ModelBricks - Model Print Page

Dashboard

Name - PDGF Src March 2012

BioModel ID - 82065439

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
PDGFR_cyto_mem+PDGF_extraPDGF_PDGFR	PDGF_binds_PDGFR cyto_mem	MassAction	PDGFR_cyto_mem+PDGF_extraPDGF_PDGFR
		reaction rate (J): (((Kf * PDGFR_cyto_mem) * PDGF_extra) - (Kr * PDGF_PDGFR))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 0.0[1] forward rate constant (Kf): 1.0[s-1.uM-1] reverse rate constant (Kr): 0.01[s-1]
PDGF_PDGFR_Srccyto_memSrc_active_cyto	Src activation cyto_mem	HMMIrreversible	PDGF_PDGFR_Srccyto_memSrc_active_cyto
		reaction rate (J): ((Vmax * PDGF_PDGFR_Srccyto_mem) / (Km + PDGF_PDGFR_Srccyto_mem))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 0.0[1] Km (1/2 max) (Km): 0.1[molecules.um-2] max reaction rate (Vmax): (kcat * PTP)[molecules.um-2.s-1] user defined (kcat): (0.01 * n)[molecules.um-2.uM-1.s-1]
Src_active_cytoSrc_cyto	Src dephosphorylation in cyto cyto	HMMIrreversible	Src_active_cytoSrc_cyto
		reaction rate (J): ((Vmax * Src_active_cyto) / (Km + Src_active_cyto))[uM.s-1] Km (1/2 max) (Km): 1.5[uM] max reaction rate (Vmax): (0.3 * Csk_cyto_active)[uM.s-1]
csk_cyto_inactiveCsk_cyto_active	r0 cyto	MassAction	csk_cyto_inactiveCsk_cyto_active
		reaction rate (J): ((Kf * csk_cyto_inactive) - (Kr * Csk_cyto_active))[uM.s-1] forward rate constant (Kf): 0.001[s-1] reverse rate constant (Kr): 0.0[s-1]
PDGF_PDGFR+Src_cytoPDGF_PDGFR_Srccyto_mem	Src association with receptor cyto_mem	MassAction	PDGF_PDGFR+Src_cytoPDGF_PDGFR_Srccyto_mem
		reaction rate (J): (((Kf * PDGF_PDGFR) * Src_cyto) - (Kr * PDGF_PDGFR_Srccyto_mem))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 0.0[1] forward rate constant (Kf): 1.0[s-1.uM-1] reverse rate constant (Kr): 0.1[s-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
extra	Compartment (+) (-)

cyto	Compartment (+) (-)

cyto_mem	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
PDGFR_cyto_mem	cyto_mem

PDGF_extra	extra

PTP	cyto

Csk_cyto_active	cyto

PDGF_PDGFR_Srccyto_mem	cyto_mem

Src_active_cyto	cyto

csk_cyto_inactive	cyto

Src_cyto	cyto

PDGF_PDGFR	cyto_mem

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications

Applications See in Dashboard
Name	Math Type	Annotation
compartmental	Deterministic (ODE) Compartmental	cloned from 'compartmental' owned by user susana compartmental model used for Fig S1
ellipse 0999	Deterministic (ODE) Spatial (2D)	(copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1
circle	Deterministic (ODE) Spatial (2D)	(copied from ellipse 0999) (copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1

Application - compartmental

Specifications(Species) - compartmental See in Dashboard
Species	Initial Condition	Diffusion Constant
PDGF_extra	1.0 [uM]	0.0 [um2/s]
PTP	0.1 [uM]	0.0 [um2/s]
Csk_cyto_active	0.0 [uM]	0.0 [um2/s]
Src_active_cyto	0.0 [uM]	0.0 [um2/s]
csk_cyto_inactive	0.1 [uM]	0.0 [um2/s]
Src_cyto	1.0 [uM]	0.0 [um2/s]
PDGFR_cyto_mem	250.0 [uM]	0.0 [um2/s]
PDGF_PDGFR_Srccyto_mem	0.0 [uM]	0.0 [um2/s]
PDGF_PDGFR	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - compartmental See in Dashboard
Name	Reaction Mapping
PDGF_binds_PDGFR	included
Src activation	included
Src dephosphorylation in cyto	included
r0	included
Src association with receptor	included

Simulations - compartmental See in Dashboard
Name	End Time	Output Options
compartmental	2700.0 [s]	OutputTimeStep 10.0

Geometry non-spatial969899354 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			cyto_mem

Application - ellipse 0999

Specifications(Species) - ellipse 0999 See in Dashboard
Species	Initial Condition	Diffusion Constant
PDGF_extra	1.0 [uM]	10.0 [um2/s]
PTP	0.1 [uM]	10.0 [um2/s]
Csk_cyto_active	0.0 [uM]	10.0 [um2/s]
Src_active_cyto	0.0 [uM]	1.0 [um2/s]
csk_cyto_inactive	0.1 [uM]	10.0 [um2/s]
Src_cyto	1.0 [uM]	10.0 [um2/s]
PDGFR_cyto_mem	250.0 [uM]	0.041 [um2/s]
PDGF_PDGFR_Srccyto_mem	0.0 [uM]	0.041 [um2/s]
PDGF_PDGFR	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - ellipse 0999 See in Dashboard
Name	Reaction Mapping
PDGF_binds_PDGFR	included
Src activation	included
Src dephosphorylation in cyto	included
r0	included
Src association with receptor	included

Simulations - ellipse 0999 See in Dashboard
Name	End Time	Output Options
Simulation0	1800.0 [s]	OutputTimeStep 10.0

Geometry ellipse sep 08 0999 See in Dashboard
(Origin: -23.5, -1.25, 0.0; Extent: 47.0, 2.5, 10.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	Cell		74.97675 [um2]	cyto
Volume	Analytical	ECM		42.52324999999999 [um2]	extra
Surface		Cell_ECM_membrane	Cell \| ECM	93.46482136095845 [um]	cyto_mem

Application - circle

Specifications(Species) - circle See in Dashboard
Species	Initial Condition	Diffusion Constant
PDGF_extra	1.0 [uM]	10.0 [um2/s]
PTP	0.1 [uM]	10.0 [um2/s]
Csk_cyto_active	0.0 [uM]	10.0 [um2/s]
Src_active_cyto	0.0 [uM]	1.0 [um2/s]
csk_cyto_inactive	0.1 [uM]	10.0 [um2/s]
Src_cyto	1.0 [uM]	10.0 [um2/s]
PDGFR_cyto_mem	250.0 [uM]	0.041 [um2/s]
PDGF_PDGFR_Srccyto_mem	0.0 [uM]	0.041 [um2/s]
PDGF_PDGFR	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - circle See in Dashboard
Name	Reaction Mapping
PDGF_binds_PDGFR	included
Src activation	included
Src dephosphorylation in cyto	included
r0	included
Src association with receptor	included

Simulations - circle See in Dashboard
Name	End Time	Output Options
Simulation1	1800.0 [s]	OutputTimeStep 10.0
Copy of Simulation1	300.0 [s]	OutputTimeStep 10.0

Geometry circle sep 08 See in Dashboard
(Origin: -5.0, -5.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	Cell		78.39 [um2]	cyto
Volume	Analytical	ECM		5.4125000000000005 [um2]	extra
Surface		Cell_ECM_membrane	Cell \| ECM	7.704697811481667 [um]	cyto_mem

Global Parameters

Global Parameters See in Dashboard
Name	Expression
n	900.0[molecules.um-2.uM-1]