E. coli core model¶
import cameo
from cameo import models
from cameo.strain_design.heuristic import GeneKnockoutOptimization, ReactionKnockoutOptimization
from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield, product_yield, number_of_knockouts
from cameo.flux_analysis.simulation import fba
from cameo.parallel import SequentialView
import inspyred
model = models.bigg.e_coli_core
objective1 = biomass_product_coupled_yield(
model.reactions.Biomass_Ecoli_core_w_GAM,
model.reactions.EX_ac_e,
model.reactions.EX_glc_e)
objective2 = number_of_knockouts()
objective = [objective1, objective2]
ko = GeneKnockoutOptimization(model=model,
simulation_method=fba,
objective_function=objective,
heuristic_method=inspyred.ec.emo.NSGA2,
seed=1234)
results = ko.run(max_evaluations=3000, popuplation_size=100, view=SequentialView())
Starting optimization at Fri, 17 Jul 2015 13:53:04
Using saved session configuration for http://localhost:5006/
To override, pass 'load_from_config=False' to Session
/Users/niko/.virtualenvs/cameo_py3/lib/python3.4/site-packages/bokeh/session.py:319 [1;31mUserWarning[0m: You need to start the bokeh-server to see this example.
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Finished after 00:00:16
results
Result:
- model: e_coli_core
- heuristic: NSGA2
- objective function: $$bpcy = \frac{(Biomass\_Ecoli\_core\_w\_GAM * EX\_ac\_e)}{EX\_glc\_e}$$
$$ min\:\#knockouts $$ - simulation method: fba
- type: gene
| Fitness | Knockouts | Reactions | Size | |
|---|---|---|---|---|
| 0 | (0.535608, 1.0) | (b3731) | (ATPS4r) | 1 |
| 1 | (0.535608, 1.0) | (b3736) | (ATPS4r) | 1 |
| 2 | (0.535608, 1.0) | (b3732) | (ATPS4r) | 1 |
| 3 | (0.655414, 0.333333) | (b0767, b3114, b0722) | (PGL, SUCDi) | 3 |
| 4 | (0.535608, 1.0) | (b3738) | (ATPS4r) | 1 |
| 5 | (0.535608, 1.0) | (b3733) | (ATPS4r) | 1 |
| 6 | (0.535608, 1.0) | (b3734) | (ATPS4r) | 1 |
| 7 | (0.535608, 0.5) | (b0875, b3736) | (ATPS4r) | 2 |
| 8 | (0.523097, 1.0) | (b3736) | (ATPS4r) | 1 |
| 9 | (0.535608, 0.5) | (b3733, b3732) | (ATPS4r) | 2 |
| 10 | (0.535608, 0.5) | (b0809, b3731) | (GLNabc, ATPS4r) | 2 |
| 11 | (0.535608, 0.5) | (b1702, b3736) | (PPS, ATPS4r) | 2 |
| 12 | (0.535608, 0.5) | (b3403, b3736) | (PPCK, ATPS4r) | 2 |
| 13 | (0.535608, 0.5) | (b3736, b0729) | (ATPS4r, SUCOAS) | 2 |
| 14 | (0.535608, 0.5) | (b3736, b3493) | (ATPS4r) | 2 |
| 15 | (0.535608, 0.5) | (b3733, b3736) | (ATPS4r) | 2 |
| 16 | (0.535608, 0.5) | (b3735, b4395) | (ATPS4r) | 2 |
| 17 | (0.535608, 0.5) | (b1524, b3736) | (ATPS4r) | 2 |
| 18 | (0.535608, 0.5) | (b3736, b4154) | (FRD7, ATPS4r) | 2 |
| 19 | (0.535608, 0.5) | (b3738, b3732) | (ATPS4r) | 2 |
| 20 | (0.535608, 0.5) | (b3736, b0722) | (ATPS4r, SUCDi) | 2 |
| 21 | (0.535608, 0.5) | (b3733, b2465) | (ATPS4r) | 2 |
| 22 | (0.535608, 0.5) | (b3736, b3732) | (ATPS4r) | 2 |
| 23 | (0.535608, 0.5) | (b3736, b3731) | (ATPS4r) | 2 |
| 24 | (0.535608, 0.5) | (b3736, b1852) | (G6PDH2r, ATPS4r) | 2 |
| 25 | (0.535608, 0.5) | (b1702, b3733) | (PPS, ATPS4r) | 2 |
| 26 | (0.535608, 0.5) | (b3736, b1852) | (G6PDH2r, ATPS4r) | 2 |
| 27 | (0.535608, 0.5) | (b3735, b1702) | (PPS, ATPS4r) | 2 |
| 28 | (0.535608, 0.5) | (b3736, b1297) | (ATPS4r) | 2 |
| 29 | (0.535608, 0.5) | (b4151, b3733) | (FRD7, ATPS4r) | 2 |
| ... | ... | ... | ... | ... |
| 70 | (0.535608, 0.5) | (b0903, b3732) | (ATPS4r) | 2 |
| 71 | (0.535608, 0.5) | (b0721, b3732) | (ATPS4r, SUCDi) | 2 |
| 72 | (0.535608, 0.5) | (b3736, b1819) | (FRUpts2, ATPS4r) | 2 |
| 73 | (0.535608, 0.5) | (b3736, b2914) | (ATPS4r) | 2 |
| 74 | (0.535608, 0.5) | (b3213, b3736) | (GLUSy, ATPS4r) | 2 |
| 75 | (0.535608, 0.5) | (b1241, b3731) | (ATPS4r) | 2 |
| 76 | (0.535608, 0.5) | (b3736, b3733) | (ATPS4r) | 2 |
| 77 | (0.535608, 0.5) | (b3213, b3736) | (GLUSy, ATPS4r) | 2 |
| 78 | (0.535608, 0.5) | (b3736, b3870) | (ATPS4r) | 2 |
| 79 | (0.535608, 0.5) | (b1101, b3736) | (ATPS4r) | 2 |
| 80 | (0.535608, 0.5) | (b1611, b3736) | (ATPS4r) | 2 |
| 81 | (0.535608, 0.5) | (b2097, b3736) | (ATPS4r) | 2 |
| 82 | (0.535608, 0.5) | (b1817, b3731) | (FRUpts2, ATPS4r) | 2 |
| 83 | (0.535608, 0.5) | (b3736, b0118) | (ATPS4r) | 2 |
| 84 | (0.535608, 0.5) | (b0809, b3731) | (GLNabc, ATPS4r) | 2 |
| 85 | (0.535608, 0.5) | (b3115, b3733) | (ATPS4r) | 2 |
| 86 | (0.535608, 0.5) | (b3738, b2987) | (ATPS4r) | 2 |
| 87 | (0.535608, 0.5) | (b0978, b3736) | (ATPS4r) | 2 |
| 88 | (0.535608, 0.5) | (b1621, b3733) | (ATPS4r) | 2 |
| 89 | (0.535608, 0.5) | (b2097, b3738) | (ATPS4r) | 2 |
| 90 | (0.535608, 0.5) | (b3736, b4077) | (GLUt2r, ATPS4r) | 2 |
| 91 | (0.535608, 0.5) | (b3733, b3731) | (ATPS4r) | 2 |
| 92 | (0.535608, 0.5) | (b2133, b3732) | (ATPS4r) | 2 |
| 93 | (0.535608, 0.5) | (b2987, b3736) | (ATPS4r) | 2 |
| 94 | (0.535608, 0.5) | (b0734, b3732) | (ATPS4r) | 2 |
| 95 | (0.535608, 0.5) | (b3735, b3493) | (ATPS4r) | 2 |
| 96 | (0.535608, 0.5) | (b1479, b3732) | (ME1, ATPS4r) | 2 |
| 97 | (0.535608, 0.5) | (b3736, b0118) | (ATPS4r) | 2 |
| 98 | (0.535608, 0.5) | (b1723, b3732) | (ATPS4r) | 2 |
| 99 | (0.535608, 0.5) | (b3731, b0722) | (ATPS4r, SUCDi) | 2 |
100 rows × 4 columns
iJO1366 model¶
model = models.bigg.iJO1366
of1 = product_yield(model.reactions.Ec_biomass_iJO1366_core_53p95M,
model.reactions.EX_glc_e)
of2 = number_of_knockouts()
of3 = biomass_product_coupled_yield(model.reactions.Ec_biomass_iJO1366_core_53p95M,
model.reactions.EX_ac_e,
model.reactions.EX_glc_e)
ko = GeneKnockoutOptimization(model=model, objective_function=[of1, of2, of3],
simulation_method=fba, heuristic_method=inspyred.ec.emo.NSGA2)
ko.run(max_evaluations=5000, n=10, mutation_rate=0.3, population_size=100)
Starting optimization at Fri, 17 Jul 2015 13:54:18
Using saved session configuration for http://localhost:5006/
To override, pass 'load_from_config=False' to Session
/Users/niko/.virtualenvs/cameo_py3/lib/python3.4/site-packages/bokeh/session.py:319 [1;31mUserWarning[0m: You need to start the bokeh-server to see this example.
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Finished after 00:07:08
Result:
- model: iJO1366
- heuristic: NSGA2
- objective function: $$yield = \frac{Ec_biomass_iJO1366_core_53p95M}{EX_glc_e}$$
$$ min\:\#knockouts $$
$$bpcy = \frac{(Ec\_biomass\_iJO1366\_core\_53p95M * EX\_ac\_e)}{EX\_glc\_e}$$ - simulation method: fba
- type: gene
| Fitness | Knockouts | Reactions | Size | |
|---|---|---|---|---|
| 0 | (0.098237, 1.0, 0.0) | (b4115) | (ARGAGMt7pp) | 1 |
| 1 | (0.040248, 1.0, 0.561171) | (b3731) | (ATPS4rpp) | 1 |
| 2 | (0.040248, 1.0, 0.561171) | (b3734) | (ATPS4rpp) | 1 |
| 3 | (0.098237, 1.0, 0.0) | (b0954) | (T2DECAI) | 1 |
| 4 | (0.040248, 1.0, 0.561171) | (b3738) | (ATPS4rpp) | 1 |
| 5 | (0.098237, 1.0, 0.0) | (b4152) | (FRD2, FRD3) | 1 |
| 6 | (0.098237, 1.0, 0.0) | (b1589) | (SELR) | 1 |
| 7 | (0.098237, 1.0, 0.0) | (b2094) | (GALTptspp) | 1 |
| 8 | (0.098237, 1.0, 0.0) | (b3902) | (RMPA) | 1 |
| 9 | (0.098237, 1.0, 0.0) | (b1393) | (DHACOAH) | 1 |
| 10 | (0.098237, 1.0, 0.0) | (b2379) | () | 1 |
| 11 | (0.098237, 1.0, 0.0) | (b2868) | (HXAND, XAND) | 1 |
| 12 | (0.098237, 1.0, 0.0) | (b0904) | () | 1 |
| 13 | (0.098237, 1.0, 0.0) | (b3833) | (AMMQLT8, OMBZLM) | 1 |
| 14 | (0.098237, 1.0, 0.0) | (b0331) | (MCITL2) | 1 |
| 15 | (0.098237, 1.0, 0.0) | (b3541) | (CGLYabcpp, PROGLYabcpp) | 1 |
| 16 | (0.098237, 1.0, 0.0) | (b1012) | (PYROX) | 1 |
| 17 | (0.098237, 1.0, 0.0) | (b2221) | (ACACCT, BUTCT, HXCT) | 1 |
| 18 | (0.098237, 1.0, 0.0) | (b0110) | (AGM4PA, AM4PA, AGM3PA, AM3PA) | 1 |
| 19 | (0.098237, 1.0, 0.0) | (b1245) | (3PEPTabcpp, 4PEPTabcpp) | 1 |
| 20 | (0.098237, 1.0, 0.0) | (b4390) | () | 1 |
| 21 | (0.098237, 1.0, 0.0) | (b3266) | (INDOLEt2pp) | 1 |
| 22 | (0.098237, 1.0, 0.0) | (b3452) | (GLYC3Pabcpp, GLYC2Pabcpp, G3PCabcpp, G3PSabcp... | 1 |
| 23 | (0.098237, 1.0, 0.0) | (b2168) | (FRUK) | 1 |
| 24 | (0.098237, 1.0, 0.0) | (b1858) | (ZNabcpp) | 1 |
| 25 | (0.098237, 1.0, 0.0) | (b3666) | (F6Pt6_2pp, G6Pt6_2pp, MAN6Pt6_2pp, GAM6Pt6_2pp) | 1 |
| 26 | (0.098237, 1.0, 0.0) | (b0871) | (POX) | 1 |
| 27 | (0.098237, 1.0, 0.0) | (b0121) | (SPMS, APCS) | 1 |
| 28 | (0.098237, 1.0, 0.0) | (b0048) | () | 1 |
| 29 | (0.098237, 1.0, 0.0) | (b0657) | (ALPATG160pp, ALPATE160pp) | 1 |
| ... | ... | ... | ... | ... |
| 70 | (0.098237, 1.0, 0.0) | (b4192) | (ASCBPL) | 1 |
| 71 | (0.098237, 1.0, 0.0) | (b2663) | (ABUTt2pp) | 1 |
| 72 | (0.098237, 1.0, 0.0) | (b3560) | (GLYTRS) | 1 |
| 73 | (0.098237, 1.0, 0.0) | (b2490) | () | 1 |
| 74 | (0.098237, 1.0, 0.0) | (b0809) | (GLNabcpp) | 1 |
| 75 | (0.098237, 1.0, 0.0) | (b3748) | () | 1 |
| 76 | (0.098237, 1.0, 0.0) | (b0394) | (HEX7) | 1 |
| 77 | (0.098237, 1.0, 0.0) | (b3580) | (3KGK) | 1 |
| 78 | (0.098237, 1.0, 0.0) | (b0388) | () | 1 |
| 79 | (0.098237, 1.0, 0.0) | (b0638) | (RZ5PP) | 1 |
| 80 | (0.098237, 1.0, 0.0) | (b2925) | (FBA3) | 1 |
| 81 | (0.098237, 1.0, 0.0) | (b2988) | (GSPMDA, GSPMDS) | 1 |
| 82 | (0.098237, 1.0, 0.0) | (b0756) | (GALM2pp) | 1 |
| 83 | (0.098237, 1.0, 0.0) | (b0837) | () | 1 |
| 84 | (0.098237, 1.0, 0.0) | (b2162) | () | 1 |
| 85 | (0.098237, 1.0, 0.0) | (b2690) | () | 1 |
| 86 | (0.098237, 1.0, 0.0) | (b1064) | (ASR) | 1 |
| 87 | (0.098237, 1.0, 0.0) | (b3052) | (GMHEPK, GMHEPAT) | 1 |
| 88 | (0.098237, 1.0, 0.0) | (b0355) | () | 1 |
| 89 | (0.098237, 1.0, 0.0) | (b4120) | (MELIBt2pp) | 1 |
| 90 | (0.098237, 1.0, 0.0) | (b0521) | () | 1 |
| 91 | (0.098237, 1.0, 0.0) | (b4014) | () | 1 |
| 92 | (0.098237, 1.0, 0.0) | (b0049) | (GP4GH, AP4AH, AP5AH) | 1 |
| 93 | (0.098237, 1.0, 0.0) | (b0733) | () | 1 |
| 94 | (0.098237, 1.0, 0.0) | (b3503) | (ASR) | 1 |
| 95 | (0.098237, 1.0, 0.0) | (b4381) | (DRPA) | 1 |
| 96 | (0.098237, 1.0, 0.0) | (b2428) | (ACM6PH) | 1 |
| 97 | (0.098237, 1.0, 0.0) | (b3431) | (GLDBRAN2) | 1 |
| 98 | (0.098237, 1.0, 0.0) | (b0160) | (NTPTP1, NTPTP2) | 1 |
| 99 | (0.098237, 1.0, 0.0) | (b0446) | () | 1 |
100 rows × 4 columns