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Merge pull request #16 from matthiaskoenig/develop
Changes for release fbc_curation-v0.1.0
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‎.travis.yml

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sudo: required
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python: 3.7
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install: pip install -r requirements.txt
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install:
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pip install -r requirements.txt
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pip install -r requirements-test.txt
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script: pytest --cov=fbc_curation
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after_success: pip install codecov; codecov
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cache:

‎README.md

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‎README.rst

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fbc_curation
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=============
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``fbc_curation`` contains helpers for reproducibility of fbc models.
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``fbc_curation``: Helpers for reproducibility of constraint-based models
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available from https://github.com/matthiaskoenig/fbc_curation.
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© 2020 Matthias König

‎fbc_curation/examples/models/LICENSE renamed to ‎examples/models/LICENSE

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‎fbc_curation/examples/models/e_coli_core.xml renamed to ‎examples/models/e_coli_core.xml

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‎examples/models/iAB_AMO1410_SARS-CoV-2.xml

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‎fbc_curation/examples/models/iJR904.xml.gz renamed to ‎examples/models/iJR904.xml.gz

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‎fbc_curation/examples/results/e_coli_core/01_objective.tsv renamed to ‎examples/results/e_coli_core/cameo/01_objective.tsv

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‎fbc_curation/examples/results/e_coli_core/02_fva.tsv renamed to ‎examples/results/e_coli_core/cameo/02_fva.tsv

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@@ -12,7 +12,7 @@ e_coli_core obj ALCD2x optimal 0.0 0.0
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e_coli_core obj ATPM optimal 8.39 8.39
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e_coli_core obj ATPS4r optimal 45.51401 45.51401
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e_coli_core obj BIOMASS_Ecoli_core_w_GAM optimal 0.873922 0.873922
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e_coli_core obj CO2t optimal -22.809833 -22.809833
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e_coli_core obj CO2t optimal 22.809833 22.809833
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e_coli_core obj CS optimal 6.00725 6.00725
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e_coli_core obj CYTBD optimal 43.598985 43.598985
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e_coli_core obj D_LACt2 optimal 0.0 0.0
@@ -26,16 +26,16 @@ e_coli_core obj EX_etoh_e optimal 0.0 0.0
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e_coli_core obj EX_for_e optimal 0.0 0.0
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e_coli_core obj EX_fru_e optimal 0.0 0.0
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e_coli_core obj EX_fum_e optimal 0.0 0.0
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e_coli_core obj EX_glc__D_e optimal -10.0 -10.0
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e_coli_core obj EX_glc__D_e optimal 10.0 10.0
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e_coli_core obj EX_gln__L_e optimal 0.0 0.0
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e_coli_core obj EX_glu__L_e optimal 0.0 0.0
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e_coli_core obj EX_h2o_e optimal 29.175827 29.175827
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e_coli_core obj EX_h_e optimal 17.530865 17.530865
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e_coli_core obj EX_lac__D_e optimal 0.0 0.0
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e_coli_core obj EX_mal__L_e optimal 0.0 0.0
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e_coli_core obj EX_nh4_e optimal -4.765319 -4.765319
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e_coli_core obj EX_o2_e optimal -21.799493 -21.799493
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e_coli_core obj EX_pi_e optimal -3.214895 -3.214895
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e_coli_core obj EX_nh4_e optimal 4.765319 4.765319
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e_coli_core obj EX_o2_e optimal 21.799493 21.799493
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e_coli_core obj EX_pi_e optimal 3.214895 3.214895
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e_coli_core obj EX_pyr_e optimal 0.0 0.0
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e_coli_core obj EX_succ_e optimal 0.0 0.0
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e_coli_core obj FBA optimal 7.477382 7.477382
@@ -51,12 +51,12 @@ e_coli_core obj GAPD optimal 16.023526 16.023526
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e_coli_core obj GLCpts optimal 10.0 10.0
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e_coli_core obj GLNS optimal 0.223462 0.223462
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e_coli_core obj GLNabc optimal 0.0 0.0
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e_coli_core obj GLUDy optimal -4.541857 -4.541857
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e_coli_core obj GLUDy optimal 4.541857 4.541857
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e_coli_core obj GLUN optimal 0.0 0.0
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e_coli_core obj GLUSy optimal 0.0 0.0
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e_coli_core obj GLUt2r optimal 0.0 0.0
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e_coli_core obj GND optimal 4.959985 4.959985
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e_coli_core obj H2Ot optimal -29.175827 -29.175827
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e_coli_core obj H2Ot optimal 29.175827 29.175827
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e_coli_core obj ICDHyr optimal 6.00725 6.00725
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e_coli_core obj ICL optimal 0.0 0.0
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e_coli_core obj LDH_D optimal 0.0 0.0
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e_coli_core obj PFK optimal 7.477382 7.477382
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e_coli_core obj PFL optimal 0.0 0.0
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e_coli_core obj PGI optimal 4.860861 4.860861
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e_coli_core obj PGK optimal -16.023526 -16.023526
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e_coli_core obj PGK optimal 16.023526 16.023526
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e_coli_core obj PGL optimal 4.959985 4.959985
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e_coli_core obj PGM optimal -14.71614 -14.71614
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e_coli_core obj PGM optimal 14.71614 14.71614
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e_coli_core obj PIt2r optimal 3.214895 3.214895
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e_coli_core obj PPC optimal 2.504309 2.504309
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e_coli_core obj PPCK optimal 0.0 0.0
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e_coli_core obj PYK optimal 1.758177 1.758177
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e_coli_core obj PYRt2 optimal 0.0 0.0
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e_coli_core obj RPE optimal 2.678482 2.678482
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e_coli_core obj RPI optimal -2.281503 -2.281503
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e_coli_core obj RPI optimal 2.281503 2.281503
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e_coli_core obj SUCCt2_2 optimal 0.0 0.0
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e_coli_core obj SUCCt3 optimal 0.0 0.0
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e_coli_core obj SUCDi optimal 5.064376 1000.0
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e_coli_core obj SUCOAS optimal -5.064376 -5.064376
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e_coli_core obj SUCOAS optimal 5.064376 5.064376
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e_coli_core obj TALA optimal 1.496984 1.496984
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e_coli_core obj THD2 optimal 0.0 0.0
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e_coli_core obj TKT1 optimal 1.496984 1.496984

‎fbc_curation/examples/results/e_coli_core/03_gene_deletion.tsv renamed to ‎examples/results/e_coli_core/cameo/03_gene_deletion.tsv

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‎fbc_curation/examples/results/e_coli_core/04_reaction_deletion.tsv renamed to ‎examples/results/e_coli_core/cameo/04_reaction_deletion.tsv

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‎examples/results/e_coli_core/cobrapy/01_objective.tsv

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model objective status value
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e_coli_core obj optimal 0.873922

‎examples/results/e_coli_core/cobrapy/02_fva.tsv

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model objective reaction status minimum maximum
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e_coli_core obj ACALD optimal 0.0 0.0
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e_coli_core obj ACALDt optimal 0.0 0.0
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e_coli_core obj ACKr optimal 0.0 0.0
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e_coli_core obj ACONTa optimal 6.00725 6.00725
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e_coli_core obj ACONTb optimal 6.00725 6.00725
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e_coli_core obj ACt2r optimal 0.0 0.0
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e_coli_core obj ADK1 optimal 0.0 0.0
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e_coli_core obj AKGDH optimal 5.064376 5.064376
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e_coli_core obj AKGt2r optimal 0.0 0.0
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e_coli_core obj ALCD2x optimal 0.0 0.0
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e_coli_core obj ATPM optimal 8.39 8.39
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e_coli_core obj ATPS4r optimal 45.51401 45.51401
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e_coli_core obj BIOMASS_Ecoli_core_w_GAM optimal 0.873922 0.873922
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e_coli_core obj CO2t optimal 22.809833 22.809833
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e_coli_core obj CS optimal 6.00725 6.00725
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e_coli_core obj CYTBD optimal 43.598985 43.598985
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e_coli_core obj D_LACt2 optimal 0.0 0.0
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e_coli_core obj ENO optimal 14.71614 14.71614
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e_coli_core obj ETOHt2r optimal 0.0 0.0
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e_coli_core obj EX_ac_e optimal 0.0 0.0
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e_coli_core obj EX_acald_e optimal 0.0 0.0
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e_coli_core obj EX_akg_e optimal 0.0 0.0
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e_coli_core obj EX_co2_e optimal 22.809833 22.809833
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e_coli_core obj EX_etoh_e optimal 0.0 0.0
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e_coli_core obj EX_for_e optimal 0.0 0.0
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e_coli_core obj EX_fru_e optimal 0.0 0.0
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e_coli_core obj EX_fum_e optimal 0.0 0.0
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e_coli_core obj EX_glc__D_e optimal 10.0 10.0
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e_coli_core obj EX_gln__L_e optimal 0.0 0.0
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e_coli_core obj EX_glu__L_e optimal 0.0 0.0
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e_coli_core obj EX_h2o_e optimal 29.175827 29.175827
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e_coli_core obj EX_h_e optimal 17.530865 17.530865
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e_coli_core obj EX_lac__D_e optimal 0.0 0.0
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e_coli_core obj EX_mal__L_e optimal 0.0 0.0
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e_coli_core obj EX_nh4_e optimal 4.765319 4.765319
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e_coli_core obj EX_o2_e optimal 21.799493 21.799493
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e_coli_core obj EX_pi_e optimal 3.214895 3.214895
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e_coli_core obj EX_pyr_e optimal 0.0 0.0
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e_coli_core obj EX_succ_e optimal 0.0 0.0
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e_coli_core obj FBA optimal 7.477382 7.477382
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e_coli_core obj FBP optimal 0.0 0.0
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e_coli_core obj FORt optimal 0.0 0.0
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e_coli_core obj FORt2 optimal 0.0 0.0
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e_coli_core obj FRD7 optimal 0.0 994.935624
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e_coli_core obj FRUpts2 optimal 0.0 0.0
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e_coli_core obj FUM optimal 5.064376 5.064376
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e_coli_core obj FUMt2_2 optimal 0.0 0.0
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e_coli_core obj G6PDH2r optimal 4.959985 4.959985
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e_coli_core obj GAPD optimal 16.023526 16.023526
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e_coli_core obj GLCpts optimal 10.0 10.0
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e_coli_core obj GLNS optimal 0.223462 0.223462
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e_coli_core obj GLNabc optimal 0.0 0.0
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e_coli_core obj GLUDy optimal 4.541857 4.541857
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e_coli_core obj GLUN optimal 0.0 0.0
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e_coli_core obj GLUSy optimal 0.0 0.0
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e_coli_core obj GLUt2r optimal 0.0 0.0
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e_coli_core obj GND optimal 4.959985 4.959985
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e_coli_core obj H2Ot optimal 29.175827 29.175827
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e_coli_core obj ICDHyr optimal 6.00725 6.00725
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e_coli_core obj ICL optimal 0.0 0.0
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e_coli_core obj LDH_D optimal 0.0 0.0
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e_coli_core obj MALS optimal 0.0 0.0
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e_coli_core obj MALt2_2 optimal 0.0 0.0
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e_coli_core obj MDH optimal 5.064376 5.064376
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e_coli_core obj ME1 optimal 0.0 0.0
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e_coli_core obj ME2 optimal 0.0 0.0
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e_coli_core obj NADH16 optimal 38.53461 38.53461
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e_coli_core obj NADTRHD optimal 0.0 0.0
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e_coli_core obj NH4t optimal 4.765319 4.765319
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e_coli_core obj O2t optimal 21.799493 21.799493
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e_coli_core obj PDH optimal 9.282533 9.282533
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e_coli_core obj PFK optimal 7.477382 7.477382
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e_coli_core obj PFL optimal 0.0 0.0
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e_coli_core obj PGI optimal 4.860861 4.860861
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e_coli_core obj PGK optimal 16.023526 16.023526
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e_coli_core obj PGL optimal 4.959985 4.959985
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e_coli_core obj PGM optimal 14.71614 14.71614
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e_coli_core obj PIt2r optimal 3.214895 3.214895
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e_coli_core obj PPC optimal 2.504309 2.504309
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e_coli_core obj PPCK optimal 0.0 0.0
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e_coli_core obj PPS optimal 0.0 0.0
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e_coli_core obj PTAr optimal 0.0 0.0
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e_coli_core obj PYK optimal 1.758177 1.758177
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e_coli_core obj PYRt2 optimal 0.0 0.0
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e_coli_core obj RPE optimal 2.678482 2.678482
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e_coli_core obj RPI optimal 2.281503 2.281503
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e_coli_core obj SUCCt2_2 optimal 0.0 0.0
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e_coli_core obj SUCCt3 optimal 0.0 0.0
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e_coli_core obj SUCDi optimal 5.064376 1000.0
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e_coli_core obj SUCOAS optimal 5.064376 5.064376
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e_coli_core obj TALA optimal 1.496984 1.496984
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e_coli_core obj THD2 optimal 0.0 0.0
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e_coli_core obj TKT1 optimal 1.496984 1.496984
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e_coli_core obj TKT2 optimal 1.181498 1.181498
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e_coli_core obj TPI optimal 7.477382 7.477382

‎examples/results/e_coli_core/cobrapy/03_gene_deletion.tsv

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model objective gene status value
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e_coli_core obj b0008 optimal 0.873922
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e_coli_core obj b0114 optimal 0.796696
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e_coli_core obj b0115 optimal 0.796696
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e_coli_core obj b0116 optimal 0.782351
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e_coli_core obj b0118 optimal 0.873922
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e_coli_core obj b0351 optimal 0.873922
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e_coli_core obj b0356 optimal 0.873922
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e_coli_core obj b0451 optimal 0.873922
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e_coli_core obj b0474 optimal 0.873922
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e_coli_core obj b0485 optimal 0.873922
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e_coli_core obj b0720 optimal 0.0
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e_coli_core obj b0721 optimal 0.814298
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e_coli_core obj b0722 optimal 0.814298
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e_coli_core obj b0723 optimal 0.814298
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e_coli_core obj b0724 optimal 0.814298
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e_coli_core obj b0726 optimal 0.858307
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e_coli_core obj b0727 optimal 0.858307
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e_coli_core obj b0728 optimal 0.858307
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e_coli_core obj b0729 optimal 0.858307
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e_coli_core obj b0733 optimal 0.873922
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e_coli_core obj b0734 optimal 0.873922
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e_coli_core obj b0755 optimal 0.873922
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e_coli_core obj b0767 optimal 0.863813
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e_coli_core obj b0809 optimal 0.873922
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e_coli_core obj b0810 optimal 0.873922
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e_coli_core obj b0811 optimal 0.873922
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e_coli_core obj b0875 optimal 0.873922
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e_coli_core obj b0902 optimal 0.873922
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e_coli_core obj b0903 optimal 0.873922
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e_coli_core obj b0904 optimal 0.873922
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e_coli_core obj b0978 optimal 0.873922
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e_coli_core obj b0979 optimal 0.873922
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e_coli_core obj b1101 optimal 0.873922
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e_coli_core obj b1136 optimal 0.0
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e_coli_core obj b1241 optimal 0.873922
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e_coli_core obj b1276 optimal 0.873922
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e_coli_core obj b1297 optimal 0.873922
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e_coli_core obj b1380 optimal 0.873922
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e_coli_core obj b1478 optimal 0.873922
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e_coli_core obj b1479 optimal 0.873922
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e_coli_core obj b1524 optimal 0.873922
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e_coli_core obj b1602 optimal 0.873922
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e_coli_core obj b1603 optimal 0.873922
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e_coli_core obj b1611 optimal 0.873922
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e_coli_core obj b1612 optimal 0.873922
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e_coli_core obj b1621 optimal 0.873922
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e_coli_core obj b1676 optimal 0.873922
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e_coli_core obj b1702 optimal 0.873922
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e_coli_core obj b1723 optimal 0.873922
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e_coli_core obj b1761 optimal 0.851389
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e_coli_core obj b1773 optimal 0.873922
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e_coli_core obj b1779 optimal 0.0
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e_coli_core obj b1812 optimal 0.873922
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e_coli_core obj b1817 optimal 0.873922
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e_coli_core obj b1818 optimal 0.873922
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e_coli_core obj b1819 optimal 0.873922
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e_coli_core obj b1849 optimal 0.873922
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e_coli_core obj b1852 optimal 0.863813
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e_coli_core obj b1854 optimal 0.873922
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e_coli_core obj b2029 optimal 0.863813
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e_coli_core obj b2097 optimal 0.873922
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e_coli_core obj b2133 optimal 0.873922
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e_coli_core obj b2276 optimal 0.211663
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e_coli_core obj b2277 optimal 0.211663
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e_coli_core obj b2278 optimal 0.211663
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e_coli_core obj b2279 optimal 0.211663
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e_coli_core obj b2280 optimal 0.211663
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e_coli_core obj b2281 optimal 0.211663
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e_coli_core obj b2282 optimal 0.211663
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e_coli_core obj b2283 optimal 0.211663
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e_coli_core obj b2284 optimal 0.211663
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e_coli_core obj b2285 optimal 0.211663
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e_coli_core obj b2286 optimal 0.211663
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e_coli_core obj b2287 optimal 0.211663
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e_coli_core obj b2288 optimal 0.211663
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e_coli_core obj b2296 optimal 0.873922
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e_coli_core obj b2297 optimal 0.873922
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e_coli_core obj b2415 infeasible
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e_coli_core obj b2416 infeasible
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e_coli_core obj b2417 optimal 0.873922
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e_coli_core obj b2458 optimal 0.873922
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e_coli_core obj b2463 optimal 0.873922
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e_coli_core obj b2464 optimal 0.873922
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e_coli_core obj b2465 optimal 0.873922
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e_coli_core obj b2492 optimal 0.873922
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e_coli_core obj b2579 optimal 0.873922
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e_coli_core obj b2587 optimal 0.873922
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e_coli_core obj b2779 optimal 0.0
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e_coli_core obj b2914 optimal 0.873922
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e_coli_core obj b2925 optimal 0.873922
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e_coli_core obj b2926 optimal 0.0
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e_coli_core obj b2935 optimal 0.873922
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e_coli_core obj b2975 optimal 0.873922
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e_coli_core obj b2976 optimal 0.873922
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e_coli_core obj b2987 optimal 0.873922
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e_coli_core obj b3114 optimal 0.873922
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e_coli_core obj b3115 optimal 0.873922
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e_coli_core obj b3212 optimal 0.873922
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e_coli_core obj b3213 optimal 0.873922
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e_coli_core obj b3236 optimal 0.825819
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e_coli_core obj b3386 optimal 0.873922
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e_coli_core obj b3403 optimal 0.873922
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e_coli_core obj b3493 optimal 0.873922
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e_coli_core obj b3528 optimal 0.873922
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e_coli_core obj b3603 optimal 0.873922
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e_coli_core obj b3612 optimal 0.873922
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e_coli_core obj b3731 optimal 0.37423
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e_coli_core obj b3732 optimal 0.37423
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e_coli_core obj b3733 optimal 0.37423
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e_coli_core obj b3734 optimal 0.37423
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e_coli_core obj b3735 optimal 0.37423
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e_coli_core obj b3736 optimal 0.37423
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e_coli_core obj b3737 optimal 0.37423
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e_coli_core obj b3738 optimal 0.37423
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e_coli_core obj b3739 optimal 0.873922
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e_coli_core obj b3870 optimal 0.873922
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e_coli_core obj b3916 optimal 0.873922
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e_coli_core obj b3919 optimal 0.704037
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e_coli_core obj b3925 optimal 0.873922
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e_coli_core obj b3951 optimal 0.873922
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e_coli_core obj b3952 optimal 0.873922
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e_coli_core obj b3956 optimal 0.870745
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e_coli_core obj b3962 optimal 0.873922
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e_coli_core obj b4014 optimal 0.873922
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e_coli_core obj b4015 optimal 0.873922
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e_coli_core obj b4025 optimal 0.86316
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e_coli_core obj b4077 optimal 0.873922
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e_coli_core obj b4090 optimal 0.873922
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e_coli_core obj b4122 optimal 0.873922
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e_coli_core obj b4151 optimal 0.873922
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e_coli_core obj b4152 optimal 0.873922
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e_coli_core obj b4153 optimal 0.873922
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e_coli_core obj b4154 optimal 0.873922
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e_coli_core obj b4232 optimal 0.873922
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e_coli_core obj b4301 optimal 0.873922
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e_coli_core obj b4395 optimal 0.873922
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e_coli_core obj s0001 optimal 0.211141

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