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earm_example.csv
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model components
L, 3000
R, 200
DISC, 0
C8A, 0
C8pro, 20000
C6A, 0
C6pro, 10000
BidU, 40000
BidT, 0
BidM, 0
flip, 100
BAR, 1000
SmacM, 100000
SmacC, 0
SmacA, 0
CytoCM, 500000
CytoCC, 0
CytoCA, 0
ApafI, 100000
ApafA, 0
C9, 100000
Apop, 0
C3A, 0
C3pro, 10000
C3ub, 0
XIAP, 100000
PARPU, 1000000
PARPC, 0
BaxC, 80000
BaxM, 0
BaxA, 0
BclxLC, 20000
BclxLM, 0
BakM, 20000
BakA, 0
Bcl2, 20000
Mcl1, 20000
Bad, 1000
Noxa, 0
required reactions
dimerization, L()[subunit_a], R()[subunit_b], DISC()[dimer], 4.8610717169040878e-09, 6.9984651157346155e-05, 0.0001004038401598357
catalysis, DISC()[catalyzer], C8pro()[substrate], C8A()[product], 1.652610985853028e-06, 0.00025515949741149136, 8.1035483807450976
catalysis, C8A()[catalyzer], BidU()[substrate], BidT()[product], 7.8693418477379699e-06, 1.3478527255190856e-05, 0.20070834648071373
inhibition, flip()[inhibitor], DISC()[inh_target], 2.0857207094671021e-06, 0.072993081874092425
inhibition, BAR()[inhibitor], C8A()[inh_target], 2.450754439292685e-05, 3.176107099863868e-05
equilibration, SmacC()[equil_a], SmacA()[equil_b], 0.68667658617411753, 0.00077853445949019686
equilibration, CytoCC()[equil_a], CytoCA()[equil_b], 0.020412343795425145, 0.0025071607534728909
catalysis, CytoCA()[catalyzer], ApafI()[substrate], ApafA()[product], 4.5927585852137639e-07, 2.8999962220310582e-05, 0.040599717918061738
conversion, C9()[subunit_d], ApafA()[subunit_c], Apop()[complex], 3.213196857547145e-07, 0.011684477645560146
catalysis, Apop()[catalyzer], C3pro()[substrate], C3A()[product], 7.8037691005466737e-10, 0.00032802481823310378, 1.1684643810480766
inhibition, XIAP()[inhibitor], Apop()[inh_target], 2.0704535531682789e-08, 0.0013859740873431536
inhibition, SmacA()[inhibitor], XIAP()[inh_target], 0.00040944017917514478, 0.0080051134954001509
catalysis, C8A()[catalyzer], C3pro()[substrate], C3A()[product], 1.9167619114268919e-06, 0.00010186532359752733, 2.7002149431488567
catalysis, XIAP()[catalyzer], C3A()[substrate], C3ub()[product], 1.8247861512403385e-07, 1.2921875123372521e-05, 0.099504980631579837
catalysis, C3A()[catalyzer], PARPU()[substrate], PARPC()[product], 1.889526802914492e-06, 0.00011387916767652634, 13.768204206283402
catalysis, C3A()[catalyzer], C6pro()[substrate], C6A()[product], 2.1334646851306905e-08, 0.0015363069332776634, 13.054054125378238
catalysis, C6A()[catalyzer], C8pro()[substrate], C8A()[product], 5.0560841288642224e-08, 9.1977396575087457e-05, 0.18488607021092679
equilibration, BidT()[equil_a], BidM()[equil_b], 0.026956531627050594, 1.1783387334989619e-05
equilibration, BaxC()[equil_a], BaxM()[equil_b], 0.0003405873853519951, 0.049750332184525257
equilibration, BclxLC()[equil_a], BclxLM()[equil_b], 0.068400564450976198, 0.14118753123479355
catalysis, BidM()[catalyzer], BaxM()[substrate], BaxA()[product], 3.9736775946970058e-09, 0.021482642730885865, 1.8203763301683924
catalysis, BidM()[catalyzer], BakM()[substrate], BakA()[product], 1.9408461301064605e-09, 0.00018094808868168103, 0.011177441271776072
self_catalyze, BaxA()[self_catalyzer], BaxM()[self_substrate], 2.0149060250585873e-06, 0.040311275999739105, 0.012192887363178946
self_catalyze, BakA()[self_catalyzer], BakM()[self_substrate], 5.3939824626322183e-06, 0.002166628073982069, 0.26475473643878961
inhibition, Bcl2()[inhibitor], BidM()[inh_target], 1.0277423337470143e-06, 2.7905757973936867
inhibition, BclxLM()[inhibitor], BidM()[inh_target], 1.6367225985110056e-07, 0.026264964906836046
inhibition, Mcl1()[inhibitor], BidM()[inh_target], 1.9428423606297654e-06, 0.0021648330129469106
inhibition, Bcl2()[inhibitor], BaxA()[inh_target], 1.4531081303335626e-08, 0.071917529283017381
inhibition, BclxLM()[inhibitor], BaxA()[inh_target], 1.2086000195405126e-06, 0.019684909992630065
inhibition, BclxLM()[inhibitor], BakA()[inh_target], 6.2674545719585416e-06, 0.067298588389140615
inhibition, Mcl1()[inhibitor], BakA()[inh_target], 1.2661363465041514e-05, 0.0002157216265888175
inhibition, Bad()[inhibitor], Bcl2()[inh_target], 5.3931067181433528e-05, 0.44013378070735282
inhibition, Bad()[inhibitor], BclxLM()[inh_target], 4.1877529969310183e-05, 0.16263349657520218
inhibition, Noxa()[inhibitor], Mcl1()[inh_target], 6.1197384627538123e-07, 0.01966269798058537
pore_formation, BaxA()[pore], 0.0067429287574002307, 1.6822795105298417e-05, 0.00029378841202344446, 0.000144616, 0.000085651, 0.002585238
pore_formation, BakA()[pore], 1.6054164088484109e-05, 0.00023979936345611174, 5.7415804556553368e-06, 0.021389853, 1.509873703e-05, 1.538796535e-05
transport, BaxA()[pore], CytoCM()[cargo_M], CytoCC()[cargo_C], 0.000106028, 0.0013725161741816323, 727.3165367902302
transport, BaxA()[pore], SmacM()[cargo_M], SmacC()[cargo_C], 2.375382573e-06, 0.00036936772401878048, 83.182122265178961
transport, BakA()[pore], CytoCM()[cargo_M], CytoCC()[cargo_C], 0.354927953e-06, 0.051294040280582424, 1.0588991714689346
transport, BakA()[pore], SmacM()[cargo_M], SmacC()[cargo_C], 2.40631696e-05, 0.00061884308859702392, 16.739408086871173