BIOMASS_Ecoli_core_w_GAM | \n", "True | \n", "
CO2t | \n", "6.952889 | \n", "6.952889 | \n", "1.891755e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "CO2t | \n", "False | \n", "
CS | \n", "0.429333 | \n", "0.429333 | \n", "0.000000e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "CS | \n", "False | \n", "
CYTBD | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "CYTBD | \n", "False | \n", "
DM_succ_e | \n", "13.905778 | \n", "13.905778 | \n", "9.128278e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "DM_succ_e | \n", "True | \n", "
D_LACt2 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "D_LACt2 | \n", "False | \n", "
ENO | \n", "20.000000 | \n", "20.000000 | \n", "6.594835e-01 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ENO | \n", "False | \n", "
ETOHt2r | \n", "0.000000 | \n", "0.000000 | \n", "-2.339592e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "True | \n", "False | \n", "False | \n", "False | \n", "ETOHt2r | \n", "False | \n", "
FBA | \n", "10.000000 | \n", "10.000000 | \n", "1.579059e-01 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "FBA | \n", "False | \n", "
FBP | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "FBP | \n", "False | \n", "
FORt2 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "FORt2 | \n", "False | \n", "
FORti | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "FORti | \n", "False | \n", "
FRD7 | \n", "13.476444 | \n", "1000.000000 | \n", "0.000000e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "FRD7 | \n", "False | \n", "
FRUpts2 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "FRUpts2 | \n", "False | \n", "
FUM | \n", "-13.476444 | \n", "-13.476444 | \n", "8.698944e+00 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "FUM | \n", "False | \n", "
FUMt2_2 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "FUMt2_2 | \n", "False | \n", "
G6PDH2r | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "G6PDH2r | \n", "False | \n", "
GAPD | \n", "20.000000 | \n", "20.000000 | \n", "4.219977e-01 | \n", "inf | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "GAPD | \n", "False | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
ME2 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "ME2 | \n", "False | \n", "
NADH16 | \n", "2.123333 | \n", "2.123333 | \n", "0.000000e+00 | \n", "6.508131 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "NADH16 | \n", "False | \n", "
NADTRHD | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "NADTRHD | \n", "False | \n", "
NH4t | \n", "1.025916 | \n", "1.025916 | \n", "0.000000e+00 | \n", "2.994683 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "NH4t | \n", "False | \n", "
O2t | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "O2t | \n", "False | \n", "
PDH | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "PDH | \n", "False | \n", "
PFK | \n", "9.812852 | \n", "9.812852 | \n", "0.000000e+00 | \n", "37.536245 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PFK | \n", "False | \n", "
PFL | \n", "15.925266 | \n", "15.925266 | \n", "0.000000e+00 | \n", "66.290142 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PFL | \n", "False | \n", "
PGI | \n", "9.961430 | \n", "9.961430 | \n", "0.000000e+00 | \n", "42.978083 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PGI | \n", "False | \n", "
PGK | \n", "-19.499855 | \n", "-19.499855 | \n", "0.000000e+00 | \n", "84.064777 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PGK | \n", "False | \n", "
PGL | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "PGL | \n", "False | \n", "
PGM | \n", "-19.218390 | \n", "-19.218390 | \n", "0.000000e+00 | \n", "82.806263 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PGM | \n", "False | \n", "
PIt2r | \n", "0.692128 | \n", "0.692128 | \n", "0.000000e+00 | \n", "2.900056 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PIt2r | \n", "False | \n", "
PPC | \n", "2.662481 | \n", "2.662481 | \n", "0.000000e+00 | \n", "7.557877 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PPC | \n", "False | \n", "
PPCK | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "PPCK | \n", "False | \n", "
PPS | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "PPS | \n", "False | \n", "
PTAr | \n", "8.669854 | \n", "8.669854 | \n", "0.000000e+00 | \n", "37.203051 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PTAr | \n", "False | \n", "
PYK | \n", "6.458243 | \n", "6.458243 | \n", "0.000000e+00 | \n", "20.745204 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PYK | \n", "False | \n", "
PYRt2 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "PYRt2 | \n", "False | \n", "
RPE | \n", "-0.135239 | \n", "-0.135239 | \n", "0.000000e+00 | \n", "-0.566657 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "RPE | \n", "False | \n", "
RPI | \n", "-0.135239 | \n", "-0.135239 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "RPI | \n", "False | \n", "
SUCCt2_2 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "True | \n", "False | \n", "SUCCt2_2 | \n", "False | \n", "
SUCCt3 | \n", "2.123333 | \n", "2.123333 | \n", "0.000000e+00 | \n", "4.915631 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "SUCCt3 | \n", "False | \n", "
SUCDi | \n", "0.000000 | \n", "997.876667 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "SUCDi | \n", "False | \n", "
SUCOAS | \n", "0.000000 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "SUCOAS | \n", "False | \n", "
TALA | \n", "-0.033659 | \n", "-0.033659 | \n", "0.000000e+00 | \n", "-0.141033 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "TALA | \n", "False | \n", "
THD2 | \n", "3.225950 | \n", "3.225950 | \n", "0.000000e+00 | \n", "4.869204 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "THD2 | \n", "False | \n", "
TKT1 | \n", "-0.033659 | \n", "-0.033659 | \n", "0.000000e+00 | \n", "-0.141033 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "TKT1 | \n", "False | \n", "
TKT2 | \n", "-0.101579 | \n", "-0.101579 | \n", "0.000000e+00 | \n", "-0.425623 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "TKT2 | \n", "False | \n", "
TPI | \n", "9.812852 | \n", "9.812852 | \n", "0.000000e+00 | \n", "42.313745 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "TPI | \n", "False | \n", "
684 rows × 12 columns
\n", "