Merge pull request #10 from cnapy-org/ecc_14bdo

1,4-butanediol strain design examples in e_coli_core

e_coli_core_14bdo/box_positions.json

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+{"Central Metabolism": {"name": "Map 0", "background": "map1.svg", "bg-size": 1, "box-size": 1.7715610000000013, "zoom": -22, "pos": [0, 0], "boxes": {"EX_glc__D_e": [985.4665102903942, 247.93584176095908], "TPI": [875.6215171051592, 1854.8111706421114], "TKT2": [1484.4766221890334, 1399.7390560175663], "TKT1": [2099.6085840263495, 1387.1853425106824], "THD2": [3459.520983943327, 603.8022353973535], "TALA": [2107.6115763869884, 1708.8742511245853], "SUCOAS": [3562.0534390108023, 2673.4388284260176], "SUCDi": [2973.441196956778, 2487.3614099702295], "SUCCt3": [4610.162979700548, 2498.753904977727], "SUCCt2_2": [4617.757976372212, 2692.42632010518], "RPI": [2164.574051424475, 1036.7170456822485], "RPE": [1974.699134632854, 1063.2995340330754], "PYRt2": [432.91481028489494, 3600.0284223691265], "PYK": [1010.8940569985881, 3381.440620660277], "PTAr": [1640.5192810796018, 3763.32085080992], "PPS": [770.8921621739796, 3368.3810238833494], "PPCK": [1306.3394275263497, 3189.8986020992256], "PPC": [1306.3394275263497, 3106.353638710913], "PIt2r": [2825.338761859314, 4222.818149445642], "PGM": [983.3242190804448, 2674.274278059901], "PGL": [1562.2908153614542, 909.8046512987293], "PGK": [987.919192066802, 2416.9557908238967], "PGI": [1001.7041110258737, 1079.8186517939464], "PFL": [1243.3996901082635, 3659.436486334889], "PFK": [980.5672352886305, 1415.2516797980234], "PDH": [1440.524031222988, 3583.619432059995], "O2t": [4523.750905068682, 1324.2712146681504], "NH4t": [3922.268941154522, 4281.136331389021], "NADTRHD": [3452.2032046501786, 924.9680621537082], "NADH16": [4589.45901877359, 2213.857984826908], "ME2": [2284.6205688168093, 3042.7911115657503], "ME1": [2072.3328168471057, 3012.4642898557927], "MDH": [2527.2351424964704, 3098.3902847006725], "MALt2_2": [2552.507493921435, 540.8283204942446], "MALS": [2893.6937319042972, 3091.1636453675824], "LDH_D": [1002.5395606597565, 3854.460810869897], "ICL": [3356.988528875851, 3394.963512234175], "ICDHyr": [3527.8759539883094, 3527.8759539883094], "H2Ot": [3216.481090450052, 4302.565614498121], "GND": [1902.5466662520378, 915.197098935611], "GLUt2r": [4591.175488021385, 3300.026053838365], "GLUSy": [4048.13322599735, 3516.4834589808124], "GLUN": [4196.235661094814, 3588.635927361628], "GLUDy": [4017.753239310691, 3281.038562159203], "GLNS": [4317.755607841451, 3505.090963973315], "GLNabc": [4367.1230862072725, 3820.283325847405], "GLCpts": [991.1470656522592, 653.1697137631746], "GAPD": [994.9445639880917, 2069.636593028664], "G6PDH2r": [1234.1869591455336, 907.6021022639462], "FUMt2_2": [2798.7562735084866, 550.6372586956995], "FUM": [2688.628821769347, 2646.8563400751905], "FRUpts2": [546.8397603598671, 1017.7295540030862], "FRD7": [3041.796167001761, 2259.5115098202846], "FORt2": [1275.95944083969, 4313.958109505618], "FORt": [1412.6693809296569, 4226.615647781473], "FBP": [759.4996671664821, 1431.656872608819], "FBA": [956.9695806297675, 1727.861742803747], "EX_succ_e": [4978.520318276291, 2548.1213833435477], "EX_pyr_e": [83.54496338831304, 3611.4209173766226], "EX_pi_e": [2813.9462668518163, 4568.39049800639], "EX_o2_e": [4887.380358216313, 1325.3269192055113], "EX_nh4_e": [3922.81578091488, 4511.428022968904], "EX_mal__L_e": [2548.1213833435477, 186.07741845578812], "EX_lac__D_e": [983.5520689805944, 4564.592999670558], "EX_h2o_e": [3186.1011037633925, 4572.1879963422225], "EX_h_e": [4894.975354887977, 1894.951669580373], "EX_glu__L_e": [4925.355341574636, 3277.2410638233705], "EX_gln__L_e": [4940.545334917966, 3820.283325847405], "EX_fum_e": [2783.566280165157, 182.2799201199557], "EX_fru_e": [121.51994674663715, 1021.5270523389185], "EX_for_e": [1382.2893942429976, 4572.1879963422225], "EX_etoh_e": [2460.7789216194024, 4549.4030063272285], "EX_akg_e": [4982.317816612123, 2889.8962335684646], "EX_co2_e": [3588.635927361628, 4583.5804913497195], "EX_acald_e": [2168.3715497603066, 4564.592999670558], "EX_ac_e": [1701.27925445292, 4583.5804913497195], "ETOHt2r": [2464.5764199552345, 4310.1606111697865], "ENO": [991.1470656522592, 2912.681223583459], "D_LACt2": [1002.5395606597565, 4294.970617826457], "CYTBD": [4553.20050466306, 1572.164311034618], "CS": [2760.7812901501625, 3539.268448995807], "CO2t": [3573.4459340182984, 4287.375621154792], "BIOMASS_Ecoli_core_w_GAM": [5255.737696792056, 4382.313079550602], "ATPS4r": [4545.605507991396, 805.0696471964711], "ATPM": [4173.45067107982, 964.5645773014323], "ALCD2x": [2312.6764865219384, 3736.738362459092], "AKGt2r": [4556.998002998893, 2886.0987352326324], "AKGDH": [3725.345867451595, 3102.55614037508], "ADK1": [4044.3357276615175, 839.2471322189627], "ACt2r": [1682.291762773758, 4332.945601184781], "ACONTb": [3246.861077136711, 3683.5733857574387], "ACONTa": [2996.226186971772, 3683.5733857574387], "ACKr": [1667.1017694304282, 3922.81578091488], "ACALDt": [2134.194064737815, 4158.26067773649], "ACALD": [1917.7366595953674, 3607.6234190407904]}}}

e_coli_core_14bdo/ecc_14bdo_example_10.sdc

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+{"model_id": "e_coli_core", "sd_modules": [{"module_type": "optknock", "constraints": [[{"BIOMASS_Ecoli_core_w_GAM": 1.0}, ">=", 0.5]], "inner_objective": {"BIOMASS_Ecoli_core_w_GAM": 1.0, "EX_14bdo_e": -0.001}, "inner_opt_sense": "maximize", "outer_objective": {"EX_14bdo_e": 1.0}, "outer_opt_sense": "maximize", "prod_id": null, "min_gcp": null, "skip_checks": true, "reac_ids": ["PFK", "PFL", "PGI", "PGK", "PGL", "ACALD", "AKGt2r", "PGM", "PIt2r", "ALCD2x", "ACALDt", "ACKr", "PPC", "ACONTa", "ACONTb", "ATPM", "PPCK", "ACt2r", "PPS", "ADK1", "AKGDH", "ATPS4r", "PTAr", "PYK", "BIOMASS_Ecoli_core_w_GAM", "PYRt2", "CO2t", "RPE", "CS", "RPI", "SUCCt2_2", "CYTBD", "D_LACt2", "ENO", "SUCCt3", "ETOHt2r", "SUCDi", "SUCOAS", "TALA", "THD2", "TKT1", "TKT2", "TPI", "EX_ac_e", "EX_acald_e", "EX_akg_e", "EX_co2_e", "EX_etoh_e", "EX_for_e", "EX_fru_e", "EX_fum_e", "EX_glc__D_e", "EX_gln__L_e", "EX_glu__L_e", "EX_h_e", "EX_h2o_e", "EX_lac__D_e", "EX_mal__L_e", "EX_nh4_e", "EX_o2_e", "EX_pi_e", "EX_pyr_e", "EX_succ_e", "FBA", "FBP", "FORt2", "FORt", "FRD7", "FRUpts2", "FUM", "FUMt2_2", "G6PDH2r", "GAPD", "GLCpts", "GLNS", "GLNabc", "GLUDy", "GLUN", "GLUSy", "GLUt2r", "GND", "H2Ot", "ICDHyr", "ICL", "LDH_D", "MALS", "MALt2_2", "MDH", "ME1", "ME2", "NADH16", "NADTRHD", "NH4t", "O2t", "PDH", "SSCOARx", "HBD", "HBCT", "HBDH", "HBDx", "BDOtpp", "BDOtex", "EX_14bdo_e", "AKGDC"]}], "gene_kos": true, "use_scenario": false, "max_solutions": "1", "max_cost": "30", "time_limit": "inf", "advanced": true, "solver": "gurobi", "solution_approach": "best", "reg_cost": {}, "ko_cost": {"EX_o2_e": 1.0}, "ki_cost": {"SSCOARx": 1.0, "AKGDC": 1.0}, "gko_cost": {"adhE": 1.0, "mhpF": 1.0, "purT": 1.0, "tdcD": 1.0, "ackA": 1.0, "acnA": 1.0, "acnB": 1.0, "adk": 1.0, "lpd": 1.0, "sucB": 1.0, "sucA": 1.0, "kgtP": 1.0, "frmA": 1.0, "adhP": 1.0, "atpA": 1.0, "atpG": 1.0, "atpF": 1.0, "atpE": 1.0, "atpI": 1.0, "atpB": 1.0, "atpH": 1.0, "atpC": 1.0, "atpD": 1.0, "gltA": 1.0, "cydA": 1.0, "cydB": 1.0, "cbdB": 1.0, "cbdA": 1.0, "lldP": 1.0, "glcA": 1.0, "eno": 1.0, "fbaA": 1.0, "ydjI": 1.0, "fbaB": 1.0, "glpX": 1.0, "fbp": 1.0, "focB": 1.0, "focA": 1.0, "frdC": 1.0, "frdA": 1.0, "frdB": 1.0, "frdD": 1.0, "manZ": 1.0, "manX": 1.0, "ptsI": 1.0, "ptsH": 1.0, "manY": 1.0, "fumC": 1.0, "fumB": 1.0, "fumA": 1.0, "dctA": 1.0, "zwf": 1.0, "gapA": 1.0, "ptsG": 1.0, "crr": 1.0, "malX": 1.0, "puuA": 1.0, "glnA": 1.0, "glnQ": 1.0, "glnH": 1.0, "glnP": 1.0, "gdhA": 1.0, "glsB": 1.0, "glsA": 1.0, "pabB": 1.0, "gltD": 1.0, "gltB": 1.0, "gltP": 1.0, "gnd": 1.0, "aqpZ": 1.0, "icd": 1.0, "aceA": 1.0, "ldhA": 1.0, "dld": 1.0, "aceB": 1.0, "glcB": 1.0, "mdh": 1.0, "maeA": 1.0, "maeB": 1.0, "nuoI": 1.0, "nuoM": 1.0, "nuoJ": 1.0, "nuoC": 1.0, "nuoB": 1.0, "nuoF": 1.0, "nuoN": 1.0, "nuoH": 1.0, "nuoK": 1.0, "nuoG": 1.0, "nuoE": 1.0, "nuoA": 1.0, "nuoL": 1.0, "pntA": 1.0, "sthA": 1.0, "pntB": 1.0, "amtB": 1.0, "aceE": 1.0, "aceF": 1.0, "pfkA": 1.0, "pfkB": 1.0, "tdcE": 1.0, "grcA": 1.0, "pflD": 1.0, "pflA": 1.0, "pflC": 1.0, "pflB": 1.0, "pgi": 1.0, "pgk": 1.0, "pgl": 1.0, "gpmM": 1.0, "ytjC": 1.0, "gpmA": 1.0, "pitA": 1.0, "pitB": 1.0, "ppc": 1.0, "pck": 1.0, "ppsA": 1.0, "pta": 1.0, "eutD": 1.0, "pykF": 1.0, "pykA": 1.0, "rpe": 1.0, "sgcE": 1.0, "rpiA": 1.0, "rpiB": 1.0, "sdhC": 1.0, "sdhD": 1.0, "sdhB": 1.0, "sdhA": 1.0, "sucD": 1.0, "sucC": 1.0, "talB": 1.0, "talA": 1.0, "tktB": 1.0, "tktA": 1.0, "tpiA": 1.0}, "gki_cost": {}}

e_coli_core_14bdo/ecc_14bdo_example_12.sdc

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+{"model_id": "e_coli_core", "sd_modules": [{"module_type": "robustknock", "constraints": [[{"BIOMASS_Ecoli_core_w_GAM": 1.0}, ">=", 0.5]], "inner_objective": {"BIOMASS_Ecoli_core_w_GAM": 1.0}, "inner_opt_sense": "maximize", "outer_objective": {"EX_14bdo_e": 1.0}, "outer_opt_sense": "maximize", "prod_id": null, "min_gcp": null, "skip_checks": true, "reac_ids": ["PFK", "PFL", "PGI", "PGK", "PGL", "ACALD", "AKGt2r", "PGM", "PIt2r", "ALCD2x", "ACALDt", "ACKr", "PPC", "ACONTa", "ACONTb", "ATPM", "PPCK", "ACt2r", "PPS", "ADK1", "AKGDH", "ATPS4r", "PTAr", "PYK", "BIOMASS_Ecoli_core_w_GAM", "PYRt2", "CO2t", "RPE", "CS", "RPI", "SUCCt2_2", "CYTBD", "D_LACt2", "ENO", "SUCCt3", "ETOHt2r", "SUCDi", "SUCOAS", "TALA", "THD2", "TKT1", "TKT2", "TPI", "EX_ac_e", "EX_acald_e", "EX_akg_e", "EX_co2_e", "EX_etoh_e", "EX_for_e", "EX_fru_e", "EX_fum_e", "EX_glc__D_e", "EX_gln__L_e", "EX_glu__L_e", "EX_h_e", "EX_h2o_e", "EX_lac__D_e", "EX_mal__L_e", "EX_nh4_e", "EX_o2_e", "EX_pi_e", "EX_pyr_e", "EX_succ_e", "FBA", "FBP", "FORt2", "FORt", "FRD7", "FRUpts2", "FUM", "FUMt2_2", "G6PDH2r", "GAPD", "GLCpts", "GLNS", "GLNabc", "GLUDy", "GLUN", "GLUSy", "GLUt2r", "GND", "H2Ot", "ICDHyr", "ICL", "LDH_D", "MALS", "MALt2_2", "MDH", "ME1", "ME2", "NADH16", "NADTRHD", "NH4t", "O2t", "PDH", "SSCOARx", "HBD", "HBCT", "HBDH", "HBDx", "BDOtpp", "BDOtex", "EX_14bdo_e", "AKGDC"]}], "gene_kos": true, "use_scenario": false, "max_solutions": "1", "max_cost": "30", "time_limit": "inf", "advanced": true, "solver": "gurobi", "solution_approach": "best", "reg_cost": {}, "ko_cost": {"EX_o2_e": 1.0}, "ki_cost": {"SSCOARx": 1.0, "AKGDC": 1.0}, "gko_cost": {"adhE": 1.0, "mhpF": 1.0, "purT": 1.0, "tdcD": 1.0, "ackA": 1.0, "acnA": 1.0, "acnB": 1.0, "adk": 1.0, "lpd": 1.0, "sucB": 1.0, "sucA": 1.0, "kgtP": 1.0, "frmA": 1.0, "adhP": 1.0, "atpA": 1.0, "atpG": 1.0, "atpF": 1.0, "atpE": 1.0, "atpI": 1.0, "atpB": 1.0, "atpH": 1.0, "atpC": 1.0, "atpD": 1.0, "gltA": 1.0, "cydA": 1.0, "cydB": 1.0, "cbdB": 1.0, "cbdA": 1.0, "lldP": 1.0, "glcA": 1.0, "eno": 1.0, "fbaA": 1.0, "ydjI": 1.0, "fbaB": 1.0, "glpX": 1.0, "fbp": 1.0, "focB": 1.0, "focA": 1.0, "frdC": 1.0, "frdA": 1.0, "frdB": 1.0, "frdD": 1.0, "manZ": 1.0, "manX": 1.0, "ptsI": 1.0, "ptsH": 1.0, "manY": 1.0, "fumC": 1.0, "fumB": 1.0, "fumA": 1.0, "dctA": 1.0, "zwf": 1.0, "gapA": 1.0, "ptsG": 1.0, "crr": 1.0, "malX": 1.0, "puuA": 1.0, "glnA": 1.0, "glnQ": 1.0, "glnH": 1.0, "glnP": 1.0, "gdhA": 1.0, "glsB": 1.0, "glsA": 1.0, "pabB": 1.0, "gltD": 1.0, "gltB": 1.0, "gltP": 1.0, "gnd": 1.0, "aqpZ": 1.0, "icd": 1.0, "aceA": 1.0, "ldhA": 1.0, "dld": 1.0, "aceB": 1.0, "glcB": 1.0, "mdh": 1.0, "maeA": 1.0, "maeB": 1.0, "nuoI": 1.0, "nuoM": 1.0, "nuoJ": 1.0, "nuoC": 1.0, "nuoB": 1.0, "nuoF": 1.0, "nuoN": 1.0, "nuoH": 1.0, "nuoK": 1.0, "nuoG": 1.0, "nuoE": 1.0, "nuoA": 1.0, "nuoL": 1.0, "pntA": 1.0, "sthA": 1.0, "pntB": 1.0, "amtB": 1.0, "aceE": 1.0, "aceF": 1.0, "pfkA": 1.0, "pfkB": 1.0, "tdcE": 1.0, "grcA": 1.0, "pflD": 1.0, "pflA": 1.0, "pflC": 1.0, "pflB": 1.0, "pgi": 1.0, "pgk": 1.0, "pgl": 1.0, "gpmM": 1.0, "ytjC": 1.0, "gpmA": 1.0, "pitA": 1.0, "pitB": 1.0, "ppc": 1.0, "pck": 1.0, "ppsA": 1.0, "pta": 1.0, "eutD": 1.0, "pykF": 1.0, "pykA": 1.0, "rpe": 1.0, "sgcE": 1.0, "rpiA": 1.0, "rpiB": 1.0, "sdhC": 1.0, "sdhD": 1.0, "sdhB": 1.0, "sdhA": 1.0, "sucD": 1.0, "sucC": 1.0, "talB": 1.0, "talA": 1.0, "tktB": 1.0, "tktA": 1.0, "tpiA": 1.0}, "gki_cost": {}}

e_coli_core_14bdo/ecc_14bdo_example_13.sdc

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+{"model_id": "e_coli_core", "sd_modules": [{"module_type": "optcouple", "constraints": [], "inner_objective": {"BIOMASS_Ecoli_core_w_GAM": 1.0}, "inner_opt_sense": "maximize", "outer_objective": null, "outer_opt_sense": null, "prod_id": {"EX_14bdo_e": 1.0}, "min_gcp": 0.3, "skip_checks": true, "reac_ids": ["PFK", "PFL", "PGI", "PGK", "PGL", "ACALD", "AKGt2r", "PGM", "PIt2r", "ALCD2x", "ACALDt", "ACKr", "PPC", "ACONTa", "ACONTb", "ATPM", "PPCK", "ACt2r", "PPS", "ADK1", "AKGDH", "ATPS4r", "PTAr", "PYK", "BIOMASS_Ecoli_core_w_GAM", "PYRt2", "CO2t", "RPE", "CS", "RPI", "SUCCt2_2", "CYTBD", "D_LACt2", "ENO", "SUCCt3", "ETOHt2r", "SUCDi", "SUCOAS", "TALA", "THD2", "TKT1", "TKT2", "TPI", "EX_ac_e", "EX_acald_e", "EX_akg_e", "EX_co2_e", "EX_etoh_e", "EX_for_e", "EX_fru_e", "EX_fum_e", "EX_glc__D_e", "EX_gln__L_e", "EX_glu__L_e", "EX_h_e", "EX_h2o_e", "EX_lac__D_e", "EX_mal__L_e", "EX_nh4_e", "EX_o2_e", "EX_pi_e", "EX_pyr_e", "EX_succ_e", "FBA", "FBP", "FORt2", "FORt", "FRD7", "FRUpts2", "FUM", "FUMt2_2", "G6PDH2r", "GAPD", "GLCpts", "GLNS", "GLNabc", "GLUDy", "GLUN", "GLUSy", "GLUt2r", "GND", "H2Ot", "ICDHyr", "ICL", "LDH_D", "MALS", "MALt2_2", "MDH", "ME1", "ME2", "NADH16", "NADTRHD", "NH4t", "O2t", "PDH", "SSCOARx", "HBD", "HBCT", "HBDH", "HBDx", "BDOtpp", "BDOtex", "EX_14bdo_e", "AKGDC"]}], "gene_kos": true, "use_scenario": false, "max_solutions": "1", "max_cost": "15", "time_limit": "inf", "advanced": true, "solver": "gurobi", "solution_approach": "best", "reg_cost": {}, "ko_cost": {"EX_o2_e": 1.0}, "ki_cost": {"SSCOARx": 1.0, "AKGDC": 1.0}, "gko_cost": {"adhE": 1.0, "mhpF": 1.0, "purT": 1.0, "tdcD": 1.0, "ackA": 1.0, "acnA": 1.0, "acnB": 1.0, "adk": 1.0, "lpd": 1.0, "sucB": 1.0, "sucA": 1.0, "kgtP": 1.0, "frmA": 1.0, "adhP": 1.0, "atpA": 1.0, "atpG": 1.0, "atpF": 1.0, "atpE": 1.0, "atpI": 1.0, "atpB": 1.0, "atpH": 1.0, "atpC": 1.0, "atpD": 1.0, "gltA": 1.0, "cydA": 1.0, "cydB": 1.0, "cbdB": 1.0, "cbdA": 1.0, "lldP": 1.0, "glcA": 1.0, "eno": 1.0, "fbaA": 1.0, "ydjI": 1.0, "fbaB": 1.0, "glpX": 1.0, "fbp": 1.0, "focB": 1.0, "focA": 1.0, "frdC": 1.0, "frdA": 1.0, "frdB": 1.0, "frdD": 1.0, "manZ": 1.0, "manX": 1.0, "ptsI": 1.0, "ptsH": 1.0, "manY": 1.0, "fumC": 1.0, "fumB": 1.0, "fumA": 1.0, "dctA": 1.0, "zwf": 1.0, "gapA": 1.0, "ptsG": 1.0, "crr": 1.0, "malX": 1.0, "puuA": 1.0, "glnA": 1.0, "glnQ": 1.0, "glnH": 1.0, "glnP": 1.0, "gdhA": 1.0, "glsB": 1.0, "glsA": 1.0, "pabB": 1.0, "gltD": 1.0, "gltB": 1.0, "gltP": 1.0, "gnd": 1.0, "aqpZ": 1.0, "icd": 1.0, "aceA": 1.0, "ldhA": 1.0, "dld": 1.0, "aceB": 1.0, "glcB": 1.0, "mdh": 1.0, "maeA": 1.0, "maeB": 1.0, "nuoI": 1.0, "nuoM": 1.0, "nuoJ": 1.0, "nuoC": 1.0, "nuoB": 1.0, "nuoF": 1.0, "nuoN": 1.0, "nuoH": 1.0, "nuoK": 1.0, "nuoG": 1.0, "nuoE": 1.0, "nuoA": 1.0, "nuoL": 1.0, "pntA": 1.0, "sthA": 1.0, "pntB": 1.0, "amtB": 1.0, "aceE": 1.0, "aceF": 1.0, "pfkA": 1.0, "pfkB": 1.0, "tdcE": 1.0, "grcA": 1.0, "pflD": 1.0, "pflA": 1.0, "pflC": 1.0, "pflB": 1.0, "pgi": 1.0, "pgk": 1.0, "pgl": 1.0, "gpmM": 1.0, "ytjC": 1.0, "gpmA": 1.0, "pitA": 1.0, "pitB": 1.0, "ppc": 1.0, "pck": 1.0, "ppsA": 1.0, "pta": 1.0, "eutD": 1.0, "pykF": 1.0, "pykA": 1.0, "rpe": 1.0, "sgcE": 1.0, "rpiA": 1.0, "rpiB": 1.0, "sdhC": 1.0, "sdhD": 1.0, "sdhB": 1.0, "sdhA": 1.0, "sucD": 1.0, "sucC": 1.0, "talB": 1.0, "talA": 1.0, "tktB": 1.0, "tktA": 1.0, "tpiA": 1.0}, "gki_cost": {}}

e_coli_core_14bdo/ecc_14bdo_example_1a.sdc

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+{"model_id": "e_coli_core", "sd_modules": [{"module_type": "protect", "inner_objective": null, "inner_opt_sense": "maximize", "constraints": [[{"BIOMASS_Ecoli_core_w_GAM": 1.0}, ">=", 0.2]], "skip_checks": null, "outer_opt_sense": null, "prod_id": null, "min_gcp": null, "outer_objective": null}, {"module_type": "suppress", "inner_objective": null, "inner_opt_sense": "maximize", "constraints": [[{"EX_14bdo_e": 1.0, "EX_glc__D_e": 0.3}, "<=", 0.0]], "skip_checks": null, "outer_opt_sense": null, "prod_id": null, "min_gcp": null, "outer_objective": null}], "gene_kos": false, "use_scenario": false, "max_solutions": "1", "max_cost": "30", "time_limit": "300", "advanced": false, "solver": "gurobi", "solution_approach": "any"}

e_coli_core_14bdo/ecc_14bdo_example_1b.sdc

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+{"model_id": "e_coli_core", "sd_modules": [{"module_type": "protect", "inner_objective": null, "inner_opt_sense": "maximize", "constraints": [[{"BIOMASS_Ecoli_core_w_GAM": 1.0}, ">=", 0.2]], "skip_checks": null, "outer_opt_sense": null, "prod_id": null, "min_gcp": null, "outer_objective": null}, {"module_type": "suppress", "inner_objective": null, "inner_opt_sense": "maximize", "constraints": [[{"EX_14bdo_e": 1.0, "EX_glc__D_e": 0.3}, "<=", 0.0]], "skip_checks": null, "outer_opt_sense": null, "prod_id": null, "min_gcp": null, "outer_objective": null}], "gene_kos": true, "use_scenario": false, "max_solutions": "1", "max_cost": "30", "time_limit": "300", "advanced": false, "solver": "gurobi", "solution_approach": "any"}

e_coli_core_14bdo/ecc_14bdo_example_1c.sdc

@@ -0,0 +1 @@
+{"model_id": "e_coli_core", "sd_modules": [{"module_type": "suppress", "inner_objective": null, "inner_opt_sense": "maximize", "constraints": [[{"EX_14bdo_e": 1.0, "EX_glc__D_e": 0.05}, "<=", 0.0]], "min_gcp": null, "prod_id": null, "outer_objective": null, "skip_checks": null, "outer_opt_sense": null}, {"module_type": "protect", "inner_objective": null, "inner_opt_sense": "maximize", "constraints": [[{"BIOMASS_Ecoli_core_w_GAM": 1.0}, ">=", 0.02]], "min_gcp": null, "prod_id": null, "outer_objective": null, "skip_checks": null, "outer_opt_sense": null}], "gene_kos": true, "use_scenario": false, "max_solutions": "20", "max_cost": "9", "time_limit": "inf", "advanced": true, "solver": "cplex", "solution_approach": "populate", "reg_cost": {"-EX_o2_e <= 1": 1.0}, "ko_cost": {"EX_o2_e": 1.0}, "ki_cost": {"SSCOARx": 5.0, "AKGDC": 1.0}, "gko_cost": {"adhE": 1.0, "mhpF": 1.0, "purT": 1.0, "tdcD": 1.0, "ackA": 1.0, "acnA": 1.0, "acnB": 1.0, "adk": 1.0, "lpd": 1.0, "sucB": 1.0, "sucA": 1.0, "kgtP": 1.0, "frmA": 1.0, "adhP": 1.0, "atpA": 1.0, "atpG": 1.0, "atpF": 1.0, "atpE": 1.0, "atpI": 1.0, "atpB": 1.0, "atpH": 1.0, "atpC": 1.0, "atpD": 1.0, "gltA": 1.0, "cydA": 1.0, "cydB": 1.0, "cbdB": 1.0, "cbdA": 1.0, "lldP": 1.0, "glcA": 1.0, "eno": 1.0, "fbaA": 1.0, "ydjI": 1.0, "fbaB": 1.0, "glpX": 1.0, "fbp": 1.0, "focB": 1.0, "focA": 1.0, "frdC": 1.0, "frdA": 1.0, "frdB": 1.0, "frdD": 1.0, "manZ": 1.0, "manX": 1.0, "ptsI": 1.0, "ptsH": 1.0, "manY": 1.0, "fumC": 1.0, "fumB": 1.0, "fumA": 1.0, "dctA": 1.0, "zwf": 1.0, "gapA": 1.0, "ptsG": 1.0, "crr": 1.0, "malX": 1.0, "puuA": 1.0, "glnA": 1.0, "glnQ": 1.0, "glnH": 1.0, "glnP": 1.0, "gdhA": 1.0, "glsB": 1.0, "glsA": 1.0, "pabB": 1.0, "gltD": 1.0, "gltB": 1.0, "gltP": 1.0, "gnd": 1.0, "aqpZ": 1.0, "icd": 1.0, "aceA": 1.0, "ldhA": 1.0, "dld": 1.0, "aceB": 1.0, "glcB": 1.0, "mdh": 1.0, "maeA": 1.0, "maeB": 1.0, "nuoI": 1.0, "nuoM": 1.0, "nuoJ": 1.0, "nuoC": 1.0, "nuoB": 1.0, "nuoF": 1.0, "nuoN": 1.0, "nuoH": 1.0, "nuoK": 1.0, "nuoG": 1.0, "nuoE": 1.0, "nuoA": 1.0, "nuoL": 1.0, "pntA": 1.0, "sthA": 1.0, "pntB": 1.0, "amtB": 1.0, "aceE": 1.0, "aceF": 1.0, "pfkA": 1.0, "pfkB": 1.0, "tdcE": 1.0, "grcA": 1.0, "pflD": 1.0, "pflA": 1.0, "pflC": 1.0, "pflB": 1.0, "pgi": 1.0, "pgk": 1.0, "pgl": 1.0, "gpmM": 1.0, "ytjC": 1.0, "gpmA": 1.0, "pitA": 1.0, "pitB": 1.0, "ppc": 1.0, "pck": 1.0, "ppsA": 1.0, "pta": 1.0, "eutD": 1.0, "pykF": 1.0, "pykA": 1.0, "rpe": 1.0, "sgcE": 1.0, "rpiA": 1.0, "rpiB": 1.0, "sdhC": 1.0, "sdhD": 1.0, "sdhB": 1.0, "sdhA": 1.0, "sucD": 1.0, "sucC": 1.0, "talB": 1.0, "talA": 1.0, "tktB": 1.0, "tktA": 1.0, "tpiA": 1.0}, "gki_cost": {}}