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

Structures

Name
Type
Electrical
cell Compartment (+)   (-)

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

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,)

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

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

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