#hoffmann2



#reactions
v1:
 {1.0}NFkB + {1.0}IkBalpha = {1.0}IkBalpha_NFkB
  cytoplasm * (a4 * IkBalpha * NFkB - d4 * IkBalpha_NFkB)
v10:
 {1.0}IkBalpha_NFkB = {1.0}NFkB
  cytoplasm * deg4 * IkBalpha_NFkB
v11:
 {1.0}IkBbeta_NFkB = {1.0}NFkB
  cytoplasm * deg4 * IkBbeta_NFkB
v12:
 {1.0}IkBeps_NFkB = {1.0}NFkB
  cytoplasm * deg4 * IkBeps_NFkB
v13:
 {1.0}NFkB = {1.0}NFkB_nuc
  cytoplasm * k1 * NFkB - nucleus * k01 * NFkB_nuc
v14:
 {1.0}NFkB_nuc + {1.0}IkBalpha_nuc = {1.0}IkBalpha_nuc_NFkB_nuc
  nucleus * (a4 * IkBalpha_nuc * NFkB_nuc - d4 * IkBalpha_nuc_NFkB_nuc)
v15:
 {1.0}NFkB_nuc + {1.0}IkBbeta_nuc = {1.0}IkBbeta_nuc_NFkB_nuc
  nucleus * (a5 * IkBbeta_nuc * NFkB_nuc - d5 * IkBbeta_nuc_NFkB_nuc)
v16:
 {1.0}NFkB_nuc + {1.0}IkBeps_nuc = {1.0}IkBeps_nuc_NFkB_nuc
  nucleus * (a6 * IkBeps_nuc * NFkB_nuc - d6 * IkBeps_nuc_NFkB_nuc)
v17:
 $pool = {1.0}IkBalpha_transcript
  nucleus * tr2a
v18:
 $pool = {1.0}IkBalpha_transcript
  nucleus * tr2 * pow(NFkB_nuc, 2)
v19:
 {1.0}IkBalpha_transcript = $pool
  nucleus * tr3 * IkBalpha_transcript
v2:
 {1.0}NFkB + {1.0}IkBbeta = {1.0}IkBbeta_NFkB
  cytoplasm * (a5 * IkBbeta * NFkB - d5 * IkBbeta_NFkB)
v20:
 $pool = {1.0}IkBbeta_transcript
  nucleus * tr2b
v21:
 {1.0}IkBbeta_transcript = $pool
  nucleus * tr3 * IkBbeta_transcript
v22:
 $pool = {1.0}IkBeps_transcript
  nucleus * tr2e
v23:
 {1.0}IkBeps_transcript = $pool
  nucleus * tr3 * IkBeps_transcript
v24:
 {1.0}IKK + {1.0}IkBalpha = {1.0}IKK_IkBalpha
  cytoplasm * (a1 * IkBalpha * IKK - d1 * IKK_IkBalpha)
v25:
 $pool = {1.0}IkBalpha
  nucleus * tr1 * IkBalpha_transcript
v26:
 {1.0}IkBalpha = $pool
  cytoplasm * deg1 * IkBalpha
v27:
 {1.0}IkBalpha = {1.0}IkBalpha_nuc
  cytoplasm * tp1 * IkBalpha - nucleus * tp2 * IkBalpha_nuc
v28:
 {1.0}IKK + {1.0}IkBbeta = {1.0}IKK_IkBbeta
  cytoplasm * (a2 * IkBbeta * IKK - d2 * IKK_IkBbeta)
v29:
 $pool = {1.0}IkBbeta
  nucleus * tr1 * IkBbeta_transcript
v3:
 {1.0}NFkB + {1.0}IkBeps = {1.0}IkBeps_NFkB
  cytoplasm * (a6 * IkBeps * NFkB - d6 * IkBeps_NFkB)
v30:
 {1.0}IkBbeta = $pool
  cytoplasm * deg1 * IkBbeta
v31:
 {1.0}IkBbeta = {1.0}IkBbeta_nuc
  cytoplasm * 0.5 * tp1 * IkBbeta - nucleus * 0.5 * tp2 * IkBbeta_nuc
v32:
 {1.0}IKK + {1.0}IkBeps = {1.0}IKK_IkBeps
  cytoplasm * (a3 * IkBeps * IKK - d3 * IKK_IkBeps)
v33:
 $pool = {1.0}IkBeps
  nucleus * tr1 * IkBeps_transcript
v34:
 {1.0}IkBeps = $pool
  cytoplasm * deg1 * IkBeps
v35:
 {1.0}IkBeps = {1.0}IkBeps_nuc
  cytoplasm * 0.5 * tp1 * IkBeps - nucleus * 0.5 * tp2 * IkBeps_nuc
v36:
 {1.0}IKK + {1.0}IkBalpha_NFkB = {1.0}IKK_IkBalpha_NFkB
  cytoplasm * (a7 * IKK * IkBalpha_NFkB - d1 * IKK_IkBalpha_NFkB)
v37:
 {1.0}IkBalpha_nuc_NFkB_nuc = {1.0}IkBalpha_NFkB
  nucleus * k2 * IkBalpha_nuc_NFkB_nuc
v38:
 {1.0}IKK + {1.0}IkBbeta_NFkB = {1.0}IKK_IkBbeta_NFkB
  cytoplasm * (a8 * IKK * IkBbeta_NFkB - d2 * IKK_IkBbeta_NFkB)
v39:
 {1.0}IkBbeta_nuc_NFkB_nuc = {1.0}IkBbeta_NFkB
  nucleus * k2_IkBbeta_nuc_NFkB_nuc * (fr_after_trigger + flag_for_after_trigger) * IkBbeta_nuc_NFkB_nuc
v4:
 {1.0}NFkB + {1.0}IKK_IkBalpha = {1.0}IKK_IkBalpha_NFkB
  cytoplasm * (a4 * IKK_IkBalpha * NFkB - d4 * IKK_IkBalpha_NFkB)
v40:
 {1.0}IKK + {1.0}IkBeps_NFkB = {1.0}IKK_IkBeps_NFkB
  cytoplasm * (a9 * IKK * IkBeps_NFkB - d3 * IKK_IkBeps_NFkB)
v41:
 {1.0}IkBeps_nuc_NFkB_nuc = {1.0}IkBeps_NFkB
  nucleus * 0.5 * k2_eps * IkBeps_nuc_NFkB_nuc
v42:
 {1.0}IKK_IkBalpha = {1.0}IKK
  cytoplasm * r1 * IKK_IkBalpha
v43:
 {1.0}IKK_IkBbeta = {1.0}IKK
  cytoplasm * r2 * IKK_IkBbeta
v44:
 {1.0}IKK_IkBeps = {1.0}IKK
  cytoplasm * r3 * IKK_IkBeps
v45:
 {1.0}IKK = $pool
  cytoplasm * k02 * IKK
v5:
 {1.0}IKK_IkBalpha_NFkB = {1.0}NFkB + {1.0}IKK
  cytoplasm * r4 * IKK_IkBalpha_NFkB
v6:
 {1.0}NFkB + {1.0}IKK_IkBbeta = {1.0}IKK_IkBbeta_NFkB
  cytoplasm * (a5 * IKK_IkBbeta * NFkB - d5 * IKK_IkBbeta_NFkB)
v7:
 {1.0}IKK_IkBbeta_NFkB = {1.0}NFkB + {1.0}IKK
  cytoplasm * r5 * IKK_IkBbeta_NFkB
v8:
 {1.0}NFkB + {1.0}IKK_IkBeps = {1.0}IKK_IkBeps_NFkB
  cytoplasm * (a6 * IKK_IkBeps * NFkB - d6 * IKK_IkBeps_NFkB)
v9:
 {1.0}IKK_IkBeps_NFkB = {1.0}NFkB + {1.0}IKK
  cytoplasm * r6 * IKK_IkBeps_NFkB


#parameters
a1 = 1.35
a2 = 0.36
a3 = 0.54
a4 = 30.0
a5 = 30.0
a6 = 30.0
a7 = 11.1
a8 = 2.88
a9 = 4.2
d1 = 0.075
d2 = 0.105
d3 = 0.105
d4 = 0.03
d5 = 0.03
d6 = 0.03
deg1 = 0.00678
deg4 = 0.00135
flag_for_after_trigger = 0.5
fr = 1.0
k01 = 0.0048
k02 = 0.0072
k1 = 5.4
k2 = 0.828
k2_beta = 0.624
k2_eps = 0.624
r1 = 0.2442
r2 = 0.09
r3 = 0.132
r4 = 1.224
r5 = 0.45
r6 = 0.66
tp1 = 0.018
tp2 = 0.012
tr1 = 0.2448
tr2 = 0.99
tr2a = 9.25e-05
tr2b = 1.068e-05
tr2e = 7.62e-06
tr3 = 0.0168
trigger_value = 0.0
v39_k2_IkBbeta_nuc_NFkB_nuc = 0.0069
cytoplasm = 1.0
nucleus = 1.0


#initial values
IKK = 0.0
IKK_IkBalpha = 0.0
IKK_IkBalpha_NFkB = 0.0
IKK_IkBbeta = 0.0
IKK_IkBbeta_NFkB = 0.0
IKK_IkBeps = 0.0
IKK_IkBeps_NFkB = 0.0
IkBalpha = 0.1
IkBalpha_NFkB = 0.0
IkBalpha_nuc = 0.0
IkBalpha_nuc_NFkB_nuc = 0.0
IkBalpha_transcript = 0.0
IkBbeta = 0.0
IkBbeta_NFkB = 0.0
IkBbeta_nuc = 0.0
IkBbeta_nuc_NFkB_nuc = 0.0
IkBbeta_transcript = 0.0
IkBeps = 0.0
IkBeps_NFkB = 0.0
IkBeps_nuc = 0.0
IkBeps_nuc_NFkB_nuc = 0.0
IkBeps_transcript = 0.0
NFkB = 0.1
NFkB_nuc = 0.001
fr_after_trigger = 0.5


#assignment rules
!F Total_NFkBn = IkBbeta_nuc_NFkB_nuc + NFkB_nuc
!F Total_IkBalpha = IkBalpha + IkBalpha_NFkB + IKK_IkBalpha + IKK_IkBalpha_NFkB
!F Total_IkBeps = IkBeps + IkBeps_NFkB + IKK_IkBeps + IKK_IkBeps_NFkB
!F Total_IkBbeta = IkBbeta + IkBbeta_NFkB + IKK_IkBbeta + IKK_IkBbeta_NFkB