from time import time
from random import Random
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
/Users/joao/.virtualenvs/cameo-env/lib/python2.7/site-packages/IPython/parallel/client/client.py:452: RuntimeWarning: Controller appears to be listening on localhost, but not on this machine. If this is true, you should specify Client(...,sshserver='you@10.32.0.166') or instruct your controller to listen on an external IP. RuntimeWarning) /Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'processing (0.52-pathos)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions. /Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'cameo (v0.2.0-51-gd721048-dirty)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions. /Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'matlabengineforpython (R2014b)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions. /Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'pyre (0.8-pathos)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.
model = load_model("/Users/joao/Documents/repos/cameo/tests/data/iJO1366.xml")
of = biomass_product_coupled_yield("Ec_biomass_iJO1366_core_53p95M", "EX_succ_lp_e_rp_", "EX_glc_lp_e_rp_")
ko = GeneKnockoutOptimization(model=model, objective_function=of,
simulation_method=fba, heuristic_method=inspyred.ec.GA)
ko.run(max_evaluations=50000, n=1, mutation_rate=0.15, indel_rate=0.185)
Starting optimization at Tue, 14 Apr 2015 13:29:21
Using saved session configuration for http://localhost:5006/ To override, pass 'load_from_config=False' to Session
Finished after 01:58:14
Fitness | Knockouts | Reactions | Size | |
---|---|---|---|---|
0 | 0.029159 | (b3835, b3397, b2907, b4036, b0721, b0616, b0945) | (OPHHX, MALTTTRtexi, 14GLUCANtexi, MALTPTtexi,... | 7 |
1 | 0.029159 | (b0341, b1270, b3006, b2937, b0721, b0841, b0945) | (CYNTt2pp, FE3DHBZStonex, CBLAT, CPGNtonex, CB... | 7 |
2 | 0.029159 | (b0341, b3006, b2937, b0721, b3791, b0841, b0945) | (CYNTt2pp, FE3DHBZStonex, DHORD2, TDPAGTA, CPG... | 7 |
3 | 0.029159 | (b0341, b1270, b2937, b0721, b0841, b1748, b0945) | (CYNTt2pp, CBLAT, SOTA, DHORD2, DHORD5, AGMT, ... | 7 |
4 | 0.029159 | (b0341, b1270, b1484, b3784, b0721, b0841, b0945) | (CYNTt2pp, ACGAMT, CBLAT, DHORD2, DHORD5, CBIA... | 7 |
5 | 0.029159 | (b3006, b2241, b2441, b0721, b0841, b0084, b0945) | (FE3DHBZStonex, CBL1tonex, CPGNtonex, CBItonex... | 7 |
6 | 0.029159 | (b0341, b3006, b2937, b2697, b0721, b0841, b0945) | (CYNTt2pp, FE3DHBZStonex, DHORD2, CPGNtonex, C... | 7 |
7 | 0.029159 | (b3006, b3542, b2241, b2441, b0721, b0841, b0945) | (FE3DHBZStonex, DHORD2, CGLYabcpp, CPGNtonex, ... | 7 |
8 | 0.029159 | (b3006, b2937, b2697, b2241, b0721, b0841, b0945) | (FE3DHBZStonex, DHORD2, ALATRS, CBItonex, CBL1... | 7 |
9 | 0.029159 | (b3390, b3542, b0722, b0038, b3849, b1197, b41... | (DHORD2, CGLYabcpp, TREHpp, DHORD5, ARGDC, CRN... | 8 |
10 | 0.029159 | (b3114, b3390, b0401, b0722, b1014, b1197, b41... | (TREHpp, P5CD, PROD2, DHORD2, DHORD5, ARGDC, I... | 8 |
11 | 0.029159 | (b3114, b4036, b3390, b0401, b0722, b1197, b41... | (DHORD2, 14GLUCANtexi, MALTPTtexi, TREHpp, DHO... | 8 |
12 | 0.029159 | (b0758, b3709, b4233, b0722, b3924, b0066, b0945) | (UM4PL, DHORD2, DHORD5, FLDR2, UM3PL, SUCDi, U... | 7 |
13 | 0.029159 | (b3709, b0722, b3924, b0066, b0945, b3493, b1007) | (PYROX, DHORD2, DHORD5, FLDR2, SUCDi, THMabcpp) | 7 |
14 | 0.029159 | (b0758, b3709, b3577, b4233, b0722, b0066, b0945) | (DHORD2, UM4PL, DHORD5, XYLUt2pp, UM3PL, THMab... | 7 |
15 | 0.029159 | (b1465, b0758, b0722, b3924, b0207, b1238, b09... | (DHORD2, DHORD5, FLDR2, DURIK1, UGLT, TMDK1, S... | 8 |
16 | 0.029159 | (b0758, b2066, b0514, b0722, b0207, b4386, b12... | (DHORD2, DHORD5, CYTDK2, DURIK1, GLYCK, LIPAMP... | 8 |
17 | 0.029159 | (b0758, b1064, b0514, b0722, b0207, b4386, b13... | (ASR, 42A12BOOXpp, DHORD5, DHORD2, TYROXDApp, ... | 8 |
18 | 0.029159 | (b0758, b2066, b0722, b0207, b2033, b4386, b12... | (O16AT, DHORD2, DHORD5, CYTDK2, DURIK1, LIPAMP... | 8 |
19 | 0.029159 | (b0758, b1453, b0514, b0651, b0722, b0207, b43... | (ASNt2rpp, DHORD5, DHORD2, PTRCORNt7pp, GLYCK,... | 9 |
20 | 0.029159 | (b0722, b0758, b1453, b0514, b2485, b0207, b41... | (ASNt2rpp, DHORD5, DHORD2, PTRCORNt7pp, ASCBpt... | 10 |
21 | 0.029159 | (b0996, b0722, b3924, b0617, b4198, b1778, b0945) | (DHORD2, DHORD5, FLDR2, METSOXR2, CITL, SUCDi) | 7 |
22 | 0.029159 | (b2092, b0494, b3222, b0996, b0722, b3924, b41... | (LPLIPAL1G160pp, LPLIPAL1E160pp, LPLIPAL1G161p... | 8 |
23 | 0.029159 | (b4198, b2964, b0996, b0724, b0945) | (GSNt2pp, DINSt2pp, DHORD2, DHORD5, INSt2pp, D... | 5 |
24 | 0.029159 | (b0723, b0945) | (DHORD2, DHORD5, SUCDi) | 2 |
25 | 0.029159 | (b0722, b0968, b2344, b0945, b0674) | (APH140, APH141, OCDCAtexi, APH160, APH161, DD... | 5 |
26 | 0.029159 | (b0722, b4485, b1380, b3789, b0945) | (DHORD2, DHORD5, SUCDi) | 5 |
27 | 0.029159 | (b0722, b2052, b4386, b0957, b0945) | (DHORD2, DHORD5, LIPAMPL, GOFUCR, OCTNLL, LIPA... | 5 |
28 | 0.029159 | (b0722, b0403, b4485, b1380, b0945) | (DHORD2, DHORD5, MLTG5, MLTG4, SUCDi, MLTG1, M... | 5 |
29 | 0.029159 | (b1297, b1611, b0722, b0451, b0155, b4015, b36... | (ICL, GLUt4pp, DHORD2, DHORD5, GGPTRCS, SUCDi) | 8 |
... | ... | ... | ... | ... |
70 | 0.029159 | (b0722, b0194, b4244, b3916, b0945, b2222) | (PFK_2, PROTRS, DHORD2, DHORD5, HXCT, PFK_3, A... | 6 |
71 | 0.029159 | (b0831, b2710, b4544, b0722, b4386, b2470, b09... | (DHORD2, DHORD5, GTHRDabcpp, LIPAMPL, NHFRBO, ... | 8 |
72 | 0.029159 | (b0722, b2470, b0945, b1857, b1623) | (ZNabcpp, DHORD5, DHORD2, DADA, ADA, SUCDi) | 5 |
73 | 0.029159 | (b0722, b4244, b0945, b4227, b2679) | (CRNabcpp, CTBTabcpp, CRNDabcpp, DHORD2, DHORD... | 5 |
74 | 0.029159 | (b4226, b0813, b0722, b0932, b1654, b0945) | (DHORD2, DHORD5, SUCDi) | 6 |
75 | 0.029159 | (b0509, b0418, b4139, b0722, b3265, b1654, b07... | (DHORD2, DHORD5, ASPT, INDOLEt2pp, SUCOAS, SUCDi) | 8 |
76 | 0.029159 | (b0722, b3224, b4069, b0311, b2470, b0945) | (DHORD2, DHORD5, ACS, ACCOAL, CHOLD, ACNAMt2pp... | 6 |
77 | 0.029159 | (b0722, b2201, b0945, b0837, b3500) | (PHEMEabcpp, DHORD2, DHORD5, GTHOr, SUCDi) | 5 |
78 | 0.029159 | (b0494, b3565, b0722, b1773, b1106, b3073, b0945) | (LPLIPAL1G160pp, LPLIPAL1E160pp, LPLIPAL1G161p... | 7 |
79 | 0.029159 | (b1713, b0418, b4139, b0722, b4035, b1654, b07... | (14GLUCANabcpp, MALTHXabcpp, MALTTTRabcpp, DHO... | 8 |
80 | 0.029159 | (b0722, b0662, b0333, b2418, b0945) | (PYDAMK, MCITS, DHORD2, DHORD5, PYDXNK, OMMBLH... | 5 |
81 | 0.029159 | (b0722, b3029, b3945, b0945, b3500) | (LALDO2x, ALR4x, QMO3, QMO2, DHORD2, DHORD5, G... | 5 |
82 | 0.029159 | (b0722, b3460, b1623, b2470, b0149, b0945) | (ILEabcpp, DADA, DHORD2, ALAabcpp, THRabcpp, A... | 6 |
83 | 0.029159 | (b1325, b2679, b0722, b2440, b0311, b1654, b18... | (CRNabcpp, CTBTabcpp, CRNDabcpp, DHORD5, DHORD... | 8 |
84 | 0.029159 | (b0494, b0722, b4069, b0311, b2470, b0945) | (LPLIPAL1G160pp, LPLIPAL1E160pp, LPLIPAL1G161p... | 6 |
85 | 0.029159 | (b2710, b4544, b0722, b1033, b1232, b4386, b03... | (DHORD2, DHORD5, PPTHpp, LIPAMPL, NHFRBO, FTHF... | 8 |
86 | 0.029159 | (b4036, b0831, b1207, b0722, b1851, b4198, b09... | (PRPPS, MALTTTRtexi, EDD, 14GLUCANtexi, MALTPT... | 8 |
87 | 0.029159 | (b3460, b3831, b0722, b1479, b1872, b0945) | (DMSOR2pp, ILEabcpp, DHORD5, DHORD2, ALAabcpp,... | 6 |
88 | 0.029159 | (b0722, b0764, b0945, b0311, b2222) | (HXCT, DHORD2, DHORD5, TUNGSabcpp, CHOLD, ACAC... | 5 |
89 | 0.029159 | (b0595, b1872, b0698, b0722, b0311, b1623, b06... | (DHORD2, DHORD5, Kabcpp, DADA, ICHORT, DMSOR1p... | 8 |
90 | 0.029159 | (b0509, b1296, b4139, b0722, b2484, b1919, b38... | (ASPT, CYSDDS, DHORD2, DHORD5, SUCDi) | 8 |
91 | 0.029159 | (b2328, b0933, b3566, b0722, b0194, b0945) | (XYLabcpp, MSO3abcpp, PROTRS, ETHSO3abcpp, DHO... | 6 |
92 | 0.029159 | (b2417, b3008, b1872, b4139, b0722, b1198, b16... | (TREptspp, ACMUMptspp, DHORD2, MALTptspp, ASPT... | 9 |
93 | 0.029159 | (b2719, b0722, b3845, b3496, b0696, b0945) | (Kabcpp, DHORD5, DHORD2, SUCDi) | 6 |
94 | 0.029159 | (b4130, b0662, b0722, b0194, b4244, b0945) | (PROTRS, DHORD5, DHORD2, OMMBLHX, SUCDi) | 6 |
95 | 0.029159 | (b0831, b2710, b0945, b1207, b0722, b2203, b15... | (PRPPS, DHORD2, NO3R1bpp, DHORD5, GTHRDabcpp, ... | 8 |
96 | 0.029159 | (b0698, b1489, b0722, b1033, b4244, b0037, b0945) | (CRNCAL2, DHORD2, Kabcpp, DHORD5, CRNDCAL2, CT... | 7 |
97 | 0.029159 | (b0722, b0194, b0945, b3429, b4244) | (PROTRS, DHORD2, DHORD5, GLCS1, SUCDi) | 5 |
98 | 0.029159 | (b1207, b0722, b1851, b1033, b1489, b0945) | (PRPPS, EDD, DHORD2, DHORD5, PDE4, PDE1, SUCDi) | 6 |
99 | 0.029159 | (b0494, b0722, b0311, b1773, b2470, b0945) | (LPLIPAL1G160pp, LPLIPAL1E160pp, LPLIPAL1G161p... | 6 |
100 rows × 4 columns