Dashboard

Name - Spine Model Final Rangamani et al PNAS 2016

BioModel ID - 102061382

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
Application0 Deterministic (ODE) Compartmental

Application - Application0

Specifications(Species) - Application0 See in Dashboard
Species Initial Condition Diffusion Constant
F_actin 0.0 [uM] 0.0 [um2/s]
CaMKII_F_actin 10.0 [uM] 0.0 [um2/s]
Il1_act 0.0 [uM] 0.0 [um2/s]
Myoppase 1.0 [uM] 0.0 [um2/s]
Myoppase_act 0.1 [uM] 0.0 [um2/s]
ROCK 1.0 [uM] 0.0 [um2/s]
Il1 1.8 [uM] 0.0 [um2/s]
RhoGTP 0.0 [uM] 0.0 [um2/s]
ROCK_act 0.0 [uM] 0.0 [um2/s]
LIMK 2.0 [uM] 0.0 [um2/s]
LIMK_P 0.0 [uM] 0.0 [um2/s]
RhoGAP_act 0.0 [uM] 0.0 [um2/s]
RhoGDP 1.0 [uM] 0.0 [um2/s]
RhoGEF 0.1 [uM] 0.0 [um2/s]
RhoGEF_act 0.0 [uM] 0.0 [um2/s]
RhoGAP 0.1 [uM] 0.0 [um2/s]
Ng 20.0 [uM] 0.0 [um2/s]
CaM_Ng 0.0 [uM] 0.0 [um2/s]
SSH1_act 0.0 [uM] 0.0 [um2/s]
cdc42GTP 0.0 [uM] 0.0 [um2/s]
WASP 1.0 [uM] 0.0 [um2/s]
PP1 0.36 [uM] 0.0 [um2/s]
PP1_act 0.0 [uM] 0.0 [um2/s]
MLC 1.0 [uM] 0.0 [um2/s]
MLC_p 0.0 [uM] 0.0 [um2/s]
arp23 1.0 [uM] 0.0 [um2/s]
WASP_act 0.0 [uM] 0.0 [um2/s]
B 30.0 [uM] 0.0 [um2/s]
R 0.0 [uM] 0.0 [um2/s]
cdc42GDP 1.0 [uM] 0.0 [um2/s]
Ca_CaM 0.0 [uM] 0.0 [um2/s]
Bp 1.0 [uM] 0.0 [um2/s]
CaM 10.0 [uM] 0.0 [um2/s]
arp23_act 0.0 [uM] 0.0 [um2/s]
SSH1 2.0 [uM] 0.0 [um2/s]
Ca ((12.0 * (t > 1.0)) && (t < 5.0)) [uM] 0.0 [um2/s]
CaMKII 0.0 [uM] 0.0 [um2/s]
CaMKIIp 0.0 [uM] 0.0 [um2/s]
G_actin 0.0 [uM] 0.0 [um2/s]
CaMKII_G_actin 10.0 [uM] 0.0 [um2/s]
Calcineurin_act 0.0 [uM] 0.0 [um2/s]
Cdc42GEF 0.1 [uM] 0.0 [um2/s]
cdc42GEF_act 0.0 [uM] 0.0 [um2/s]
Cofilin_p 2.0 [uM] 0.0 [um2/s]
Calcineurin 1.0 [uM] 0.0 [um2/s]
cofilin_act 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - Application0 See in Dashboard
Name Reaction Mapping
Myoppase inactivation by ROCK included
Cofilin inactivation by LIMK included
PP1 inactivation by CaMKII included
calcium binding calmodulin included
calcinuerin inactivation included
Cofilin activation through SSH1 dephosphorylation included
RhoGTP hydrolysis included
SSH1 dephosphorylation by CaN included
cdc42 activates WASP included
cdc42 hydrolysis included
LIMK activation by ROCK included
MLC Phosphorylation by ROCK included
Cdc42 GEF inactivation included
Arp23 inactivation included
Barbed ends included
RhoGEF activation by CaMKII included
Il1 inactivation included
Il1 activation by CaN included
Arp23 activation included
severing included
CaMKII activation by CaM included
PP1 activation by IL1 included
cdc42 activation included
pushing barbed ends included
CaMKII sequestration of G-actin included
Calmodulin binding neurogranin included
Radius included
RhoGAP inactivation by PP1 included
RhoGTP activation by RhoGEF included
Myoppase activation by autodephosphorylation included
Rho GEF inactivation included
Calcineurin activation by CaM included
LIMK inactivation by ROCK included
MLC dephosphorylation included
CaMKII inactivation included
ROCK activation by Rho included
cdc42 GEF activation included
myosin phosphatase activation basal included
MLC phosphorylation basal included
ROCK inactivation 1 included
RhoGAP activation by CaMKII included
CaMKII sequestration of F-actin included
SSH1 phosphorylation by CaMKIIp included
Actin growth included
Simulations - Application0 See in Dashboard
Name End Time Output Options
basic simulation 300.0 [s]

OutputTimeStep 1.0

Arp23 variation 300.0 [s]

OutputTimeStep 1.0

Nuc-Sev phase 300.0 [s]

OutputTimeStep 1.0

cofilin variation 300.0 [s]

OutputTimeStep 1.0

CaM variation 300.0 [s]

OutputTimeStep 1.0

Ng variation 300.0 [s]

OutputTimeStep 1.0

PP1 variation 300.0 [s]

OutputTimeStep 1.0

CaN variation 300.0 [s]

OutputTimeStep 1.0

Rho GTP level 300.0 [s]

OutputTimeStep 1.0

sensitivity kage 240.0 [s]

OutputTimeStep 1.0

sensitivity with cofilin 240.0 [s]

OutputTimeStep 1.0

sensitivity with Arp2/3 240.0 [s]

OutputTimeStep 1.0

CaN sensitivity 240.0 [s]

OutputTimeStep 1.0

CaMKII-f-actin 240.0 [s]

OutputTimeStep 1.0

CaMKII-G-actin sensitivity 240.0 [s]

OutputTimeStep 1.0

cdc42GTP sensitivity 240.0 [s]

OutputTimeStep 1.0

Cdc42 GEF sensitivity 240.0 [s]

OutputTimeStep 1.0

I1 sensitivity 240.0 [s]

OutputTimeStep 1.0

LIMK sensitivity 240.0 [s]

OutputTimeStep 1.0

MLC sensitivity 240.0 [s]

OutputTimeStep 1.0

Myoppase active sens 240.0 [s]

OutputTimeStep 1.0

Myoppase sens 240.0 [s]

OutputTimeStep 1.0

Ng sens 240.0 [s]

OutputTimeStep 1.0

phi sens 240.0 [s]

OutputTimeStep 1.0

PP1 sens 240.0 [s]

OutputTimeStep 1.0

Rho GAP sens 240.0 [s]

OutputTimeStep 1.0

Rho GEF sens 240.0 [s]

OutputTimeStep 1.0

Rho GDP sens 240.0 [s]

OutputTimeStep 1.0

ROCK sens 240.0 [s]

OutputTimeStep 1.0

SSH1 sens 240.0 [s]

OutputTimeStep 1.0

VO sens 240.0 [s]

OutputTimeStep 1.0

w sens 240.0 [s]

OutputTimeStep 1.0

WASP sens 240.0 [s]

OutputTimeStep 1.0

k-arp23 inactivation 240.0 [s]

OutputTimeStep 1.0

k-calcineurin-activation-by-cam 240.0 [s]

OutputTimeStep 1.0

kcap 240.0 [s]

OutputTimeStep 1.0

kdeg 240.0 [s]

OutputTimeStep 1.0

knuc 240.0 [s]

OutputTimeStep 1.0

ksev 240.0 [s]

OutputTimeStep 1.0

kshrink 240.0 [s]

OutputTimeStep 1.0

KAPPA 240.0 [s]

OutputTimeStep 1.0

kcat1 240.0 [s]

OutputTimeStep 1.0

kcat2 240.0 [s]

OutputTimeStep 1.0

kcat 3 240.0 [s]

OutputTimeStep 1.0

Kcat CaMKII activation by CAM 240.0 [s]

OutputTimeStep 1.0

kcat camkii inactivation 240.0 [s]

OutputTimeStep 1.0

kcat cd42 acticaion 240.0 [s]

OutputTimeStep 1.0

kcat cdc42 gef activation 240.0 [s]

OutputTimeStep 1.0

kcat cdc42 gef inactivation 240.0 [s]

OutputTimeStep 1.0

kcat cdc42 hydrolysis 240.0 [s]

OutputTimeStep 1.0

kcat cofilin activation through ssh1 240.0 [s]

OutputTimeStep 1.0

kcat cofilin inactivation through LIMK 240.0 [s]

OutputTimeStep 1.0

kcat i1 inactivation 240.0 [s]

OutputTimeStep 1.0

kcat limk rock 240.0 [s]

OutputTimeStep 1.0

kcat mlc rock 240.0 [s]

OutputTimeStep 1.0

kcat myoppase dephos 240.0 [s]

OutputTimeStep 1.0

kcat myoppase rock1 240.0 [s]

OutputTimeStep 1.0

kcat myoppase rock 240.0 [s]

OutputTimeStep 1.0

kcat pp1 by camkii 240.0 [s]

OutputTimeStep 1.0

kcat rhogap camkii 240.0 [s]

OutputTimeStep 1.0

kcat rho gef camkii 240.0 [s]

OutputTimeStep 1.0

kcat Rho gtp by Rho gef 240.0 [s]

OutputTimeStep 1.0

kf 240.0 [s]

OutputTimeStep 1.0

kf arp23 activation 240.0 [s]

OutputTimeStep 1.0

kf CaM NG 240.0 [s]

OutputTimeStep 1.0

camkii f-actin 240.0 [s]

OutputTimeStep 1.0

camkii g-actin 240.0 [s]

OutputTimeStep 1.0

kf cdc42 wasp 240.0 [s]

OutputTimeStep 1.0

kf MLC phosphorylation 240.0 [s]

OutputTimeStep 1.0

kf myoppase basal 240.0 [s]

OutputTimeStep 1.0

kf rock act by rho 240.0 [s]

OutputTimeStep 1.0

kf rock inact 240.0 [s]

OutputTimeStep 1.0

Km 240.0 [s]

OutputTimeStep 1.0

km1 camkii activation by cam 240.0 [s]

OutputTimeStep 1.0

km1 PP1 activation by i1 240.0 [s]

OutputTimeStep 1.0

km2 240.0 [s]

OutputTimeStep 1.0

km can cam 240.0 [s]

OutputTimeStep 1.0

CaN inactivation 240.0 [s]

OutputTimeStep 1.0

CaMKii activation by CaM 240.0 [s]

OutputTimeStep 1.0

Km CaMKII inactivation 240.0 [s]

OutputTimeStep 1.0

km cdc42 activation 240.0 [s]

OutputTimeStep 1.0

km cdc42 gef activation 240.0 [s]

OutputTimeStep 1.0

km cdc42 gef 240.0 [s]

OutputTimeStep 1.0

km cdc42 hydrolysis 240.0 [s]

OutputTimeStep 1.0

km cofilin actiation ssh1 240.0 [s]

OutputTimeStep 1.0

km i1 activation by CaN 240.0 [s]

OutputTimeStep 1.0

Km i1 inactivation 240.0 [s]

OutputTimeStep 1.0

km limk activation by rock 240.0 [s]

OutputTimeStep 1.0

km limk inactivation by rock 240.0 [s]

OutputTimeStep 1.0

km mlc dephosphorylation 240.0 [s]

OutputTimeStep 1.0

km myoppase activation dephos 240.0 [s]

OutputTimeStep 1.0

km myoppase inactivation rock 240.0 [s]

OutputTimeStep 1.0

km pp1 inct by camkii 240.0 [s]

OutputTimeStep 1.0

km rho gef inactivation 240.0 [s]

OutputTimeStep 1.0

km rhogap camkii 240.0 [s]

OutputTimeStep 1.0

km rho gap pp1 240.0 [s]

OutputTimeStep 1.0

km rhogef camkii 240.0 [s]

OutputTimeStep 1.0

km rhogtp by rhogef 240.0 [s]

OutputTimeStep 1.0

km rhogtp hhydrolysis 240.0 [s]

OutputTimeStep 1.0

km ssh1 dephos 240.0 [s]

OutputTimeStep 1.0

km ssh1 phos camkii 240.0 [s]

OutputTimeStep 1.0

kr 240.0 [s]

OutputTimeStep 1.0

kr arp activation 240.0 [s]

OutputTimeStep 1.0

kr CaM binding NG 240.0 [s]

OutputTimeStep 1.0

kr caMkii binding f-actin 240.0 [s]

OutputTimeStep 1.0

kr camkii g-actin 240.0 [s]

OutputTimeStep 1.0

kr cdc42 wasp 240.0 [s]

OutputTimeStep 1.0

kr MLCp basal 240.0 [s]

OutputTimeStep 1.0

kr myosin ppase basal 240.0 [s]

OutputTimeStep 1.0

kr rock by rho 240.0 [s]

OutputTimeStep 1.0

kr rock inacivation 240.0 [s]

OutputTimeStep 1.0

Geometry non-spatial256678770 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 plasma membrane

Global Parameters

Global Parameters See in Dashboard
Name Expression
k_sev 0.01[tbd]
C0 0.5[tbd]
l 0.255[tbd]
k_nuc 60.0[tbd]
Km 2.0[uM]
V0 0.07[tbd]
w 25.0[tbd]
phi 10.0[tbd]
k_cap 0.04[s-1]
k_shrink 0.01[uM-1.s-1]
Vmb (V0 * Bp / (Bp + (phi * exp((w / Bp)))))[s-1]
f_nuc (k_nuc * arp23_act * l * F_actin * G_actin / (Km + arp23_act))[tbd]