Module Expr Str ImportFrom alias ImportFrom alias Expr Call NameLoad Expr Call NameLoad NameLoad Str Str Expr Call NameLoad NameLoad Str Str Assign NameStore Num Assign NameStore Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Assign NameStore BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Call NameLoad keyword NameLoad Assign NameStore BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Assign NameStore Call NameLoad keyword NameLoad Expr Call NameLoad NameLoad CompareNotEq BinOpAdd NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad NameLoad BinOpRShift NameLoad BinOpAdd NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Assign NameStore BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore BinOpMod Str AttributeLoad NameLoad attr Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Call NameLoad keyword NameLoad Assign NameStore BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Assign NameStore Call NameLoad keyword NameLoad Expr Call NameLoad NameLoad CompareNotEq BinOpAdd NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad NameLoad BinOpRShift NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Expr Str Assign NameStore BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Call NameLoad keyword NameLoad Assign NameStore BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Expr Call NameLoad NameLoad CompareNotEq BinOpAdd NameLoad NameLoad NameLoad NameLoad NameLoad decorator_list Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str NameLoad Expr Call NameLoad Str NameLoad Expr Call NameLoad Str CompareNotEq Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad NameLoad NameLoad Expr Call NameLoad Str BinOpDiv Num NameLoad Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str BinOpMult BinOpDiv Num NameLoad Num Expr Call NameLoad Str Num Expr Call NameLoad Str CompareNotEq BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad NameLoad NameLoad Expr Call NameLoad Str BinOpDiv Num NameLoad Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str BinOpMult BinOpDiv Num NameLoad Num Expr Call NameLoad Str Num Expr Call NameLoad Str CompareNotEq BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad NameLoad NameLoad Expr Call NameLoad Str BinOpDiv Num NameLoad Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str BinOpDiv Num NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str BinOpDiv Num NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str BinOpDiv Num NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str NameLoad Expr Call NameLoad Str NameLoad Expr Call NameLoad Str CompareNotEq Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str CompareNotEq BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str NameLoad Expr Call NameLoad Str NameLoad Expr Call NameLoad Str CompareNotEq Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad Str Call NameLoad keyword NameLoad Expr Call NameLoad Str Call NameLoad keyword NameLoad Expr Call NameLoad Str Call NameLoad keyword NameLoad Expr Call NameLoad Str Call NameLoad Expr Call NameLoad Str Call NameLoad Expr Call NameLoad Str Call NameLoad For NameStore AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str AttributeLoad NameLoad attr If CompareIsNot NameLoad NameLoad body Assign NameStore Dict For NameStore AttributeLoad NameLoad attr body If CompareIn NameLoad AttributeLoad NameLoad attr body Assign SubscriptStore NameLoad Index NameLoad SubscriptLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Index Num orelse Assign SubscriptStore NameLoad Index NameLoad NameLoad Expr Call NameLoad Call NameLoad NameLoad NameLoad If CompareEq NameLoad Str body Expr Call NameLoad NameLoad Str NameLoad Expr Call NameLoad Str
N/A N/A EARM 1.0 (extrinsic apoptosis reaction model)

Albeck JG, Burke JM, Spencer SL, Lauffenburger DA, Sorger PK, 2008
Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic
Cell Death. PLoS Biol 6(12): e299. doi:10.1371/journal.pbio.0060299

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0060299
 __future__ print_function pysb * N/A N/A Model N/A N/A Annotation model http://identifiers.org/biomodels.db/BIOMD0000000220 is N/A N/A Annotation model http://identifiers.org/doi/10.1371/journal.pbio.0060299 isDescribedBy N/A transloc 0.01 N/A v 0.07 N/A N/A Parameter L_0 3000 N/A N/A Parameter pR_0 200 N/A N/A Parameter flip_0 100.0 N/A N/A Parameter pC8_0 20000.0 N/A N/A Parameter BAR_0 1000.0 N/A N/A Parameter pC3_0 10000.0 N/A N/A Parameter pC6_0 10000.0 N/A N/A Parameter XIAP_0 100000.0 N/A N/A Parameter PARP_0 1000000.0 N/A N/A Parameter Bid_0 40000.0 N/A N/A Parameter Bcl2c_0 20000.0 N/A N/A Parameter Bax_0 100000.0 N/A N/A Parameter Bcl2_0 20000.0 N/A N/A Parameter Mito_0 500000.0 N/A N/A Parameter mCytoC_0 500000.0 N/A N/A Parameter mSmac_0 100000.0 N/A N/A Parameter pC9_0 100000.0 N/A N/A Parameter Apaf_0 100000.0 N/A N/A Monomer L N/A b N/A N/A Monomer pR N/A b N/A N/A Monomer DISC N/A b N/A N/A Monomer flip N/A b N/A N/A Monomer pC8 N/A b N/A N/A Monomer C8 N/A b N/A N/A Monomer BAR N/A b N/A N/A Monomer pC3 N/A b N/A N/A Monomer C3 N/A b N/A N/A Monomer pC6 N/A b N/A N/A Monomer C6 N/A b N/A N/A Monomer XIAP N/A b N/A N/A Monomer C3_U N/A b N/A N/A Monomer PARP N/A b N/A N/A Monomer CPARP N/A b N/A N/A Monomer Bid N/A b N/A N/A Monomer tBid N/A b N/A N/A Monomer Bcl2c N/A b N/A N/A Monomer Bax N/A b N/A N/A Monomer aBax N/A b N/A N/A Monomer MBax N/A b N/A N/A Monomer Bcl2 N/A b N/A N/A Monomer Bax2 N/A b N/A N/A Monomer Bax4 N/A b N/A N/A Monomer Mito N/A b N/A N/A Monomer AMito N/A b N/A N/A Monomer mCytoC N/A b N/A N/A Monomer ACytoC N/A b N/A N/A Monomer mSmac N/A b N/A N/A Monomer ASmac N/A b N/A N/A Monomer cCytoC N/A b N/A N/A Monomer Apaf N/A b N/A N/A Monomer aApaf N/A b N/A N/A Monomer pC9 N/A b N/A N/A Monomer Apop N/A b N/A N/A Monomer cSmac N/A b catalyze N/A N/A enz sub prod kf kr kc N/A N/A N/A 2-step catalytic process N/A r1_name N/A bind_%s_%s N/A N/A sub name N/A enz name N/A r2_name N/A produce_%s_via_%s N/A N/A prod name N/A enz name N/A E N/A enz b None N/A S N/A sub b None N/A ES N/A N/A enz b 1 N/A sub b 1 N/A P N/A prod b None N/A N/A Rule r1_name N/A N/A E S ES kf kr N/A N/A Rule r2_name N/A ES N/A E P kc N/A catalyze_convert N/A N/A s1 s2 p kf kr kc N/A N/A N/A 2-step catalytic-type process, but the "catalyst" is effectively consumed N/A r1_name N/A bind_%s_%s N/A N/A s1 name N/A s2 name N/A r2_name N/A produce_%s N/A p name N/A A N/A s1 b None N/A B N/A s2 b None N/A AB N/A N/A s1 b 1 N/A s2 b 1 N/A C N/A p b None N/A N/A Rule r1_name N/A N/A A B AB kf kr N/A N/A Rule r2_name N/A AB C kc N/A inhibit N/A N/A targ inh kf kr N/A N/A N/A inhibition by complexation/sequestration N/A r_name N/A inhibit_%s_by_%s N/A N/A targ name N/A inh name N/A T N/A targ b None N/A I N/A inh b None N/A TI N/A N/A targ b 1 N/A inh b 1 N/A N/A Rule r_name N/A N/A T I TI kf kr N/A N/A N/A Parameter kf1 4e-07 N/A N/A Parameter kr1 0.001 N/A N/A Parameter kc1 1e-05 N/A N/A catalyze_convert L pR DISC kf1 kr1 kc1 N/A N/A Parameter kf2 1e-06 N/A N/A Parameter kr2 0.001 N/A N/A inhibit DISC flip kf2 kr2 N/A N/A Parameter kf3 1e-06 N/A N/A Parameter kr3 0.001 N/A N/A Parameter kc3 1.0 N/A N/A catalyze DISC pC8 C8 kf3 kr3 kc3 N/A N/A Parameter kf4 1e-06 N/A N/A Parameter kr4 0.001 N/A N/A inhibit BAR C8 kf4 kr4 N/A N/A Parameter kf5 1e-07 N/A N/A Parameter kr5 0.001 N/A N/A Parameter kc5 1.0 N/A N/A catalyze C8 pC3 C3 kf5 kr5 kc5 N/A N/A Parameter kf6 1e-06 N/A N/A Parameter kr6 0.001 N/A N/A Parameter kc6 1.0 N/A N/A catalyze C3 pC6 C6 kf6 kr6 kc6 N/A N/A Parameter kf7 3e-08 N/A N/A Parameter kr7 0.001 N/A N/A Parameter kc7 1.0 N/A N/A catalyze C6 pC8 C8 kf7 kr7 kc7 N/A N/A Parameter kf8 2e-06 N/A N/A Parameter kr8 0.001 N/A N/A Parameter kc8 0.1 N/A N/A catalyze XIAP C3 C3_U kf8 kr8 kc8 N/A N/A Parameter kf9 1e-06 N/A N/A Parameter kr9 0.01 N/A N/A Parameter kc9 1.0 N/A N/A catalyze C3 PARP CPARP kf9 kr9 kc9 N/A N/A Parameter kf10 1e-07 N/A N/A Parameter kr10 0.001 N/A N/A Parameter kc10 1.0 N/A N/A catalyze C8 Bid tBid kf10 kr10 kc10 N/A N/A Parameter kf11 1e-06 N/A N/A Parameter kr11 0.001 N/A N/A inhibit tBid Bcl2c kf11 kr11 N/A N/A Parameter kf12 1e-07 N/A N/A Parameter kr12 0.001 N/A N/A Parameter kc12 1.0 N/A N/A catalyze tBid Bax aBax kf12 kr12 kc12 N/A N/A Parameter kf13 transloc N/A N/A Parameter kr13 transloc N/A N/A Rule transloc_MBax_aBax N/A N/A aBax b None N/A MBax b None kf13 kr13 N/A N/A Parameter kf14 N/A 1e-06 v N/A N/A Parameter kr14 0.001 N/A N/A inhibit MBax Bcl2 kf14 kr14 N/A N/A Parameter kf15 N/A N/A 1e-06 v 2 N/A N/A Parameter kr15 0.001 N/A N/A Rule dimerize_MBax_to_Bax2 N/A N/A N/A MBax b None N/A MBax b None N/A Bax2 b None kf15 kr15 N/A N/A Parameter kf16 N/A 1e-06 v N/A N/A Parameter kr16 0.001 N/A N/A inhibit Bax2 Bcl2 kf16 kr16 N/A N/A Parameter kf17 N/A N/A 1e-06 v 2 N/A N/A Parameter kr17 0.001 N/A N/A Rule dimerize_Bax2_to_Bax4 N/A N/A N/A Bax2 b None N/A Bax2 b None N/A Bax4 b None kf17 kr17 N/A N/A Parameter kf18 N/A 1e-06 v N/A N/A Parameter kr18 0.001 N/A N/A inhibit Bax4 Bcl2 kf18 kr18 N/A N/A Parameter kf19 N/A 1e-06 v N/A N/A Parameter kr19 0.001 N/A N/A Parameter kc19 1.0 N/A N/A catalyze_convert Bax4 Mito AMito kf19 kr19 kc19 N/A N/A Parameter kf20 N/A 2e-06 v N/A N/A Parameter kr20 0.001 N/A N/A Parameter kc20 10.0 N/A N/A catalyze AMito mCytoC ACytoC kf20 kr20 kc20 N/A N/A Parameter kf21 N/A 2e-06 v N/A N/A Parameter kr21 0.001 N/A N/A Parameter kc21 10.0 N/A N/A catalyze AMito mSmac ASmac kf21 kr21 kc21 N/A N/A Parameter kf22 transloc N/A N/A Parameter kr22 transloc N/A N/A Rule transloc_cCytoC_ACytoC N/A N/A ACytoC b None N/A cCytoC b None kf22 kr22 N/A N/A Parameter kf23 5e-07 N/A N/A Parameter kr23 0.001 N/A N/A Parameter kc23 1.0 N/A N/A catalyze cCytoC Apaf aApaf kf23 kr23 kc23 N/A N/A Parameter kf24 5e-08 N/A N/A Parameter kr24 0.001 N/A N/A Rule bind_aApaf_pC9_as_Apop N/A N/A N/A aApaf b None N/A pC9 b None N/A Apop b None kf24 kr24 N/A N/A Parameter kf25 5e-09 N/A N/A Parameter kr25 0.001 N/A N/A Parameter kc25 1.0 N/A N/A catalyze Apop pC3 C3 kf25 kr25 kc25 N/A N/A Parameter kf26 transloc N/A N/A Parameter kr26 transloc N/A N/A Rule transloc_cSmac_ASmac N/A N/A ASmac b None N/A cSmac b None kf26 kr26 N/A N/A Parameter kf27 2e-06 N/A N/A Parameter kr27 0.001 N/A N/A inhibit Apop XIAP kf27 kr27 N/A N/A Parameter kf28 7e-06 N/A N/A Parameter kr28 0.001 N/A N/A inhibit cSmac XIAP kf28 kr28 N/A N/A Observable Bid_unbound N/A Bid b None N/A N/A Observable PARP_unbound N/A PARP b None N/A N/A Observable mSmac_unbound N/A mSmac b None N/A N/A Observable tBid_total N/A tBid N/A N/A Observable CPARP_total N/A CPARP N/A N/A Observable cSmac_total N/A cSmac N/A m N/A model monomers N/A N/A ic_param N/A N/A N/A model parameters get N/A %s_0 N/A m name N/A N/A ic_param None N/A N/A sites N/A N/A s N/A m sites N/A N/A N/A s N/A m site_states N/A N/A N/A sites N/A s N/A N/A N/A m site_states N/A s N/A 0 N/A N/A N/A sites N/A s None N/A N/A Initial N/A m sites ic_param N/A N/A __name__ __main__ N/A N/A N/A print __doc__ model N/A N/A print 
NOTE: This model code is designed to be imported and programatically
manipulated, not executed directly. The above output is merely a
diagnostic aid. Please see run_earm_1_0.py for example usage.