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EARM_2_0_M1a.sbml
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EARM_2_0_M1a.sbml
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model name="Lopez2013_extrinsic_apoptosis_M1a_embedded">
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<rdf:li rdf:resource="http://identifiers.org/uniprot/Q16611" />
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q07817" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s53" metaid="metaid_s53" name="Bak(bf=1, s1=None, s2=None, state=A) ._br_Mcl1(bf=1, state=M)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s53">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q16611" />
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q07820" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s54" metaid="metaid_s54" name="Bax(bf=None, s1=1, s2=None, state=A) ._br_Bax(bf=None, s1=None, s2=1, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s54">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q07812" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s55" metaid="metaid_s55" name="Bak(bf=None, s1=1, s2=None, state=A) ._br_Bak(bf=None, s1=None, s2=1, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s55">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q16611" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s56" metaid="metaid_s56" name="Bax(bf=None, s1=1, s2=2, state=A) ._br_Bax(bf=None, s1=2, s2=3, state=A) ._br_Bax(bf=None, s1=3, s2=1, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s56">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q07812" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s57" metaid="metaid_s57" name="Bak(bf=None, s1=1, s2=2, state=A) ._br_Bak(bf=None, s1=2, s2=3, state=A) ._br_Bak(bf=None, s1=3, s2=1, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s57">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q16611" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s58" metaid="metaid_s58" name="Bax(bf=None, s1=1, s2=2, state=A) ._br_Bax(bf=None, s1=2, s2=3, state=A) ._br_Bax(bf=None, s1=3, s2=4, state=A) ._br_Bax(bf=None, s1=4, s2=1, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s58">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q07812" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s59" metaid="metaid_s59" name="Bak(bf=None, s1=1, s2=2, state=A) ._br_Bak(bf=None, s1=2, s2=3, state=A) ._br_Bak(bf=None, s1=3, s2=4, state=A) ._br_Bak(bf=None, s1=4, s2=1, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s59">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q16611" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s60" metaid="metaid_s60" name="Bax(bf=1, s1=2, s2=3, state=A) ._br_Bax(bf=None, s1=3, s2=4, state=A) ._br_Bax(bf=None, s1=4, s2=5, state=A) ._br_Bax(bf=None, s1=5, s2=2, state=A) ._br_CytoC(bf=1, state=M)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s60">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P99999" />
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q07812" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s61" metaid="metaid_s61" name="Bax(bf=1, s1=2, s2=3, state=A) ._br_Bax(bf=None, s1=3, s2=4, state=A) ._br_Bax(bf=None, s1=4, s2=5, state=A) ._br_Bax(bf=None, s1=5, s2=2, state=A) ._br_Smac(bf=1, state=M)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s61">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q07812" />
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q9NR28" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s62" metaid="metaid_s62" name="Bak(bf=1, s1=2, s2=3, state=A) ._br_Bak(bf=None, s1=3, s2=4, state=A) ._br_Bak(bf=None, s1=4, s2=5, state=A) ._br_Bak(bf=None, s1=5, s2=2, state=A) ._br_CytoC(bf=1, state=M)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s62">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q16611" />
<rdf:li rdf:resource="http://identifiers.org/uniprot/P99999" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s63" metaid="metaid_s63" name="Bak(bf=1, s1=2, s2=3, state=A) ._br_Bak(bf=None, s1=3, s2=4, state=A) ._br_Bak(bf=None, s1=4, s2=5, state=A) ._br_Bak(bf=None, s1=5, s2=2, state=A) ._br_Smac(bf=1, state=M)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s63">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q16611" />
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q9NR28" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s64" metaid="metaid_s64" name="CytoC(bf=None, state=C)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s64">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P99999" />
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s65" metaid="metaid_s65" name="Smac(bf=None, state=C)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s65">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q9NR28" />
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s66" metaid="metaid_s66" name="Smac(bf=None, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s66">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q9NR28" />
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s67" metaid="metaid_s67" name="CytoC(bf=None, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s67">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P99999" />
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s68" metaid="metaid_s68" name="Apaf(bf=1, state=I) ._br_CytoC(bf=1, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s68">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/O14727" />
<rdf:li rdf:resource="http://identifiers.org/uniprot/P99999" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s69" metaid="metaid_s69" name="Smac(bf=1, state=A) ._br_XIAP(bf=1)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s69">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P98170" />
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q9NR28" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s70" metaid="metaid_s70" name="Apaf(bf=None, state=A)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s70">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/O14727" />
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s71" metaid="metaid_s71" name="Apop(bf=None)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s71">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0043293" />
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s72" metaid="metaid_s72" name="Apop(bf=1) ._br_C3(bf=1, state=pro)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s72">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P42574" />
<rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0043293" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species id="s73" metaid="metaid_s73" name="Apop(bf=1) ._br_XIAP(bf=1)" compartment="default" initialAmount="0">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_s73">
<bqbiol:hasPart>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P98170" />
<rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0043293" />
</rdf:Bag>
</bqbiol:hasPart>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
<listOfParameters>
<parameter id="bind_L_R_to_LR_kf" metaid="metaid_bind_L_R_to_LR_kf" name="bind_L_R_to_LR_kf" value="3.9999999999999998e-07"/>
<parameter id="bind_L_R_to_LR_kr" metaid="metaid_bind_L_R_to_LR_kr" name="bind_L_R_to_LR_kr" value="0.001"/>