In [1]:
from cameo.strain_design.heuristic import GeneKnockoutOptimization
from cameo import load_model
from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield
from cameo.flux_analysis.simulation import fba
import inspyred
In [2]:
model = load_model("iJO1366")
In [3]:
of = biomass_product_coupled_yield(model.reactions.Ec_biomass_iJO1366_core_53p95M,
model.reactions.EX_ac_e,
model.reactions.EX_glc_e)
In [4]:
of
Out[4]:
$$bpcy = \frac{(Ec\_biomass\_iJO1366\_core\_53p95M * EX\_ac\_e)}{EX\_glc\_e}$$
In [5]:
ko = GeneKnockoutOptimization(model=model, objective_function=of,
simulation_method=fba, heuristic_method=inspyred.ec.GA)
In [6]:
ko.run(max_evaluations=1000, n=1)
Starting optimization at Wed, 15 Jul 2015 15:56:42
Using saved session configuration for http://localhost:5006/
To override, pass 'load_from_config=False' to Session
0%
Finished after 00:01:04
Out[6]:
Result:
- model: iJO1366
- heuristic: GA
- objective function: $$bpcy = \frac{(Ec\_biomass\_iJO1366\_core\_53p95M * EX\_ac\_e)}{EX\_glc\_e}$$
- simulation method: fba
- type: gene
Fitness
Knockouts
Reactions
Size
0
0.574833
(b2913, b3734, b1764, b1226, b3665, b2797)
(ATPS4rpp, PGCD, ADD, SELNPS)
6
1
0.574833
(b2913, b3734, b1764, b1226, b2797, b2963)
(ATPS4rpp, SELNPS, PGCD)
6
2
0.574833
(b2913, b3734, b1764, b3600, b1226, b3665)
(ATPS4rpp, PGCD, ADD, M1PD, SELNPS)
6
3
0.574833
(b2149, b2913, b0474, b2521, b3734, b3665, b2797)
(MCPST, DADK, ADK4, ADK3, ADK1, GLCabcpp, PGCD...
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4
0.574833
(b2913, b2963, b3734, b1226, b3057, b2797)
(ATPS4rpp, PGCD)
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5
0.574833
(b2913, b3734, b0200, b1226, b2797, b2963)
(GMHEPPA, ATPS4rpp, PGCD)
6
6
0.574833
(b2422, b2913, b3734, b1226, b2797, b2963)
(SELtpp, ATPS4rpp, PGCD, TSULabcpp, SLNTtpp)
6
7
0.574833
(b3619, b2913, b3734, b4033, b1226, b2797, b2963)
(14GLUCANabcpp, MALTHXabcpp, MALTTTRabcpp, AGM...
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0.574833
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(ATPS4rpp, PGCD, ACGAMK)
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0.574833
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(AGMHE, ATPS4rpp, SELNPS, NTRIR2x, PGCD)
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0.574833
(b2913, b2963, b3734, b4244, b3057, b2797)
(ATPS4rpp, PGCD)
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0.574833
(b2913, b3734, b1764, b1621, b1226, b2797)
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12
0.570274
(b0007, b3736, b1612, b2551, b4471)
(GHMT2r, ATPS4rpp, ALAt4pp, THFAT, GLYt4pp)
5
13
0.570274
(b0007, b2260, b0809, b1612, b3736, b2551)
(GHMT2r, ALAt4pp, GLYt4pp, SUCBZL, ATPS4rpp, G...
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14
0.568817
(b3821, b2738, b3734, b1764, b3665, b0529, b2797)
(PLIPA2A120pp, PLIPA2G120pp, PLIPA2G180pp, PLI...
7
15
0.566916
(b2913, b3734, b1764, b1226, b3665, b2797)
(ATPS4rpp, PGCD, ADD, SELNPS)
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16
0.561642
(b3619, b2913, b3734, b1764, b1226, b2797, b2963)
(AGMHE, ATPS4rpp, SELNPS, PGCD)
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17
0.561404
(b3736, b1486, b2551, b1612)
(GHMT2r, ATPS4rpp, THFAT)
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18
0.561171
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(GTHRDabc2pp, ATPS4rpp, CYSabc2pp, GLYOX, ASCB...
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19
0.561171
(b0007, b3940, b2243, b1612, b3736, b4138)
(ATPS4rpp, ALAt4pp, G3PD7, GLYt4pp, G3PD6)
6
20
0.561171
(b1589, b0194, b3736, b2481, b1681, b3909, b0729)
(DDGLCNt2rpp, PROTRS, S2FE2SR, S2FE2SS, S2FE2S...
7
21
0.561171
(b0019, b1101, b2379, b2035, b2490, b3733)
(ATPS4rpp, NAt3_2pp, O16AP3pp, O16AP2pp, O16AP...
6
22
0.561171
(b0194, b3736, b2481, b1681, b3528, b3909, b0729)
(DDGLCNt2rpp, MALDt2_2pp, MALt2_2pp, PROTRS, O...
7
23
0.561171
(b1589, b0194, b3736, b2481, b1855, b3909, b0729)
(EDTXS4, DDGLCNt2rpp, EDTXS2, PROTRS, SUCOAS, ...
7
24
0.561171
(b1227, b0474, b3734, b1764, b3665, b2797)
(DADK, ADK4, ADK3, ADK1, ADD, SELNPS, ATPS4rpp...
6
25
0.561171
(b0019, b1101, b2379, b2035, b3733, b3126)
(O16AP1pp, O16AP2pp, NAt3_2pp, O16AP3pp, GLCRA...
6
26
0.561171
(b0474, b3734, b1764, b3665, b2039, b2797)
(DADK, ADK4, ADK3, ADK1, ADD, SELNPS, ATPS4rpp...
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0.561171
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28
0.561171
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6
29
0.561171
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(DADK, ADK4, ADK3, ADK1, SELNPS, ATPS4rpp, ADNK1)
6
...
...
...
...
...
70
0.561171
(b0007, b4471, b2243, b1612, b3785, b3736)
(ECAP2pp, ALAt4pp, GLYt4pp, ECAP1pp, G3PD7, G3...
6
71
0.561171
(b0474, b3734, b1764, b1227, b2797, b4513)
(DADK, ADK4, ADK3, ADK1, SELNPS, ATPS4rpp, ADNK1)
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72
0.561171
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5
73
0.561171
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(ALAt4pp, GLYt4pp, FE3DHBZSabcpp, G3PD7, G3PD6...
6
74
0.561171
(b0573, b0759, b3012, b3583, b1483, b3736, b1681)
(S2FE2SS, S2FE2SR, UDPG4E, S2FE2ST, S4FE4ST, S...
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75
0.561171
(b1246, b2817, b0474, b3734, b1764, b2039, b3909)
(4PEPTabcpp, 3PEPTabcpp, DADK, DDGLCNt2rpp, AD...
7
76
0.561171
(b0007, b4227, b2243, b1612, b3736, b4138)
(ATPS4rpp, ALAt4pp, G3PD7, GLYt4pp, G3PD6)
6
77
0.561171
(b0007, b2720, b1612, b3736, b0121, b0861)
(APCS, ATPS4rpp, ALAt4pp, GLYt4pp, SPMS)
6
78
0.561171
(b1441, b3736, b2558, b1612, b4471)
(ATPS4rpp)
5
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0.561171
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(ALAt4pp, GLYt4pp, MAN6PI, G3PD7, G3PD6, AKGt2...
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80
0.561171
(b0007, b2279, b2720, b1612, b3736, b0121)
(NADH16pp, ALAt4pp, GLYt4pp, SPMS, APCS, ATPS4...
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81
0.561171
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(S2FE2SS, PROTRS, S2FE2SR, UDPG4E, S2FE2ST, S4...
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0.561171
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(MCITD, S2FE2SS, PROTRS, S2FE2SR, UDPG4E, S2FE...
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0.561171
(b4053, b3829, b0194, b3736, b3528, b0729, b0171)
(MALDt2_2pp, MALt2_2pp, PROTRS, OROTt2_2pp, FU...
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0.561171
(b4088, b0576, b3734, b0197, b1897, b2797)
(ATPS4rpp, METDabcpp, TRE6PP, METabcpp, ALLabcpp)
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0.561171
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(ATPS4rpp, DSBDR, TDSR1, TDSR2)
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0.561171
(b2919, b3222, b2243, b4138, b3736, b3654)
(AMANK, GUAt2pp, G3PD7, G3PD6, MMCD, ATPS4rpp)
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87
0.561171
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(NADH16pp, ALAt4pp, GLYt4pp, GPDDA4, GPDDA5, A...
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0.561171
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0.561171
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(DADK, ADK4, ADK3, ADK1, ADD, ADNK1, GLNTRS, A...
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0.561171
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0.561171
(b1441, b3417, b0474, b3734, b1764, b3665)
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0.561171
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0.561171
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7
94
0.561171
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(ALAt4pp, GLYt4pp, FE3DHBZSabcpp, G3PD7, G3PD6...
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95
0.561171
(b1296, b2243, b1612, b0887, b3736, b4138)
(GTHRDabc2pp, CYSabc2pp, ATPS4rpp, G3PD7, G3PD6)
6
96
0.561171
(b2328, b2917, b4138, b3736, b4367, b3057)
(FEOXAMR2, MMM, ATPS4rpp, FEOXAMR1, FEOXAMR3)
6
97
0.561171
(b1395, b3416, b3224, b0394, b3734, b2797, b1124)
(AMALT4, AMALT3, AMALT2, AMALT1, ATPS4rpp, ACN...
7
98
0.561171
(b3734, b2797, b1388, b4122, b1226)
(ATPS4rpp, PACCOAE, DTARTD)
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99
0.561171
(b4069, b0033, b3736, b3908, b4471)
(ACS, ATPS4rpp, ACCOAL, CBPS)
5
100 rows × 4 columns
In [7]:
from bokeh import io
In [12]:
io._state.session
In [ ]:
Content source: KristianJensen/cameo
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