Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
MekMek_act Mek_Activation cell GeneralKinetics
Mek_actMek Mek_Deactivation cell GeneralKinetics
MekMek_act Mek_Activation_bRaf cell GeneralKinetics

Mek_Activation Universal ID's

Mek_Activation Text Annotations

Mek_Deactivation Universal ID's

Mek_Deactivation Text Annotations

Mek_Activation_bRaf Universal ID's

Mek_Activation_bRaf Text Annotations

Expressions for Mek_Activation

reaction rate

J

(Kcat * Raf1_act * Mek / (km + Mek)) [mmol.ml-1.min-1]

local

km

4768350.0 [mmol.ml-1]

local

Kcat

185.759 [min-1]

Expressions for Mek_Deactivation

reaction rate

J

(Kcat * PP2A_act * Mek_act / (km + Mek_act)) [mmol.ml-1.min-1]

local

km

518753.0 [mmol.ml-1]

local

Kcat

2.83243 [min-1]

Expressions for Mek_Activation_bRaf

reaction rate

J

(kcat * bRaf_act * Mek / (km + Mek)) [mmol.ml-1.min-1]

local

km

4768350.0 [mmol.ml-1]

local

kcat

185.759 [min-1]

Structures

Name
Type
Electrical
cell Compartment (+)   (-)

cell Universal ID's

cell Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Raf1_act cell Raf(Active~yes!-,). cell
Mek_act cell MEK(Active~yes!-,). cell
Mek cell MEK(Active~no!-,). cell
bRaf_act cell B_Raf(Active~yes!-,). cell
PP2A_act cell PP2A(Active~yes!-,). cell

Raf1_act Universal ID's

Raf1_act Text Annotations

Mek_act Universal ID's

Mek_act Text Annotations

Mek Universal ID's

Mek Text Annotations

bRaf_act Universal ID's

bRaf_act Text Annotations

PP2A_act Universal ID's

PP2A_act Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
Raf Raf(Active~yes~no,)
MEK MEK(Active~yes~no,)
B_Raf B_Raf(Active~yes~no,)
PP2A PP2A(Active~yes~no,)

Raf Universal ID's

Raf Text Annotations

MEK Universal ID's

MEK Text Annotations

B_Raf Universal ID's

B_Raf Text Annotations

PP2A Universal ID's

PP2A Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Deterministic Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental cloned from 'Deterministic' owned by user savi06 cloned from 'Deterministic' owned by user mblinov cloned from 'Deterministic' owned by user cab15130

Deterministic Universal ID's

Deterministic Text Annotations

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Raf1_act (1800.0 * (t > 1.0) * (t < 3.0)) [mmol] 0.0 [m2/min] cell
Mek_act 0.0 [mmol] 0.0 [m2/min] cell
Mek 600000.0 [mmol] 0.0 [m2/min] cell
bRaf_act (14000.0 * (t > 1.0) * (t < 7.0)) [mmol] 0.0 [m2/min] cell
PP2A_act 120000.0 [mmol] 0.0 [m2/min] cell

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
Mek_Activation included
Mek_Deactivation included
Mek_Activation_bRaf included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 10.0

KeepEvery 1

KeepAtMost 1000

Deterministic Universal ID's

Deterministic Text Annotations

Assignments

Name Variable Assignment Function Expression
assignmentRule0 Raf1_act (1800.0 * (t > 1.0) * (t < 3.0))
assignmentRule1 bRaf_act (14000.0 * (t > 1.0) * (t < 7.0))

Events

Name Trigger Type Variable Assignment

Geometry Compartmental1162560315

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [m])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment cell

Events

Name Variable Rate Expression

Global Parameters

Name
Expression

Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Deterministic.bngl
SBML Deterministic.sbml
Matlab Deterministic.m
NFSim XML Deterministic.xml