APPENDIX II.

PARAMETERS IN THE REVISED MODEL

Parameters for entities:

Name Variable Initial concentration

c-FLIPl m9 0.293669
DISCbs:FLIPl m19 0
DISCbs:FLIPl:pro8 m42 0
DISCbs:pro8 m7 0
DISCbs:pro8:pro8 m6 0
BID m11 1.046746
FADD m4 1.343079
BID C terminal in mitochondrion m14 0
BID C terminal m13 0
caspase-8 m8 0
cytochrome c in mitochondrion m15 0
Fas ligand trimer m2 9
DISCbs:p43/p41 m41 0
FasL:Fas m3 0
DISCbs m40 0
p43/p41 m43 0
blocked DISCbs m44 0
c-FLIPs m45 0.293669
procaspase-8 m5 2
apoptosome m22 0
caspase-3 m27 0
procaspase-9 m21 1.107
caspase-9 m23 0
procaspase-3 m25 0.5079
Apaf1:CyC m20 0
cytochrome c m16 0
Apaf1:dATP m17 4.13
Fas trimer m48 2
procaspase-6 m24 0.08488
caspase-6 m49 0
cPARP m10 0
PARP m12 1.050411
Parameters for transitions:

Name reaction rate

n58 m2*m48*0.017748
n87 m13 *0.012970
p1 and
n112 m14 *0.012970
n77 m4 *0.012970
p3 and
p4 and
n111 m15/10
p5 m6*0.913561
n43 (2.14041*m8*m11)/(18.12865+m11)
n75 m2 *0.012970
n83 m11 *0.012970
n109 m14 / 10
n44 m13*0.05
p6 and
n110 m15 *0.012970
p9 and
n76 m5 *0.012970
n90 m16 *0.012970
n59 and
n100 m25 *0.012970
n93 m20 *0.012970
n73 m23 *0.012970
n45 and
n94 m22 *0.012970
n96 m21 *0.012970
n46 and
n72 m27 *0.012970
n69 (12.794051*m27*m12)/(25.273+m12)
n47 and
n49 and
n114 m17*0.012970
p13 and
p14 and
n66 and
p11 and
p8 and
p7 and
p10 and
p2 and
n79 m48 *0.012970
n81 m3 *0.012970
n82 m40 *0.012970
n63 m19 *0.012970
n84 m9 *0.012970
n85 m45 *0.012970
n86 m7 *0.012970
n88 m42 *0.012970
n74 m6 *0.012970
n95 m41 *0.012970
n97 m44 *0.012970
n98 m43 *0.012970
n99 m24 *0.012970
n104 m49 *0.012970
n61 m8 * 0.012970
p30 and
p31 m12 *0.012970
p32 m10 *0.01448
p33 and

Parameters for arcs:

Name Kinetic Script threshold

c75 (0.03*m8*m5)/(30+m5)/2 0
c77 0 0
c76 (0.03*m8*m5)/(30+m5) 0
c74 c74 0
c73 c73 0
c69 3.5*m22*0.0016087 0
c70 m22*0.0016087 0
c68 m22*0.0016087 0
c67 c67 0
c37 c37 0
c66 c66 0
c65 c65 0
c64 c64 0
c63 c63 0
c58 c58 0
c59 c59 0
c57 c57 0
c62 c62 0
c61 c61 0
c60 c60 0
c56 c56 0
c55 c55 0
c50 c50 0
c19 m40*pow(m9,3)*2.083467 0
c21 m40*pow(m9,3)*2.083467 0
c18 m40*pow(m9,3)*2.083467*3 0
c31 m40*pow(m45,3)*2.083467 0
c30 m40*pow(m45,3)*2.083467 0
c29 m40*pow(m45,3)*2.083467*3 0
c22 pow(m5,3)*m19*8.223242 0
c53 3*pow(m5,3)*m19*8.223242 0
c20 pow(m5,3)*m19*8.223242 0
c25 m7*pow(m9,3)*2.083467 0
c24 m7*pow(m9,3)*2.083467 0
c23 m7*pow(m9,3)*2.083467*3 0
c34 m7*pow(m45,3)*2.083467 0
c33 m7*pow(m45,3)*2.083467 0
c32 m7*pow(m45,3)*2.083467*3 0
c44 (1.5*m23*m21)/(8+m21)/2 0
c49 (1.5*m23*m21)/(8+m21) 0
c51 0 0
c42 (0.1*m49*m5)/(0.1+m5)/2 0
c43 (0.1*m49*m5)/(0.1+m5) 0
c46 0 0
c41 (0.07012*m27*m24)/(0.251+m24)/2 0
c40 (0.07012*m27*m24)/(0.251+m24) 0
c39 0 0
a123 a123 0
c47 (1.012*m23*m25)/(0.4021+m25)/2 0
a26 0 0
a25 (1.012*m23*m25)/(0.4021+m25) 0
a22 3.5*(0.2144*m27*m22)/(0.251+m22) 0
c38 (0.2144*m27*m22)/(0.251+m22) 0
a21 (0.2144*m27*m22)/(0.251+m22) 0
c52 0 0
c72 c72 0
a71 a71 0
c71 c71 0
a77 a77 0
a20 m20*pow(m21,7)*0.02043 0
a19 m20*pow(m21,7)*0.02043 0
a18 m20*pow(m21,7)*0.02043*7 0
a101 a101 0
a99 a99 0
a17 pow(m16*m17,7)*0.213 0
c15 pow(m16*m17,7)*0.213*7 0
a15 pow(m16*m17,7)*0.213*7 0
a78 a78 0
a98 a98 0
a105 a105 0
c54 (1.90358*m8*m25)/(0.4021+m25)/2 0
a47 (1.90358*m8*m25)/(0.4021+m25) 0
a46 0 0
a95 a95 0
a81 a81 0
c27 0.01113*m42*3 0
c28 0.01113*m42 0
c26 0.01113*m42 0
a116 a116 0
c14 m41*4.70967 0
c13 m41*4.70967*3 0
c12 m41*4.70967 0
a14 a14 0
a13 a13 0
a115 a115 0
a114 a114 0
a88 a88 0
a80 a80 0
c45 c45 0
a11 a11 0
a10 a10 0
c11 c11 0
c10 c10 0
a118 a118 0
a117 a117 0
c9 pow(m5,3)*m7*8.223242 0
c8 pow(m5,3)*m7*8.223242*3 0
c7 pow(m5,3)*m7*8.223242 0
c6 pow(m5,3)*m40*0.028354 0
c5 pow(m5,3)*m40*0.028354*3 0
c4 pow(m5,3)*m40*0.028354 0
a82 a82 0
a119 a119 0
c2 m3*pow(m4,3)*9.2913466 0
c3 3*m3*pow(m4,3)*9.2913466 0
c1 m3*pow(m4,3)*9.2913466 0
a92 a92 0
a45 a45 0
a44 a44 0
c36 c36 0
Overview of the model structure