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University of Connecticut Health Center - Know Better Care VCell - The Virtual Cell

VCell Published Models






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2014

Using Markov State Models to Develop a Mechanistic Understanding of Protein Kinase A-RIα Activation in Response to cAMP Binding
Britton W. Boras, Alexandr Kornev, Susan S. Taylor, Andrew D. McCulloch
J Biol Chem. 2014 Sep 8. pii: jbc.M114.568907
PubMed
BioModels
Boras_PKA-Dimer Boras_PKA-CBD-B
Boras_PKA-CBD-A Boras_PKA-Dual
Boras_PKA-Unconstrained Boras_PKA-Dimer_mutant_A-inhibited
Boras_PKA_Dimer_mutant_B-inhibited Boras_PKA_CBD-A_mutant_A-inhibited
Boras_PKA_CBD-A_mutant_B-inhibited Boras_PKA_CBD-B_mutant_A-inhibited
Boras_PKA_CBD-B_mutant_B-inhibited
Boras_PKA_Dual_mutant_A-inhibited
Boras_PKA_Dual_mutant_B-inhibited
Synaptic excitation is regulated by the postsynaptic dSK channel at the Drosophila larval NMJ
Daniel M. Gertner , Sunil Desai , Gregory A. Lnenicka
Journal of NeurophysiologyPublished 15 June 2014Vol. 111no. 2533-2543
DOI: 10.1152/jn.00903.2013
PubMed
BioModel: gregl: epsp_gcs
Interconnected Network Motifs Control Podocyte Morphology and Kidney Function
Evren U. Azeloglu, Simon V. Hardy, Narat John Eungdamrong, Yibang Chen, Gomathi Jayaraman, Peter Y. Chuang, Wei Fang, Huabao Xiong, Susana R. Neves, Mohit R. Jain, Hong Li, Avi Ma’ayan, Ronald E. Gordon, John Cijiang He, and Ravi Iyengar
Sci. Signal., 4 February 2014
Vol. 7, Issue 311, p. ra12
[DOI: 10.1126/scisignal.2004621]
PubMed

2013

Tension modulates actin filament polymerization mediated by formin and profilin.
Courtemanche N, Lee JY, Pollard TD, & Greene EC
Proceedings of the National Academy of Sciences 110(24):9752-9757.
PubMed
Differential triggering of spontaneous glutamate release by P/Q-, N- and R-type Ca2+ channels.
Ermolyuk YS, Alder FG, Surges R, Pavlov IY, Timofeeva Y, Kullmann DM, Volynski KE.
Nat Neurosci. 2013 Dec;16(12):1754-63. doi: 10.1038/nn.3563. Epub 2013 Nov 3.
PubMed
Mutations in DNA binding and transactivation domains affect the dynamics of parvovirus NS1 protein.
Niskanen EA, Kalliolinna O, Ihalainen TO, Häkkinen M, Vihinen-Ranta M.
J Virol. 2013 Nov;87(21):11762-74. doi: 10.1128/JVI.01678-13. Epub 2013 Aug 28.
PubMed
Recycling of Kinesin-1 Motors by Diffusion after Transport.
Blasius T. L., Reed N., SlepchenkoB. M., Verhey K. J.
2013 PLoS One, 8(9): 76081 (pp.1-11). doi: 10.1371/journal.pone.0076081.
PubMed
MathModel: boris: ‘VerheyProblem_PLoS1_loose bucket brigade’
MathModel: boris: ‘VerheyProblem_PLoS1_diligent workers’
MathModel: boris: ‘VerheyProblem_PLoS1_hybrid1’
MathModel: boris: ‘VerheyProblem_PLoS1_hybrid2’
Protein artifacts of pathogen, vector and host.
Mark R. McGary
1 Nov 2013, ThyenMed Library
BioModel:mcgama88:'Mark W2X'
Modeling and Simulation of Intracellular Drug Transport and Disposition Pathways with Virtual Cell.
Baik J and Rosania, GR.
2013;1(1): 8., J Pharmaceu Pharmacol, June 2013 Vol.:1, Issue:1
Publicaton
BioModel:jsbaik:'Baik & Rosania 2013 JPP – 01 Suspension model no lysosome'
BioModel:jsbaik:'Baik & Rosania 2013 JPP – 02 Transcellular model no lysosome'
BioModel:jsbaik:'Baik & Rosania 2013 JPP – 03 Transcellular model with lysosome. '
ERK regulation of phosphodiesterase 4 enhances dopamine-stimulated AMPA receptor membrane insertion.
Song RS, Massenburg B, Wenderski W, Jayaraman V, Thompson L, Neves SR.
Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15437-42. doi: 10.1073/pnas.1311783110. Epub 2013 Aug 28.
PubMed
BioModel:rsong:'Song_PNAS_2013'
Decoding Information in Cell Shape
Rangamani, P., A. Lipshtat, Evren U. Azeloglu, Rhodora C. Calizo, M. Hu, S. Ghassemi, J. Hone, S. Scarlata, Susana R. Neves, and R. Iyengar.
Cell, 2013, 154:1356-1369.
PubMed
BioModel:prangamani:'Rangamani Cell 2013 B2R signaling'
BioModel:prangamani:'PDGF Src March 2012'
BioModel:prangamani:'EGF ras Sep 2012'
Ion channels and regulation of insulin secretion in human β-cells: a computational systems analysis.
Fridlyand LE, Jacobson DA, Philipson LH.
Islets. 2013 Jan-Feb;5(1):1-15. doi: 10.4161/isl.24166.
PubMed
MathModel:Fridlyand:'Human_Beta_cell'
Protein Equilibration Through Somatic Ring Canals in Drosophila.
McLean PF, Cooley L.
Science. 2013 Jun 21;340(6139):1445-1447. Epub 2013 May 23.
PubMed
BioModel:peterfoster: '2 Cell Spatial CORRR 1/4Cell_01'
BioModel:peterfoster: 'PAGFP Diffusion COMPARTMENTAL_3Cell_01'
BioModel:peterfoster: 'PAGFP Diffusion COMPARTMENTAL_3Cell_02'
BioModel:peterfoster: 'PAGFP Diffusion COMPARTMENTAL_4Cell_01'
Computational Analysis of Rho GTPase Cycling
Cibele V Falkenberg, Leslie M Loew
PLoS Comput Biol. 2013 9(1): e1002831. doi:10.1371/journal.pcbi.1002831 PLoS Comput Biol 9(1): e1002831. doi:10.1371/journal.pcbi.1002831
PubMed
BioModel:'Falkenberg_GTPases_Rac_betaCell'
Quantitative properties and receptor reserve of the DAG and PKC branch of Gq-coupled receptor signaling
Björn H. Falkenburger, Eamonn J. Dickson, and Bertil Hille
J. Gen. Physiol. 2013; 141:537-555.
PubMed
BioModel: bfalken:FalkenburgerDicksonHille2013
Quantitative properties and receptor reserve of the IP3 and calcium branch of Gq-coupled receptor signaling.
Eamonn J. Dickson, Björn H. Falkenburger, and Bertil Hille
J. Gen. Physiol. 2013; 141:521-535.
PubMed
BioModel: bfalken:FalkenburgerDicksonHille2013

2012

Determinants of Formin Homology 1 (FH1) domain function in actin filament elongation by formins.
Courtemanche N, Pollard TD.
J Biol Chem. 2012 Mar 2;287(10):7812-20. doi: 10.1074/jbc.M111.322958. Epub 2012 Jan 14.
PubMed
Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia.
Brown SA, Loew LM.
BMC Syst Biol. 2012 Jun 15;6:70. doi: 10.1186/1752-0509-6-70.
PubMed
BioModel: les: Brown et al. 2011 Analysis of SCA15-SCA16 with IC4 Peptide Application
BioModel: les: Brown et al. 2011 SCA1 Compensation Analysis
BioModel: les: Brown et al. 2011 Analysis of SCA1-SCA2-SCA3 with IC-G2736X Peptide
BioModel: les: Brown et al. 2011 Purkinje Biochem-Electrophysiol SCA
BioModel: les: Brown et al. 2011 Purkinje 3D Spine – Spinocerebellar Ataxia study
BioModel: les: Brown et al. 2011 Combined Purkinje - Several Spines - Current Injection
A computational systems analysis of factors regulating α cell glucagon secretion.
Fridlyand LE, Philipson LH.
Islets. 2012 Jul 1;4(4):262-83. doi: 10.4161/isl.22193. Epub 2012 Jul 1.
PubMed
MathModel: Fridlyand: Alpha and beta cells glucose sensing
MathModel: Fridlyand: Glucagon secretion
CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation.
Michalski PJ, Loew LM.
Phys Biol. 2012 Jun 8;9(3):036010. [Epub ahead of print]
PubMed
BioModel: pjmichal: BioNetGen CaMKII – Trimer – 6 states – with phosphatase
BioModel: pjmichal: CaMKII – Infinite Lattice – 6 states
BioModel: pjmichal: BioNetGen CaMKII – Dimer – 3 states – with phosphatase
BioModel: pjmichal: BioNetGen CaMKII – Trimer – 3 states – with phosphatase
BioModel: pjmichal: BioNetGen CaMKII – Tetramer – 3 states – with phosphatase
BioModel: pjmichal: BioNetGen CaMKII – Pentamer – 3 states – with phosphatase
BioModel: pjmichal: BioNetGen CaMKII – Hexamer – 3 states – with phosphatase
Stoichiometry of Nck-dependent actin polymerization in living cells
Ditlev, J.A., Michalski, P.J., Huber, G., Rivera, G.M., Mohler, W.A., Loew, L.M., Mayer, B.J.
J Cell Biol 197 (5): 643-658, May 21, 2012
PubMed
Biomodel:'JDitlev: Nck Induces Actin Comet Tail Formation Single NWASP Activation of Arp2/3 Simplified Actin Dendritic Nucleation (1:1:1 model)
Biomodel:'JDitlev: Nck Induces Actin Comet Tail Formation Dimer NWASP Activation of Arp2/3 Simplified Actin Dendritic Nucleation (2:2:1 model)
Biomodel:'JDitlev: Nck Induces Actin Comet Tail Formation Dimer Nck Binds NWASP With Dimer NWASP Activation of Arp2/3 Simplified Actin Dendritic Nucleation (4:2:1 model)
Live-cell fluorescence microscopy with molecular biosensors: What are we really measuring?
Haugh, JM
Biophys J, 102 (9): 2003-2011 (2012).
PubMed
Biomodel: 'jmhaugh: Biosensor simple'
Spatial modeling of cell signaling networks
Cowan AE, Moraru II, Schaff JC, Slepchenko BM, Loew LM.
Methods Cell Biol. 2012;110:195-221
PubMed
Biomodel: 'les: Membrane Flux for meth cell biology'
Assessment of cellular mechanisms contributing to cAMP compartmentalization in pulmonary microvascular endothelial cells
Wei P Feinstein, Bing Zhu, Silas J Leavesley, Sarah L. Sayner, and Thomas C Rich
Am J Physiol Cell Physiol. 2012 Mar;302(6):C839-52. Epub 2011 Nov 23.
PubMed
BioModel: 'wfeinstein: PMVEC cAMP model'
BioModel: 'wfeinstein: PMVEC cAMP model with point source'

2011

System analysis shows distinct mechanisms and common principles of nuclear envelope protein dynamics.
Nikolaj Zuleger, David A. Kelly, A. Christine Richardson, Alastair R. W. Kerr, Martin W. Goldberg, Andrew B. Goryachev, and Eric C. Schirmer
J Cell Biol 2011 193:109-123. Published March 28, 2011, doi:10.1083/jcb.201009068
PubMed
Cooperative Nuclear Localization Sequences Lend a Novel Role to the N-Terminal Region of MSH6.
Gassman NR, Clodfelter JE, McCauley AK, Bonin K, Salsbury FR Jr, et al.
(2011) PLoS ONE 6(3): e17907. doi:10.1371/journal.pone.0017907.
PubMed
Coupling of metabolic, second messenger pathways and insulin granule dynamics in pancreatic beta-cells: A computational analysis
Fridlyand LE, Philipson LH.
Prog Biophys Mol Biol. 2011 Nov;107(2):293-303. Ep ub 2011 Sep 8.
PubMed
MathModels: "Fridlyand" and "Traffic1"
Triggering Actin Comets Versus Membrane Ruffles: Distinctive Effects of Phosphoinositides on Actin Reorganization.
Ueno T, Falkenburger BH, Pohlmeyer C, Inoue T.
Sci Signal. 2011;4(203):ra87.
PubMed
BioModel: 'bfalken: Ueno2011'
System analysis shows distinct mechanisms and common principles of nuclear envelope protein dynamics.
Zuleger, N., Kelly, D.A., Richardson, A.C., Kerr, A.R.W., Goldberg, M.W., Goryachev, A.B., Schirmer, E.C.
The Journal of Cell Biology 193, 109-123, 2011.
PubMed
The emergence of sarcomeric, graded-polarity and spindle-like patterns in bundles of short cytoskeletal polymers and two opposite molecular motors.
Craig, E.M., Dey, S., and Mogilner, A.
J Phys Condens Matter 23, 374102, (2011).
PubMed
MathModel: ‘ecraig: Cytoskeletal bundle_1-motor’
MathModel: ‘ecraig: Cytoskeletal bundle_2-motor’ (for the extended model described in section 6)
Astrocytes as regulators of synaptic function: a quest for the Ca2+ master key.
Rusakov, D.A., Zheng, K., and Henneberger, C.
Neuroscientist 17, 513-523, (2011).
PubMed
Protein Diffusion in Mammalian Cell Cytoplasm.
Kühn, T., T.O. Ihalainen, J. Hyväluoma, N. Dross, S.F. Willman, J. Langowski, M. Vihinen-Ranta, and J. Timonen.
2011, PLoS ONE. 6:e22962.
PubMed
Quantifying the Waddington landscape and biological paths for development and differentiation.
Wang J, Zhang K, Xu L, Wang E.
Proc Natl Acad Sci U S A. 2011 May 17;108(20):8257-62. Epub 2011 May 2.
PubMed
The effect of compressive deformations on the rate of build-up of oxygen in isolated skeletal muscle cells.
Leopold E, Sopher R, Gefen A.
Med Eng Phys. 33, 1072-1078, 2011
PubMed
Coupling of the phosphatase activity of Ci-VSP to its voltage sensor activity over the entire range of voltage sensitivity.
Sakata S, Hossain MI, Okamura Y.
J Physiol. 589:2687-2705, 2011
PubMed
Public Biomodel: "ssvcell1548: sakata_JP2011-Kir2.1"
Public Biomodel: "ssvcell1548: sakata_JP2011-PHDGFP"
Ca2+ buffering at a drosophila larval synaptic terminal.
He, T., and Lnenicka, G.A.
(2011) Synapse 65, 687-693.
PubMed
Cooperative Nuclear Localization Sequences Lend a Novel Role to the N-Terminal Region of MSH6.
Gassman, N.R., Clodfelter, J.E., McCauley, A.K., Bonin, K., Salsbury, F.R., Jr., and Scarpinato, K.D.
(2011). PLoS One 6, e17907.
PubMed
Signaling network triggers and membrane physical properties control the actin cytoskeleton-driven isotropic phase of cell spreading.
Rangamani P, Fardin MA, Xiong Y, Lipshtat A, Rossier O, Sheetz MP, Iyengar R.
Biophys J. 2011 Feb 16;100(4):845-57.
PubMed
BioModel: 'prangamani: Rangamani et al, BJ Feb 2011'
Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling.
Brown SA, Moraru II, Schaff JC, Loew LM.
J Comput Neurosci. 31:385-400, 2011
PubMed
BioModel: 'Brown:GBrown et al 2010 Purkinje MultiCompartmental Combined Biochem and Electrophysiol'
Potassium (K+) gradients serve as a mobile energy source in plant vascular tissues.
Gajdanowicz P, Michard E, Sandmann M, Rocha M, Corrêa LG, Ramírez-Aguilar SJ, Gomez-Porras JL, González W, Thibaud JB, van Dongen JT, Dreyer I.
Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):864-9. Epub 2010 Dec 27.
PubMed
BioModel: 'IngoDreyer: Gajdanowicz_et_al_20119'
Purification of Actin from Fission Yeast Schizosaccharomyces pombe and Characterization of Functional Differences from Muscle Actin.
Shih-Chieh Ti and Thomas D. Pollard
Journal of Biological Chemistry, 2011, 286(7), 5784-92 Publication Date: Dec 9, 2010
PubMed
BioModel: 'SCT: PiRelease'

2010

Bursting and calcium oscillations in pancreatic beta-cells: specific pacemakers for specific mechanisms.
Fridlyand, L.E., Tamarina, N., and Philipson, L.H.
Am J Physiol Endocrinol Metab 299, E517-532, 2010. PMID 20628025
PubMed
MathModel: Chicago1
Glucose sensing in the pancreatic beta cell: a computational systems analysis.
Fridlyand LE, Philipson LH.
Theoritical Biology and Medical Modeling, 2010, May 24;7:15
PubMed
MathModel: GlucoseSensitivity-1
MathModel: GlucoseSensitivity-2
Lysosomal Pathology and Osteopetrosis upon Loss of H+-Driven Lysosomal Cl– Accumulation
Stefanie Weinert, Sabrina Jabs, Chayarop Supanchart, Michaela Schweizer, Niclas Gimber, Martin Richter, Jörg Rademann, Tobias Stauber, Uwe Kornak, and Thomas J. Jentsch
Science 11 June 2010: 1401-1403.Published online 29 April 2010 [DOI:10.1126/science.1188072]
PubMed
Effect of ATP Binding and Hydrolysis on Dynamics of Canine Parvovirus NS1.
Niskanen, E.A., Ihalainen, T.O., Kalliolinna, O., Hakkinen, M.M., and Vihinen-Ranta, M.
J Virol 84, 5391-5403. (2010).
PubMed
The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation.
Wang J, Xu L, Wang E, Huang S.
Biophys J. 2010 Jul 7;99(1):29-39.
PubMed
MathModel: 'xuli: BJ_cellfate_2010'
Purification of actin from fission yeast Schizosaccharomyces pombe and characterization of functional differences from muscle actin.
Ti SC, Pollard TD.
J Biol Chem. 2011 Feb 18;286(7):5784-92. Epub 2010 Dec 9.
PMID: 21148484 [PubMed - in process]
PubMed
BioModel: 'SCT: PiRelease'
Putting one step before the other: Distinct activation pathways for Cdk1 and Cdk2 bring order to the mammalian cell cycle.
Merrick, K.A., and Fisher, R.P.
Cell Cycle 9, 706-714, (2010).
PubMed
Cingulin and paracingulin show similar dynamic behaviour, but are recruited independently to junctions
Paschoud S, Yu D, Pulimeno P, Jond L, Turner JR, Citi S. Mol Membr Biol. 2010 Dec 17. [Epub ahead of print]
PubMed
BioModel: 'dyu: final cingulin model'
Quantitative Measurement of Ca2+ in the Sarcoplasmic Reticulum Lumen of Mammalian Skeletal Muscle
Ziman, A.P., C.W. Ward, G.G. Rodney, W.J. Lederer, and R.J. Bloch.
Biophys J, 2010. 99(8): p. 2705-2714.
PubMed
BioModel: 'dyu: final cingulin model'
Quantifying a pathway: kinetic analysis of actin dendritic nucleation.
Kraikivski P, Slepchenko BM.
Biophys J.2010 Aug 4;99(3):708-15.
PubMed
MathModel: 'pavelkr: Actin_Polymerization and NPF_ARP2/3_Actin'
Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics
Kapustina M, Vitriol E, Elston TC, Loew LM, Jacobson K.
Cytoskeleton (Hoboken).2010 Aug;67(8):519-34.
PubMed
BioModel: 'marynka: CALI'
MLCK-dependent exchange and actin binding region-dependent anchoring of ZO-1 regulate tight junction barrier function
Dan Yu, Amanda M. Marchiando, Christopher R. Weber, David R. Raleigh, Yingmin Wang, Le Shen, and Jerrold R. Turner.
PNAS, vol. 107, no. 18, 8237-8241 (2010). Published online, April 19, 2010, doi:10.1072/pnas.0908869107.
PubMed
BioModel: 'dyu: cacodeltaABR'
BioModel: 'dyu: latrunculin'
BioModel: 'dyu: mouseZO1control&PIK'
A Mitotic Kinesin-6, PavKLP, Mediates Interdependent Cortical Reorganization and Spindle Dynamics in Drosophila Embryos
P. Sommi, R. Ananthakrishnan, D. K. Cheerambathur, M. Kwon, S. Morales-Mulia, I. Brust-Mascher, A. Mogilner.
J Cell Sci., 123: 1862-1872 (2010).
PubMed
BioModel: 'ananth: furrowsinglepathwayconstconcabsorbingbcscaling'
Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues.
Lipshtat, A., G. Jayaraman, J.C. He, and R. Iyengar.
Proceedings of the National Academy of Sciences. 107:1247-1252, 2010.
PubMed
BioModel: 'azilipshtat: PNAS_switch'
BioModel: 'azilipshtat: Rap1_switch'
Kinetics of M1 muscarinic receptor and G protein signaling to phospholipase C in iving cells.
Bjorn H. Falkenburger, Jill B. Jensen, and Bertil Hille
J. Gen. Physiol. 2010; 135 81-97, Published online Jan 25 2010, 10.1085/jgp.200910344.
PubMed
BioModel: 'hillelab: FalkenburgerJGP2010'
Kinetics of PIP2 metabolism and KCNQ2/3 channel regulation studied with a voltage-sensitive phosphatase in iving cells.
Bjorn H. Falkenburger, Jill B. Jensen, and Bertil Hille
J. Gen. Physiol. 2010; 135 99-114, Published online Jan 25 2010, 10.1085/jgp.200910345.
PubMed
BioModel: 'hillelab: FalkenburgerJGP2010'

2009

Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives
Wang J, Xu L, Wang E.
Biophys J. 2009 Dec 2;97(11):3038-46.
PubMed
MathModel: 'xuli: BJ_Circadian_2009'
Phosphodiesterase 1C is dispensable for rapid response termination of olfactory sensory neurons.
Cygnar, K.D., and H. Zhao.
Nat Neurosci. 12:454-62, 2009. PMID 19305400 2712288. 
PubMed
BioModel: 'cygnar: NatureNeuroscience2009'
A genetically encoded reporter of synaptic activity in vivo.
Dreosti E, Odermatt B, Dorostkar MM, Lagnado L.
Nat Methods. 2009 Dec;6(12):883-9. Epub 2009 Nov 8.
PubMed PMID: 19898484.
PubMed
BioModel: 'Leon: Fig.1v7'
BioModel: 'Leon: GECI_Synapse'

Effects of excluded volume due to internal membranes and cytoskeletal structures.
Novak, I.L., Kraikivski, P., Slepchenko, B.M.
Biophysical Journal 97(3): 758-767(2009).
PubMed
This paper employed a customized VCell-based application. The code is available upon request from Igor Novak.
Modeling Spatial and Temporal Dynamics of Chemotactic Networks
Liu Yang and Pablo A. Iglesias
Chemotaxis: Methods and Protocols, Methods in Molecular Biology, vol. 571, pp. 489-505, 2009.
PubMed
BioModel: 'LiuYang: LEGI'.
Subcellular dynamics of type II PKA in neurons.
Zhong, H., G.M. Sia, T.R. Sato, N.W. Gray, T. Mao, Z. Khuchua, R.L. Huganir, and K. Svoboda.
Neuron. 62:363-374, 2009.
Neuron
BioModel: globus: CAT diffusion
BioModel: globus: PKA2D
BioModel: globus: PKA2D with AKAP
Intracellular fluid flow in rapidly moving cells
Kinneret Keren, Patricia T. Yam, Anika Kinkhabwala, Alex Mogilner & Julie A. Theriot
Nature Cell Biology 11, 1219 - 1224 (2009) Published online: 20 September 2009
Nature
MathModel: 'mogilner: JulyConc'
MathModel: 'mogilner: JulyPressure'
Affinity for phosphatidylinositol 4,5-bisphosphate determines muscarinic agonist sensitivity of Kv7 K+ channels
Ciria C. Hernandez, Bjorn Falkenburger, and Mark S. Shapiro
J. Gen. Physiol. 2009;134 437-448, Published online Oct 26 2009, 10.1085/jgp.200910313.
JGP
BioModel: 'bfalken :HernandexFalkenburgerShapiro2009'.
A Tridimensional Model of Proangiogenic Calcium Signals in Endothelial Cells
Luca Munaron
The Open Biology Journal, 2009, 2, 114-129 Publication Date: October 2009
PubMed
BioModel: 'Annalisa03: Imunaron'.
Persistent cAMP-Signals Triggered by Internalized G-Protein-Coupled Receptors.
Calebiro D, Nikolaev VO, Gagliani MC, de Filippis T, Dees C, Tacchetti C, Persani L, Lohse MJ.
PLoS Biol. 2009 Aug;7(8):e1000172 Publication Date: Epub 2009 Aug 18
PubMed
BioModel: 'davide.calebiro: Calebiro_Plos-Biol_2009'
An open model of actin dendritic nucleation.
Ditlev, J.A., N.M. Vacanti, I.L. Novak, and L.M. Loew.
Biophys J. 2009 96:3529-3542.
PubMed
BioModel: 'les: Actin Dendritic Nucleation_Detailed Branching'
BioModel: 'les: Actin Dendritic Nucleation'
MathModel: 'les: Actin Advection and Diffusion'
MathModel: 'les: Actin Advection and Diffusion 2D Cylindrical Transform'
A model of action potentials and fast Ca2+ dynamics in pancreatic beta-cells.
Fridlyand LE, Jacobson DA, Kuznetsov A, Philipson LH.
Biophys J. 2009 Apr 22;96(8):3126-39.
PubMed
MathModel: 'Fridlyand: MouseSpike'
Energetic requirements for processive elongation of actin filaments by FH1FH2-formins
Aditya S. Paul and Thomas D. Pollard
J. Biol. Chem. 284:12533-40, 2009
PubMed
BioModel: 'abiggiep: Formin FH1FH2-Profilin-Actin Elongation'

2008

Analog Modulation of Mossy Fiber Transmission Is Uncoupled from Changes in Presynaptic Ca2
Ricardo Scott, Arnaud Ruiz, Christian Henneberger, Dimitri M. Kullmann, and Dmitri A. Rusakov
The Journal of Neuroscience, 30 July 2008, 28(31): 7765-7773; doi: 10.1523/​JNEUROSCI.1296-08.2008.
PubMed
Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectives.
Wang J, Xu L, Wang E.
PMC Biophys. 2008 Dec 30;1(1):7.
PubMed
MathModel: 'xuli: PMCBiophysics2008'
Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations.
Wang J, Xu L, Wang E.
Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12271-6. Epub 2008 Aug 21.
PubMed
MathModel:'xuli: PNAS2008'.
Quantitative analysis of G-actin transport in motile cells
I.L. Novak, B.M. Slepchenko, A. Mogilner
Biophysical Journal, 95(4):1627-38, 2008
PubMed
MathModel: 'ignovak: Analysis of G_actin transport in 2D fragment'
MathModel: 'ignovak: Analysis of G_actin transport in keratocyte'
Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity
A.B. Goryachev, and A.V. Pokhilkos
FEBS Letters, v. 582, p.1437, (2008)
PubMed
BioModel: 'alex1: full01'.
Analysis of phosphatidylinositol-4,5-bisphosphate signaling in cerebellar Purkinje spines.
Brown, S., F. Morgan, J. Watras, and L.M. Loew.
Biophys J. 95:1795-1812,2008.
PubMed
BioModel: 'brown: Purkinje Compartmental-adapted from Hernjak et al.'
BioModel: 'brown: Purkinje 1D'
BioModel: 'brown: Purkinje 3D-12 PF Stimuli'
BioModel: 'brown: Purkinje 3D-4 PF Stimuli'
BioModel: 'brown: Purkinje 3D Several Spines-12 PF Stimuli'
BioModel: 'brown: PIP2 Diffusion 1D and 3D'
Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks.
Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, Taubenfeld SM, Alberini CM, Schaff JC, Blitzer RD, Moraru II, Iyengar R.
Cell. 2008 May 16;133(4):666-80.
PubMed
BioModel: 'susana: neves_cell_2008'.
The tight junction protein complex undergoes rapid and continuous molecular remodeling at steady state.
Shen L, Weber CR, Turner JR.
J Cell Biol. 2008 May 19;181(4):683-95. Epub 2008 May 12.
PubMed
BioModel: 'leshen: intracellular bleach FLIP'
BioModel: 'leshen: large area membrane bleach FRAP
BioModel: 'leshen: membrane bleach FLIP'
BioModel: 'leshen: small area membrane bleach FRAP'
Calcium Transport Mechanisms of PC12 Cells.
Duman, J.G., L. Chen, and B. Hille.
J. Gen. Physiol. 131:307-323, 2008.
PubMed
BioModel: 'hillelab: DumanJGP2008Fig1A-4block'
BioModel: 'hillelab: DumanJGP2008Fig1A-control'
BioModel: 'hillelab: DumanJGP2008Fig9diff'
BioModel: 'hillelab: DumanJGP2008Fig9undiff'
Calcium signal transmission in chick sensory neurones is diffusion based.
Coatesworth W, Bolsover S.
Cell Calcium. 2008 Mar;43(3):236-49. Epub 2007 Jul 12
PubMed
BioModel: 'coatesworth: 120504_SCAB100B'
BioModel: 'coatesworth: 140105_SCAB100B'
BioModel: 'coatesworth: 190105_SCAB100B'
BioModel: 'coatesworth: 190105_SCAB100P'
BioModel: 'coatesworth: 221204_SCAB100B'
BioModel: 'coatesworth: 240604_SCAB100B'
The role of the FH1 domain and profilin in formin-mediated actin-filament elongation and nucleation.
Paul, A., Pollard, T.
Current Biology, 2008 Jan 8;18(1):9-19.
PubMed
BioModel: 'abiggiep: Formin-Profilin-Actin Polymerization'
Pathway of actin filament branch formation by Arp2/3 complex.
Beltzner CC, Pollard TD.
J Biol Chem 283: 7135-7144.2008.
PubMed
Contact author regarding access to model.

2007

Coordination of Chromosome Alignment and Mitotic Progression Chromosome-Based Ran Signal
Hoi Y. Li, Win Pin Ng, Wong Chi Hang, Pablo A. Iglesias and Yixian Zheng
Cell Cycle. 6(15):1886-1895, 2007.
PubMed
BioModel: 'piglesias: Gorlich6'
Membrane-binding/modification model of signaling protein activation and analysis of its control by cell morphology.
Haugh, J.M.
Biophys J 92, L93-95, 2007.
PubMed
BioModel: 'jmhaugh: Cell shape control'
Switching of membrane organelles between cytoskeletal transport systems is determined by regulation of the microtubule-based transport.
Slepchenko, B.M., Semenova, I., Zaliapin, I., and Rodionov, V.
J. Cell Biol., jcb.200705146, 2007.
PubMed
MathModel: 'boris: fish_melanophore_pigment_aggregation'
MathModel: 'boris: 'fish_melanophore_pigment_dispersion'
Regulation of cAMP dynamics by Ca2+ and G-protein coupled receptors in the pancreatic beta-cell: A computational approach.
Fridlyand, L.E., M.C. Harbeck, M.W. Roe, and L.H. Philipson
Am J Physiol Cell Physiol:293:C1924-C1933, 2007.
PubMed
MathModel: 'Fridlyand: cAMP'
Compartment-Specific Feedback Loop and Regulated Trafficking Can Result in Sustained Activation of Ras at the Golgi.
Narat J. Eungdamrong and Ravi Iyengar
Biophys. J. 2007; 92(3): p. 808-815
PubMed
BioModel: 'eungdamr: eungdamrong and iyengar BiophysJ'

2006

Rapid redistribution of synaptic PSD-95 in the neocortex in vivo.
Gray, N, Weimer R.M., Bureau, I. Svoboda, K
PLoS, v4, Iss 11, e370, 2006.
PubMed
BioModel: 'rweimer: 10 spines'
Does diacylglycerol regulate KCNQ channels?
Suh, B.-C., and B. Hille.
Pflügers Archiv European Journal of Physiology. 453:293-301,2006.
PubMed
BioModel: 'hillelab: SuhHilleEJP2006Fig1b'
Modeling the impact of store-operated Ca2+ entry on intracellular Ca2+ oscillations.
Kowalewski, J.M., P. Uhlen, H. Kitano, and H. Brismar.
Mathematical Biosciences. 204:232-249, 2006.
PubMed
In vivo dynamics of Rac-membrane interactions.
Moissoqlu K, Slepchenko BM, Meller N, Horwitz AF, Schwartz, MAA
Mol Biol Cell. 2006 Jun; 17(6):2770-9. Epub 2006 Apr.5
PubMed
MathModel: 'boris: Schwartz_2D_membrane_diffusion'
MathModel: 'boris: Schwartz_3D_FLIP'
Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes.
J.J. Saucerman, J. Zhang, J.C. Martin, L.X. Peng, A.E. Stenbit, R.Y. Tsien, and A.D. McCulloch..
Proceedings of the National Academy of Sciences. 103:12923-12928.
PubMed
BioModel: 'jsaucer: AKARmyocyte'
BioModel: 'jsaucer: AKARmyocyte_2compart’
BioModel: 'jsaucer: AKARmyocyte_no_cAMP_buffering’
Analysis of a RanGTP-regulated gradient in mitotic somatic cells.
Kalab, P., A. Pralle, E.Y. Isacoff, R. Heald, and K. Weis.
Nature 2006. 440:(7084)697-701.
PubMed
BioModel: 'Pralle: MitoticExtract_added_ImportinB'
BioModel: 'Pralle: MitoticExtract_added_RanQ69L'

2005

Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts.
Schneider, I.C. and Haugh, J.M.
J.Cell B 171:883-892 (2005)
PubMed
BioModel: 'jmhaugh: pdgf gradient sensing'
Modeling and Analysis of Calcium Signaling Events Leading to Long-Term Depression in Cerebellar Purkinje Cells.
N. Hernjak, B. M. Slepchenko, K. Fernald, C.C. Fink, D. Fortin, I.I. Moraru, J. Watras, and L.M. Loew.
Biophysical Journal Volume 89, Dec. 2005, pp. 3790-3806
PubMed
BioModel: 'hernjak: purkinje_compartmental'
BioModel: 'hernjak: purkinje_2d'
Mathmodel: 'hernjak: purkinje_1d'
STAT module can function as a biphasic amplitude filter.
V. Mayya and L.M. Loew.
IEE Proceedings Systems Biology, March 2005, Volume 2, Issue 1, p. 43-52
PubMed
BioModel: 'mayya: STATmodulePaper'
Phospholipase C in living cells: activation, inhibition, Ca2+ requirement, and regulation of M current.
Horowitz LF, Hirdes W, Suh B-C, Hilgemann DW, Mackie K, Hille B.
J. Gen. Physiol. 2005. 126(3):243-262.
PubMed
BioModel: 'hillelab: Horowitz2005JGPprobes'
Rearrangement of the endoplasmic reticulum and calcium transient formation: The computational approach.
Pomorski P, Targos B, Baranska J.
Biochem Biophys Res Commun. 2005 Mar 25;328(4):1126-32.
PubMed
Adenine nucleotide regulation in pancreatic beta cells: Modelling of ATP/ADP - Ca2+ interaction
Fridlyand L., Li Ma, Philipson LH.
Am J Physiol Endocrinol Metab. 289, E839-E848, 2005.
PubMed
MathModel: 'Fridlyand: Chicago2'

2004

Bio-switches: what makes them robust?
Slepchenko, B. M. and Terasaki, M.
Opin. Genet. Dev. 2004; 14/4: 428-434.
PubMed
MathModel: 'boris: MPF_2D Tyson's Model, all speices mobile, slightly different inits in nucleus and outside' MathModel: 'boris: MPF_ODEs_simplified, no aggregates or buffers'
MathModel: 'boris: MPF_ODEs_simplified1, with aggregates'
MathModel: 'boris: MPF_ODEs_simplified2, with buffers'
BioModel: 'boris: Terasaki_MPF1'
A multi-enzyme model for pyrosequencing.
Ali Agah, Mariam Aghajan, Foad Mashayekhi, Sasan Amini, Ronald W. Davis, James D. Plummer, Mostafa Ronaghi, and Peter B. Griffin.
Nucleic Acids Research 2004 32(21):e166
PubMed
BioModel:'Foad:pyro_fin'
Two Complementary, Local Excitation, Global Inhibition Mechanisms Acting in Parallel Can Explain the Chemoattractant-Induced Regulation of PI(3,4,5)P3 Response in Dictyostelium Cells.
Lan Ma, Chris Janetopoulos, Liu Yang, Peter N. Devreotes and Pablo A. Iglesias.
Biophys. J. 2004; 87(6): p. 3764-3774
PubMed
BioModel: 'LiuYang: uniform_public'
BioModel: 'LiuYang: needle_public'
A Signal Transduction Pathway Model Prototype I: Application to Ca2+-Calmodulin Signaling and Myosin Light Chain Phosphorylation.
Lukas, TJ
Biophys. J. 2004;87 1417-1425
PubMed
BioModel: 'tjlukas: Ca_Release_Coupled_MLC'
A Signal Transduction Pathway Model Prototype I: From Agonist to Cellular Endpoint.
Lukas, TJ
Biophys. J. 2004; 87 1406-1416
PubMed
BioModel: 'tjlukas: Ca_Release_Coupled_MLC'
High Mobility of Vesicles Supports Continuous Exocytosis at a Ribbon Synapse.
Matthew Holt, Anne Cooke, Andreas Neef, and Leon Lagnado.
Current Biology, Vol. 14, 173-183, February 3, 2004
PubMed
BioModel: 'Lagnado Lab: TIR_FRAP'
Regulation of KCNQ2/KCNQ3 Current by G Protein Cycling: the kinetics of receptor-mediated signaling by Gq.
Byung-Chang Suh, Lisa R. Horowitz, Wiebke Hirdes, Ken Mackie and Bertil Hille.
Journal of General Physiology, Volume 123, Number 6, June 2004 663-683
PubMed
BioModel: 'hillelab: SuhJGP2004Fig11A
BioModel: 'hillelab: SuhJGP2004Fig12
BioModel: 'hillelab: SuhJGP2004Fig13B'
BioModel: 'hillelab: SuhJGP2004Fig15'

2003

Cyclin aggregation and robustness of bio-switching.
Slepchenko, B. M. and Terasaki, M.
Mol. Biol. Cell 2003;14: 4695 - 4706.
PubMed
MathModel: 'boris: MPF_2D Tyson's Model, all speices mobile, slightly different inits in nucleus and outside'
MathModel: 'boris: MPF_ODEs_simplified, no aggregates or buffers
MathModel: 'boris: MPF_ODEs_simplified1, with aggregates
MathModel: 'boris: MPF_ODEs_simplified2, with buffers
BioModel: 'boris: Terasaki_MPF1'
Kinetic analysis of receptor-activated phosphoinositide turnover
Chang Xu, James Watras and Leslie M. Loew
Journal of Cell Biology, vol. 161, no. 4, May 26, 2003
PubMed
BioModel:'les: PIP2 Hydrolysis JCB Submission'.
Alternatively, the model is available here in an XML-compliant format that can be imported directly into you own workspace within the Virtual Cell. Download the XML file (Do not open this link, use your right mouse button and Save Target As.). Alternatively you may use the html version,(open the link and select all within the browser, copy and paste into a text editor and save as an xml file). Using either version, access the 'Import' dialog box under the 'File' menu item within the Virtual Cell.
Centrosome positioning in interphase cells.
Anton Burakov, Elena Nadezhdina, Boris Slepchenko, and Vladimir Rodionov
Journal of Cell Biology, 2003 Sep 15;162(6):963-9..
PubMed
MathModel: 'boris: NocodazoleTubulin_3D'
Alternatively, the model is available here in an XML-compliant format that can be imported directly into you own workspace within the Virtual Cell. Download the XML file (Do not open this link, use your right mouse button and Save Target As.). Alternatively you may use the html version,(open the link and select all within the browser, copy and paste into a text editor and save as an xml file) Using either version, access the 'Import' dialog box under the 'File' menu item within the Virtual Cell.
Modeling Ca2+ flux in pancreaticB-cells: role of the plasma membrane and intracellular stores
Leonid E. Fridlyand, Natalia Tamarina, and Louis H. Philipson
Am J Physiol Endocrinol Metab, Jul 2003;285: E138-154
PubMed
MathModel: 'Fridlyand: Chicago'

2002

Systems Analysis of Ran Transport
Alicia E. Smith, Boris M. Slepchenko, James C. Schaff, Leslie M. Loew, Ian G. Macara.
Science. 2002 Jan 18;295(5554):488-91
PubMed
MathModel: 'boris: AliciaProblem1_5; basic nonspatial model used to obtain results published in the Science paper'
MathModel: 'boris: AliciaProblem1_5Fast; as in AliciaProblem1_5 but the reactions with mass action kinetics are treated as fast; this model was used to obtain initial conditions for spatial simulations'
MathModel: 'boris: AliciaSpatial_NewFast; the basic spatial model used in the Science paper'
Biomodel: 'les: Smith et al System Analysis of Ran Transport'. This is a later version and is corrected for the competiton between RanGDP and NTF2:RanGDP for the same site on RCC1.
Targeting of rough endoplasmic reticulum membrane proteins and ribosomes in invertebrate neurons.
Rolls MM, Hall DH, Victor M, Stelzer EH, Rapoport TA.
Mol Biol Cell. 2002 May;13(5):1778-91.PMID: 12006669 [PubMed - indexed for MEDLINE]
PubMed
Please contact author for access to this model.
Distinct intracellular calcium transients in neurites and somata integrate neuronal signals.
Johenning FW, Zochowski M, Conway SJ, Holmes AB, Koulen P, Ehrlich BE.
J Neurosci 22: 5344-5353.2002.
PubMed
Please contact author for access to this model.
Computational Cell Biology
Christopher P. Fall, Eric S. Marland, John M. Wagner, John J. Tyson.
The models from the text were implemented into the Virtual Cell by Johann Frederick Cutiongco.
Computational Cell Biology

The following BioModels are available from user: 'CompCell'
Chay-Keizer ER - Models pancreatic beta-cell bursting. Described in 5.4 and illustrated in Figure 5.21.
Hodgkin-Huxley - Models electrical behavior of the squid giant axon. Used to demonstrate interacting ion channels. Described in 2.5.
Keizer-Levine Open-Cell - Models calcium oscillations in bullfrog sympathetic ganglion neurons via RyR channel kinetics. Described in 5.2.3 and illustrated in Figure 5.8.
L-Type Calcium Channels - Models L-type calcium channel kinetics in the Aplysia neuron. Used to demonstrate the rapid equilibrium approximation. Described in 4.1 and illustrated in Figure 4.3.
Morris-Lecar Coincidence Detection - Demonstrates coincidence detection for excitatory inputs. Described in 6.4 and illustrated in Figure 6.9.
Morris-Lecar Gap Junction Coupled - Demonstrates electrical coupling and gap junctions. Described in 6.1.
Morris-Lecar Mutual Excitation - Demonstrates how fast excitatory synapses lead to synchrony and slow excitatory synapses lead to asynchrony in two identically electrically coupled cells. The only parameter modified is beta (=1000/s in Figure 6.6A and =100/s in Figure 6.6C). Described in 6.3.
Morris-Lecar Mutual Inhibition - Demonstrates how fast inhibition leads to antiphase behavior (for t<0.8, beta=1000/s) and slow inhibition leads to in-phase behavior (for t>0.8s, beta=100/s). SurfToVol_PlasmaMembrane 1 and SurfToVol_PlasmaMembrane 2 were changed to 1806 to cancel out KMOLE in the equations for s1 and s2 kinetics. Described in 6.3 and illustrated in Figure 6.7.
Morris-Lecar Mutual Type II - Models electrical behavior of barnacle muscle fiber. Used to demonstrate interacting ion channels. Described in 2.4.

2001

Local Photorelease of Caged Thymosin beta4 in Locomoting Keratocytes Causes Cell Turning
Roy P, Rajfur Z, Jones D, Marriott G, Loew L, Jacobson K.
J Cell Biol. 2001 May 28;153(5):1035-48
PubMed
BioModel: 'partharoy: 7_12_00_model1'.

2000

An image-based model of calcium waves in differentiated neuroblastoma cells.
Fink, C. C., B. Slepchenko, I. I. Moraru, J. Watras, J. Schaff, and L. M. Loew.
Biophys. J. 2000 79:163-183.2000.
PubMed
There are five mathematical descriptions from the following two publications that were generated using the Virtual Cell software. Refer to the detailed model description that describes the following mathematical descriptions. NE_Full is best described in the model description while the other models have slight variations to the description. See Virtual Cell Calcium Dynamics for an introduction to the experiment and to view the experimental and simulation data.
MathModels: 'Boris'
'NE_DifferentGeom1'
Basic model for simulations presented in Biophys. J., July 2000. It uses experimental ER and BkR distributions. Geometry from the image cellmnucnew2.tif
'NE_DifferentGeom2_1'
Simulation presented in Biophys. J. July 2000 with bipolar geometry from the image bpolargeo2.tif
'NE_DifferentGeom3'
Simulation presented in Biophys. J., July 2000 with geometry from the image 525am.tif
'NE_Full'
Simulation provides the best fit to experimental data presented in J. Cell Biol., November 1999 and on WWW (Calcium Dynamics). It uses ER and BkR distributions that are slightly different from experimental. Geometry from the image mask2_smallnucl.tif
'NE_Full_best'
Best fit to experimental data presented in Biophys. J., July 2000. Geometry from the image cellmnucnew2.tif

1999

Morphological control of inositol-1,4,5-triphosphate-dependent signals.
Fink, C. C., B. Slepchenko, I. I. Moraru, J. Schaff, J. Watras, and L. M. Loew.
J. Cell Biol. 147:929-936, 1999.
There are five mathematical descriptions from the following two publications that were generated using the Virtual Cell software. Refer to the detailed model description that describes the following mathematical descriptions. NE_Full is best described in the model description while the other models have slight variations to the description.
See Virtual Cell Calcium Dynamics for an introduction to the experiment and to view the experimental and simulation data.
MathModels: 'Boris'
'NE_DifferentGeom1'
Basic model for simulations presented in Biophys. J., July 2000. It uses experimental ER and BkR distributions. Geometry from the image cellmnucnew2.tif
'NE_DifferentGeom2_1'
Simulation presented in Biophys. J. July 2000 with bipolar geometry from the image bpolargeo2.tif
'NE_DifferentGeom3'
Simulation presented in Biophys. J., July 2000 with geometry from the image 525am.tif
'NE_Full'
Simulation provides the best fit to experimental data presented in J. Cell Biol., November 1999 and on WWW (Calcium Dynamics). It uses ER and BkR distributions that are slightly different from experimental. Geometry from the image mask2_smallnucl.tif
'NE_Full_best'
Best fit to experimental data presented in Biophys. J., July 2000. Geometry from the image cellmnucnew2.tif

How to Access the Published Models

The Virtual Cell is being referenced in published articles since it was used to create the experimental models discussed in these articles. The models have been made public so that other Virtual Cell users may access them and view the results. To access a public model proceed as follows:

BioModels

  1. log on to the Virtual Cell software.
  2. In the Database pane (lower left), Select the BioModels tab from within the VCell Database.
  3. Published models are within the Public Biomodels folder; models are organized by "user name: model name". Open the Search box to search by user name or model name.
  4. Double click the model to open.
  5. If you wish to modify the model or run new simulations, copy it into your VC Workspace under your own User account.

MathModels

  1. log on to the Virtual Cell software.
  2. In the Database pane (lower left), Select the MathModels tab from within the VCell Database.
  3. Published models are within the Public Mathmodels folder; models are organized by "user name: model name". Open the Search box to search by user name or model name.
  4. Double click the model to open.
  5. If you wish to modify the model or run new simulations, copy it into your VC Workspace under your own User account.

Software Support

vcell_support@uchc.edu

The Virtual Cell, a project of NRCAM, is developed by the Center for Cell Analysis & Modeling (CCAM)