Dashboard

Name - Surve_et_al_RAF1

BioModel ID - 147699816

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
-sorafenib Deterministic (ODE) Compartmental cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995
+sorafenib Deterministic (ODE) Compartmental cloned from 'Raf-1 activation, +sorafenib' owned by user pmyers1995 (copied from Raf-1 activation, -sorafenib)
+sorafenib after 60 min EGF pretreatment Deterministic (ODE) Compartmental (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995
+sorafenib after 15 min EGF pretreatment Deterministic (ODE) Compartmental (copied from +sorafenib after 60 min EGF pretreatment) (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995
+sorafenib after 30 min EGF pretreatment Deterministic (ODE) Compartmental (copied from Copy of +sorafenib after 60 min EGF pretreatment) (copied from +sorafenib after 60 min EGF pretreatment) (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995
+sorafenib after 5 min EGF pretreatment Deterministic (ODE) Compartmental (copied from Copy of Copy of +sorafenib after 60 min EGF pretreatment) (copied from Copy of +sorafenib after 60 min EGF pretreatment) (copied from +sorafenib after 60 min EGF pretreatment) (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995
const. active Ras-GTP, -sorafenib Deterministic (ODE) Compartmental (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995

Application - -sorafenib

Specifications(Species) - -sorafenib See in Dashboard
Species Initial Condition Diffusion Constant
sorafenib 0.0 [uM] 0.0 [um2/min]
Raf1 12000.0 [uM] 0.0 [um2/min]
pRaf1 0.0 [uM] 0.0 [um2/min]
iRaf1 0.0 [uM] 0.0 [um2/min]
BRaf 1000.0 [uM] 0.0 [um2/min]
MEK 500000.0 [uM] 0.0 [um2/min]
pMEK 0.0 [uM] 0.0 [um2/min]
ERK 600000.0 [uM] 0.0 [um2/min]
iBRaf 0.0 [uM] 0.0 [um2/min]
pERK 0.0 [uM] 0.0 [um2/min]
nfpRaf1 0.0 [uM] 0.0 [um2/min]
nfpBRaf 0.0 [uM] 0.0 [um2/min]
nfpiBRaf 0.0 [uM] 0.0 [um2/min]
nfpiRaf1 0.0 [uM] 0.0 [um2/min]
GTP_Ras ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] 0.0 [um2/min]
Ras_Raf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Braf_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Raf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
BRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_iBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpRaf1 0.0 [uM] 0.0 [um2/min]
Ras_nfpBRaf 0.0 [uM] 0.0 [um2/min]
BRaf_iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_nfpiBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpiRaf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_iBRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Specifications(Reaction) - -sorafenib See in Dashboard
Name Reaction Mapping
Ras_Raf1_bind included
BRaf_Raf1_bind included
BRaf_Raf1_phosph included
Ras_pRaf1_unbind included
Ras_BRaf_bind included
pRaf1_Raf1_bind included
pRaf1_Raf1_phosph included
sorafenib_Raf1_bind_cyt excluded
Ras_iRaf1_bind excluded
iRaf1_iRaf1_bind excluded
BRaf_iRaf1_bind excluded
pRaf1_dephosph included
pRaf1_pRaf1_unbind included
BRaf_pRaf1_unbind included
sorafenib_BRaf_bind_cyt excluded
MEK_p included
MEK_dp included
ERK_p included
ERK_dp included
Ras_iBRaf_b excluded
iBRaf_dim excluded
iBRaf_Raf1_bind excluded
Raf1_iBRaf_p excluded
pRaf1_iBRaf_ub excluded
BRaf_dim included
Ras_pRaf1_dp included
Ras_Raf1_nfp included
nfpRaf1_ub included
nfpRaf1_dp included
BRaf_nfp included
nfpBRaf_ub included
nfpBRaf_dp included
BRaf_iBRaf_dim excluded
Ras_iRaf_nfp excluded
nfpiRaf1_ub excluded
nfpiRaf_dp excluded
Ras_iBRaf_nfp excluded
nfpiBRaf_ub excluded
nfpiBRaf_dp excluded
iRaf_iBRaf_dim excluded
Simulations - -sorafenib See in Dashboard
Name End Time Output Options
60 min 60.0 [min]

KeepEvery 1

KeepAtMost 1000

Fitted binding rates 60.0 [min]

KeepEvery 1

KeepAtMost 1000

Geometry non-spatial1069339151 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment pm

Application - +sorafenib

Specifications(Species) - +sorafenib See in Dashboard
Species Initial Condition Diffusion Constant
sorafenib 10.0 [uM] 0.0 [um2/min]
Raf1 12000.0 [uM] 0.0 [um2/min]
pRaf1 0.0 [uM] 0.0 [um2/min]
iRaf1 0.0 [uM] 0.0 [um2/min]
BRaf 1000.0 [uM] 0.0 [um2/min]
MEK 500000.0 [uM] 0.0 [um2/min]
pMEK 0.0 [uM] 0.0 [um2/min]
ERK 600000.0 [uM] 0.0 [um2/min]
iBRaf 0.0 [uM] 0.0 [um2/min]
pERK 0.0 [uM] 0.0 [um2/min]
nfpRaf1 0.0 [uM] 0.0 [um2/min]
nfpBRaf 0.0 [uM] 0.0 [um2/min]
nfpiBRaf 0.0 [uM] 0.0 [um2/min]
nfpiRaf1 0.0 [uM] 0.0 [um2/min]
GTP_Ras ((As * t * exp(( - t / Bs))) + (Cs * t / (t + Ds))) [uM] 0.0 [um2/min]
Ras_Raf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Braf_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Raf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
BRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_iBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpRaf1 0.0 [uM] 0.0 [um2/min]
Ras_nfpBRaf 0.0 [uM] 0.0 [um2/min]
BRaf_iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_nfpiBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpiRaf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_iBRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Specifications(Reaction) - +sorafenib See in Dashboard
Name Reaction Mapping
Ras_Raf1_bind included
BRaf_Raf1_bind included
BRaf_Raf1_phosph included
Ras_pRaf1_unbind included
Ras_BRaf_bind included
pRaf1_Raf1_bind included
pRaf1_Raf1_phosph included
sorafenib_Raf1_bind_cyt included
Ras_iRaf1_bind included
iRaf1_iRaf1_bind included
BRaf_iRaf1_bind included
pRaf1_dephosph included
pRaf1_pRaf1_unbind included
BRaf_pRaf1_unbind included
sorafenib_BRaf_bind_cyt included
MEK_p included
MEK_dp included
ERK_p included
ERK_dp included
Ras_iBRaf_b included
iBRaf_dim included
iBRaf_Raf1_bind included
Raf1_iBRaf_p included
pRaf1_iBRaf_ub included
BRaf_dim included
Ras_pRaf1_dp included
Ras_Raf1_nfp included
nfpRaf1_ub included
nfpRaf1_dp included
BRaf_nfp included
nfpBRaf_ub included
nfpBRaf_dp included
BRaf_iBRaf_dim included
Ras_iRaf_nfp included
nfpiRaf1_ub included
nfpiRaf_dp included
Ras_iBRaf_nfp included
nfpiBRaf_ub included
nfpiBRaf_dp included
iRaf_iBRaf_dim included
Simulations - +sorafenib See in Dashboard
Name End Time Output Options
Fitted binding 60.0 [min]

KeepEvery 1

KeepAtMost 1000

Geometry non-spatial1102832951 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment pm

Application - +sorafenib after 60 min EGF pretreatment

Specifications(Species) - +sorafenib after 60 min EGF pretreatment See in Dashboard
Species Initial Condition Diffusion Constant
sorafenib (10.0 * (t > 60.0)) [uM] 0.0 [um2/min]
Raf1 12000.0 [uM] 0.0 [um2/min]
pRaf1 0.0 [uM] 0.0 [um2/min]
iRaf1 0.0 [uM] 0.0 [um2/min]
BRaf 1000.0 [uM] 0.0 [um2/min]
MEK 500000.0 [uM] 0.0 [um2/min]
pMEK 0.0 [uM] 0.0 [um2/min]
ERK 600000.0 [uM] 0.0 [um2/min]
iBRaf 0.0 [uM] 0.0 [um2/min]
pERK 0.0 [uM] 0.0 [um2/min]
nfpRaf1 0.0 [uM] 0.0 [um2/min]
nfpBRaf 0.0 [uM] 0.0 [um2/min]
nfpiBRaf 0.0 [uM] 0.0 [um2/min]
nfpiRaf1 0.0 [uM] 0.0 [um2/min]
GTP_Ras ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] 0.0 [um2/min]
Ras_Raf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Braf_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Raf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
BRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_iBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpRaf1 0.0 [uM] 0.0 [um2/min]
Ras_nfpBRaf 0.0 [uM] 0.0 [um2/min]
BRaf_iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_nfpiBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpiRaf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_iBRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Specifications(Reaction) - +sorafenib after 60 min EGF pretreatment See in Dashboard
Name Reaction Mapping
Ras_Raf1_bind included
BRaf_Raf1_bind included
BRaf_Raf1_phosph included
Ras_pRaf1_unbind included
Ras_BRaf_bind included
pRaf1_Raf1_bind included
pRaf1_Raf1_phosph included
sorafenib_Raf1_bind_cyt included
Ras_iRaf1_bind included
iRaf1_iRaf1_bind included
BRaf_iRaf1_bind included
pRaf1_dephosph included
pRaf1_pRaf1_unbind included
BRaf_pRaf1_unbind included
sorafenib_BRaf_bind_cyt included
MEK_p included
MEK_dp included
ERK_p included
ERK_dp included
Ras_iBRaf_b included
iBRaf_dim included
iBRaf_Raf1_bind included
Raf1_iBRaf_p included
pRaf1_iBRaf_ub included
BRaf_dim included
Ras_pRaf1_dp included
Ras_Raf1_nfp included
nfpRaf1_ub included
nfpRaf1_dp included
BRaf_nfp included
nfpBRaf_ub included
nfpBRaf_dp included
BRaf_iBRaf_dim included
Ras_iRaf_nfp included
nfpiRaf1_ub included
nfpiRaf_dp included
Ras_iBRaf_nfp included
nfpiBRaf_ub included
nfpiBRaf_dp included
iRaf_iBRaf_dim included
Simulations - +sorafenib after 60 min EGF pretreatment See in Dashboard
Name End Time Output Options
60 min EGF pretreat 80.0 [min]

KeepEvery 1

KeepAtMost 1000

Geometry non-spatial1069339151 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment pm

Application - +sorafenib after 15 min EGF pretreatment

Specifications(Species) - +sorafenib after 15 min EGF pretreatment See in Dashboard
Species Initial Condition Diffusion Constant
sorafenib (10.0 * (t > 15.0)) [uM] 0.0 [um2/min]
Raf1 12000.0 [uM] 0.0 [um2/min]
pRaf1 0.0 [uM] 0.0 [um2/min]
iRaf1 0.0 [uM] 0.0 [um2/min]
BRaf 1000.0 [uM] 0.0 [um2/min]
MEK 500000.0 [uM] 0.0 [um2/min]
pMEK 0.0 [uM] 0.0 [um2/min]
ERK 600000.0 [uM] 0.0 [um2/min]
iBRaf 0.0 [uM] 0.0 [um2/min]
pERK 0.0 [uM] 0.0 [um2/min]
nfpRaf1 0.0 [uM] 0.0 [um2/min]
nfpBRaf 0.0 [uM] 0.0 [um2/min]
nfpiBRaf 0.0 [uM] 0.0 [um2/min]
nfpiRaf1 0.0 [uM] 0.0 [um2/min]
GTP_Ras ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] 0.0 [um2/min]
Ras_Raf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Braf_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Raf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
BRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_iBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpRaf1 0.0 [uM] 0.0 [um2/min]
Ras_nfpBRaf 0.0 [uM] 0.0 [um2/min]
BRaf_iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_nfpiBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpiRaf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_iBRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Specifications(Reaction) - +sorafenib after 15 min EGF pretreatment See in Dashboard
Name Reaction Mapping
Ras_Raf1_bind included
BRaf_Raf1_bind included
BRaf_Raf1_phosph included
Ras_pRaf1_unbind included
Ras_BRaf_bind included
pRaf1_Raf1_bind included
pRaf1_Raf1_phosph included
sorafenib_Raf1_bind_cyt included
Ras_iRaf1_bind included
iRaf1_iRaf1_bind included
BRaf_iRaf1_bind included
pRaf1_dephosph included
pRaf1_pRaf1_unbind included
BRaf_pRaf1_unbind included
sorafenib_BRaf_bind_cyt included
MEK_p included
MEK_dp included
ERK_p included
ERK_dp included
Ras_iBRaf_b included
iBRaf_dim included
iBRaf_Raf1_bind included
Raf1_iBRaf_p included
pRaf1_iBRaf_ub included
BRaf_dim included
Ras_pRaf1_dp included
Ras_Raf1_nfp included
nfpRaf1_ub included
nfpRaf1_dp included
BRaf_nfp included
nfpBRaf_ub included
nfpBRaf_dp included
BRaf_iBRaf_dim included
Ras_iRaf_nfp included
nfpiRaf1_ub included
nfpiRaf_dp included
Ras_iBRaf_nfp included
nfpiBRaf_ub included
nfpiBRaf_dp included
iRaf_iBRaf_dim included
Simulations - +sorafenib after 15 min EGF pretreatment See in Dashboard
Name End Time Output Options
15 min EGF pretreat 35.0 [min]

KeepEvery 1

KeepAtMost 1000

Geometry non-spatial1069339151 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment pm

Application - +sorafenib after 30 min EGF pretreatment

Specifications(Species) - +sorafenib after 30 min EGF pretreatment See in Dashboard
Species Initial Condition Diffusion Constant
sorafenib (10.0 * (t > 30.0)) [uM] 0.0 [um2/min]
Raf1 12000.0 [uM] 0.0 [um2/min]
pRaf1 0.0 [uM] 0.0 [um2/min]
iRaf1 0.0 [uM] 0.0 [um2/min]
BRaf 1000.0 [uM] 0.0 [um2/min]
MEK 500000.0 [uM] 0.0 [um2/min]
pMEK 0.0 [uM] 0.0 [um2/min]
ERK 600000.0 [uM] 0.0 [um2/min]
iBRaf 0.0 [uM] 0.0 [um2/min]
pERK 0.0 [uM] 0.0 [um2/min]
nfpRaf1 0.0 [uM] 0.0 [um2/min]
nfpBRaf 0.0 [uM] 0.0 [um2/min]
nfpiBRaf 0.0 [uM] 0.0 [um2/min]
nfpiRaf1 0.0 [uM] 0.0 [um2/min]
GTP_Ras ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] 0.0 [um2/min]
Ras_Raf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Braf_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Raf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
BRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_iBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpRaf1 0.0 [uM] 0.0 [um2/min]
Ras_nfpBRaf 0.0 [uM] 0.0 [um2/min]
BRaf_iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_nfpiBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpiRaf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_iBRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Specifications(Reaction) - +sorafenib after 30 min EGF pretreatment See in Dashboard
Name Reaction Mapping
Ras_Raf1_bind included
BRaf_Raf1_bind included
BRaf_Raf1_phosph included
Ras_pRaf1_unbind included
Ras_BRaf_bind included
pRaf1_Raf1_bind included
pRaf1_Raf1_phosph included
sorafenib_Raf1_bind_cyt included
Ras_iRaf1_bind included
iRaf1_iRaf1_bind included
BRaf_iRaf1_bind included
pRaf1_dephosph included
pRaf1_pRaf1_unbind included
BRaf_pRaf1_unbind included
sorafenib_BRaf_bind_cyt included
MEK_p included
MEK_dp included
ERK_p included
ERK_dp included
Ras_iBRaf_b included
iBRaf_dim included
iBRaf_Raf1_bind included
Raf1_iBRaf_p included
pRaf1_iBRaf_ub included
BRaf_dim included
Ras_pRaf1_dp included
Ras_Raf1_nfp included
nfpRaf1_ub included
nfpRaf1_dp included
BRaf_nfp included
nfpBRaf_ub included
nfpBRaf_dp included
BRaf_iBRaf_dim included
Ras_iRaf_nfp included
nfpiRaf1_ub included
nfpiRaf_dp included
Ras_iBRaf_nfp included
nfpiBRaf_ub included
nfpiBRaf_dp included
iRaf_iBRaf_dim included
Simulations - +sorafenib after 30 min EGF pretreatment See in Dashboard
Name End Time Output Options
30 min EGF pretreat 50.0 [min]

KeepEvery 1

KeepAtMost 1000

Geometry non-spatial1069339151 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment pm

Application - +sorafenib after 5 min EGF pretreatment

Specifications(Species) - +sorafenib after 5 min EGF pretreatment See in Dashboard
Species Initial Condition Diffusion Constant
sorafenib (10.0 * (t > 5.0)) [uM] 0.0 [um2/min]
Raf1 12000.0 [uM] 0.0 [um2/min]
pRaf1 0.0 [uM] 0.0 [um2/min]
iRaf1 0.0 [uM] 0.0 [um2/min]
BRaf 1000.0 [uM] 0.0 [um2/min]
MEK 500000.0 [uM] 0.0 [um2/min]
pMEK 0.0 [uM] 0.0 [um2/min]
ERK 600000.0 [uM] 0.0 [um2/min]
iBRaf 0.0 [uM] 0.0 [um2/min]
pERK 0.0 [uM] 0.0 [um2/min]
nfpRaf1 0.0 [uM] 0.0 [um2/min]
nfpBRaf 0.0 [uM] 0.0 [um2/min]
nfpiBRaf 0.0 [uM] 0.0 [um2/min]
nfpiRaf1 0.0 [uM] 0.0 [um2/min]
GTP_Ras ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] 0.0 [um2/min]
Ras_Raf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Braf_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Raf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
BRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_iBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpRaf1 0.0 [uM] 0.0 [um2/min]
Ras_nfpBRaf 0.0 [uM] 0.0 [um2/min]
BRaf_iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_nfpiBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpiRaf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_iBRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Specifications(Reaction) - +sorafenib after 5 min EGF pretreatment See in Dashboard
Name Reaction Mapping
Ras_Raf1_bind included
BRaf_Raf1_bind included
BRaf_Raf1_phosph included
Ras_pRaf1_unbind included
Ras_BRaf_bind included
pRaf1_Raf1_bind included
pRaf1_Raf1_phosph included
sorafenib_Raf1_bind_cyt included
Ras_iRaf1_bind included
iRaf1_iRaf1_bind included
BRaf_iRaf1_bind included
pRaf1_dephosph included
pRaf1_pRaf1_unbind included
BRaf_pRaf1_unbind included
sorafenib_BRaf_bind_cyt included
MEK_p included
MEK_dp included
ERK_p included
ERK_dp included
Ras_iBRaf_b included
iBRaf_dim included
iBRaf_Raf1_bind included
Raf1_iBRaf_p included
pRaf1_iBRaf_ub included
BRaf_dim included
Ras_pRaf1_dp included
Ras_Raf1_nfp included
nfpRaf1_ub included
nfpRaf1_dp included
BRaf_nfp included
nfpBRaf_ub included
nfpBRaf_dp included
BRaf_iBRaf_dim included
Ras_iRaf_nfp included
nfpiRaf1_ub included
nfpiRaf_dp included
Ras_iBRaf_nfp included
nfpiBRaf_ub included
nfpiBRaf_dp included
iRaf_iBRaf_dim included
Simulations - +sorafenib after 5 min EGF pretreatment See in Dashboard
Name End Time Output Options
5 min EGF pretreat 25.0 [min]

KeepEvery 1

KeepAtMost 1000

Geometry non-spatial1069339151 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment pm

Application - const. active Ras-GTP, -sorafenib

Specifications(Species) - const. active Ras-GTP, -sorafenib See in Dashboard
Species Initial Condition Diffusion Constant
sorafenib 0.0 [uM] 0.0 [um2/min]
Raf1 12000.0 [uM] 0.0 [um2/min]
pRaf1 0.0 [uM] 0.0 [um2/min]
iRaf1 0.0 [uM] 0.0 [um2/min]
BRaf 1000.0 [uM] 0.0 [um2/min]
MEK 500000.0 [uM] 0.0 [um2/min]
pMEK 0.0 [uM] 0.0 [um2/min]
ERK 600000.0 [uM] 0.0 [um2/min]
iBRaf 0.0 [uM] 0.0 [um2/min]
pERK 0.0 [uM] 0.0 [um2/min]
nfpRaf1 0.0 [uM] 0.0 [um2/min]
nfpBRaf 0.0 [uM] 0.0 [um2/min]
nfpiBRaf 0.0 [uM] 0.0 [um2/min]
nfpiRaf1 0.0 [uM] 0.0 [um2/min]
GTP_Ras 27000.0 [uM] 0.0 [um2/min]
Ras_Raf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_Raf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Braf_iRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_BRaf_pRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_Raf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
Ras_pRaf1_iBRaf_tetramer 0.0 [uM] 0.0 [um2/min]
iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
BRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_iBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpRaf1 0.0 [uM] 0.0 [um2/min]
Ras_nfpBRaf 0.0 [uM] 0.0 [um2/min]
BRaf_iBRaf_dimer 0.0 [uM] 0.0 [um2/min]
Ras_nfpiBRaf 0.0 [uM] 0.0 [um2/min]
Ras_nfpiRaf1 0.0 [uM] 0.0 [um2/min]
Ras_iRaf1_iBRaf1_tetramer 0.0 [uM] 0.0 [um2/min]
Specifications(Reaction) - const. active Ras-GTP, -sorafenib See in Dashboard
Name Reaction Mapping
Ras_Raf1_bind included
BRaf_Raf1_bind included
BRaf_Raf1_phosph included
Ras_pRaf1_unbind included
Ras_BRaf_bind included
pRaf1_Raf1_bind included
pRaf1_Raf1_phosph included
sorafenib_Raf1_bind_cyt excluded
Ras_iRaf1_bind excluded
iRaf1_iRaf1_bind excluded
BRaf_iRaf1_bind excluded
pRaf1_dephosph included
pRaf1_pRaf1_unbind included
BRaf_pRaf1_unbind included
sorafenib_BRaf_bind_cyt included
MEK_p included
MEK_dp included
ERK_p included
ERK_dp included
Ras_iBRaf_b excluded
iBRaf_dim excluded
iBRaf_Raf1_bind excluded
Raf1_iBRaf_p excluded
pRaf1_iBRaf_ub excluded
BRaf_dim included
Ras_pRaf1_dp included
Ras_Raf1_nfp included
nfpRaf1_ub included
nfpRaf1_dp included
BRaf_nfp included
nfpBRaf_ub included
nfpBRaf_dp included
BRaf_iBRaf_dim excluded
Ras_iRaf_nfp excluded
nfpiRaf1_ub excluded
nfpiRaf_dp excluded
Ras_iBRaf_nfp excluded
nfpiBRaf_ub excluded
nfpiBRaf_dp excluded
iRaf_iBRaf_dim excluded
Simulations - const. active Ras-GTP, -sorafenib See in Dashboard
Name End Time Output Options
Simulation0 60.0 [min]

KeepEvery 1

KeepAtMost 1000

10x Ras 60.0 [min]

KeepEvery 1

KeepAtMost 1000

Geometry non-spatial757173534 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment pm

Global Parameters

Global Parameters See in Dashboard
Name Expression
kSon 100000.0[uM-1.min-1]
kSoff 420.0[min-1]
kpR1 186.0[min-1]
kdR1f 0.0191[molecules-1.min-1]
kR1f 1.84E-7[molecules.min-1]
kR1r 0.212[min-1]
kBf 2.47E-7[min-1.molecules-1]
kBr 0.0367[min-1]
kdR1r 111.0[min-1]
kdpR1 0.6[min-1]
boundRaf_frac_parameter (Raf1_pm_param / (Raf1_cyt_param + Raf1_pm_param))[tbd]
A 20671.0[tbd]
B 3.6724[tbd]
C 6.7089E16[tbd]
RasGTP_parameter (GTP_Ras + (2.0 * (Ras_iRaf1_tetramer + Ras_Braf_iRaf1_tetramer + Ras_BRaf_Raf1_tetramer + Ras_pRaf1_Raf1_tetramer + Ras_BRaf_pRaf1_tetramer + Ras_pRaf1_tetramer + BRaf_dimer + BRaf_iBRaf_dimer + iBRaf_dimer + Ras_iRaf1_iBRaf1_tetramer + Ras_Raf1_iBRaf_tetramer + Ras_pRaf1_iBRaf_tetramer)) + Ras_BRaf + Ras_iRaf1 + Ras_pRaf1 + Ras_Raf1 + Ras_nfpRaf1 + Ras_nfpiRaf1 + Ras_iBRaf + Ras_nfpiBRaf + Ras_nfpBRaf)[tbd]
kiR1f 1.84E-7[min-1.molecules-1]
kiR1r 0.212[min-1]
Raf1_pm_param (Ras_pRaf1 + (2.0 * Ras_pRaf1_Raf1_tetramer) + Ras_BRaf_Raf1_tetramer + Ras_iRaf1 + Ras_Raf1 + (2.0 * Ras_iRaf1_tetramer) + Ras_Braf_iRaf1_tetramer + Ras_BRaf_pRaf1_tetramer + (2.0 * Ras_pRaf1_tetramer) + Ras_nfpiRaf1 + Ras_nfpRaf1 + Ras_iRaf1_iBRaf1_tetramer + Ras_Raf1_iBRaf_tetramer + Ras_pRaf1_iBRaf_tetramer)[tbd]
Raf1_cyt_param (Raf1 + pRaf1 + iRaf1 + nfpRaf1 + nfpiRaf1)[tbd]
kMEKp 6.0E-6[molecules-1.min-1]
active_Raf ((2.0 * BRaf_dimer) + Ras_BRaf_Raf1_tetramer + (2.0 * Ras_BRaf_pRaf1_tetramer) + Ras_pRaf1_iBRaf_tetramer + Ras_pRaf1 + Ras_pRaf1_Raf1_tetramer + (2.0 * Ras_pRaf1_tetramer) + pRaf1 + BRaf_iBRaf_dimer + Ras_Braf_iRaf1_tetramer)[tbd]
kERKp 6.0E-5[min-1.molecules-1]
kERKdp 0.6[min-1]
kMEKdp 0.6[min-1]
kiBf 2.47E-7[molecules-1.min-1]
kiBr 0.0367[min-1]
kfpR1r 2.12[min-1]
kfpBr 0.367[min-1]
knfpBR1 6.0E-7[min-1.molecules-1]
D 1.1735E15[tbd]
As 21930.665775907[tbd]
Bs 3.30082007598438[tbd]
Cs 5.37755813880742E16[tbd]
Ds 1.42262832362309E15[tbd]