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VCell compute cluster online

November 21st, 2017|Comments Off on VCell compute cluster online

11/21/2017 10:06am EST:  VCell compute cluster is back online.

VCell compute cluster offline

November 21st, 2017|Comments Off on VCell compute cluster offline

11/21/2017 9:00AM:  The VCell compute cluster upgrade is in progress, expect full functionality by 10:30AM EST today.  Sorry for any inconvenience.

New published model of the PLC/PKC pathway

July 10th, 2017|Comments Off on New published model of the PLC/PKC pathway

2017-07-10. A new publication in Biophysical Journal by Mohan et al. uses a VCell model to define mechanisms for signal amplification in the PLC/PKC pathway during chemotaxis.  Link to the publication and view model details from our Published Models listing.

Summer Research Projects

July 1st, 2017|Comments Off on Summer Research Projects

7-1-2017.  CCAM welcomes several undergraduates and a graduate rotation student who are working on projects related to VCell this summer . Undergraduate students include Keeyan Ghoreshi, Anvin Thomas, Natalie de la Garrique and Shahan Kamal from UConn Storrs and Kevin Gaffney from the University of Oklahoma. Joe Masison is a new MD/PhD student from University of Maryland. Keeyan is working on the infrastructure for Sloppy Modeling projects, Shahan is modeling pathways using high-throuput data, Natalie is building Model Bricks, and Anvin is building VCell models for analyzing optogenetic experiments and developing general tools for assessing parameter identifiability in VCell. Kevin’s […]

18th Annual VCell Short Course

June 15th, 2017|Comments Off on 18th Annual VCell Short Course

VCell was pleased and honored to host its 18th annual VCell Short Course on June 12-14, 2017. Twelve national and international scientists traveled to work with VCell developers and administrators to construct Virtual Cell models based on their own, personal research interests. Thanks to all for a successful time!

VCell model of Plant and fungal transporters

May 10th, 2017|Comments Off on VCell model of Plant and fungal transporters

2017-05-10. A VCell model has recently been published by Wittek et al. that describes the battle between fungal and plant  sugar transporters. View model details from our Published Models listing.

New VCell model of kidney podocyte cytoskeleton

March 10th, 2017|Comments Off on New VCell model of kidney podocyte cytoskeleton

2017-03-10. A new model from the Iyengar and Loew laboratories examines how cytoskeletal dynamics effect local changes in the complex morphology of kidney podocytes. Link to the publication and view model details from our Published Models listing.

SpringSaLaD Update

January 8th, 2017|Comments Off on SpringSaLaD Update

Update released August 4, 2016. It fixes a minor bug in cluster size statistics. Go to CCAM Software to replace your current version.

New publication describes hybrid deterministic – stochastic spatial solver

December 28th, 2016|Comments Off on New publication describes hybrid deterministic – stochastic spatial solver

A new publication in PLoS Computational Biology from Boris Slepchenko and coworkers describes the new hybrid deterministic stochastic spatial solver used in VCell.  Schaff, J.C., F. Gao, Y. Li, I.L. Novak, and B.M. Slepchenko. 2016. Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology. PLoS Comput Biol. 12:e1005236. PMID 27959915

 

VCell 6.1 released to beta site

October 25th, 2016|Comments Off on VCell 6.1 released to beta site

2016-10-14.  A new version of VCell (6.1) was released to beta site. The new version replaces VCell 6.0 in beta, and enhances the new Rule-Based Modeling capabilities available in VCell. Advantages of Rule-Based Modeling in VCell are

  • Specify rule-based models in a GUI, no scripting language required
  • Rule-based models can span multiple compartments
  • Reactions and rules can be mixed in one model
  • Full support for rules in all VCell Application types (spatial, nonspatial, deterministic, stochastic).
  • A set of rules can be simulated with Network-Free Simulator NFSim
  • “Molecular Anchors” in rule-based models that keeps membrane-bound receptors attached to the membranes.

Visit the Download page to try the […]

September 15th, 2016|Comments Off on

2016-09-15 A new publication in Bioinformatics by Jim Schaff and Michael Blinov describes the new Rule-based modeling features in VCell 6.0. See Schaff et al., 2016. Rule-based modeling with Virtual Cell. BioInformatrics 23:2880-2882, PMID 27497444

New VCell model of PDE role in AMPAR trafficking

September 10th, 2016|Comments Off on New VCell model of PDE role in AMPAR trafficking

2016-09-10. A new publication in JBC describes a new VCell model used by Song et al. to study the role of PDE1 and PDE2 in AMPA receptor trafficking in medium spiny neurons.  Link to the publication and view model details from our Published Models listing.

New VCell model of dendritic spines

August 30th, 2016|Comments Off on New VCell model of dendritic spines

2016-08-30 A recent publication in PNAS describes a VCell model developed as collaboration between the Rangamini group at UC Davis and the Oster lab at UC Berkeley.  The model couples biochemical signaling machinery with actin remodeling events in the dendritic spine; view the details on our Published Models list.

New VCell models of chemotactic networks

July 27th, 2016|Comments Off on New VCell models of chemotactic networks

2016-07-27   A new publication from Sayak Bhattacharya and Pablo Iglesias at Johns Hopkins University describes the step-by-step construction of dynamical models of chemotactic networks using VCell (Bhattacharya and Iglesias 2016. Methods Mol. Biol. 1407:397, PMID 27271916).  Publically available VCell models associated with the paper can be found on our list of published models here.

New VCell models of cAMP domains

July 15th, 2016|Comments Off on New VCell models of cAMP domains

2016-07-15 VCell models were used to test possible mechanisms for maintenance of subcellular microdomains of cAMP in cardiomyocytes in a recent publication in PLoS Computational Biology by Yang et al. Find the publication and details of the models on our Published Models listing.

VCell 3-day course June 20-22, 2016

June 9th, 2016|Comments Off on VCell 3-day course June 20-22, 2016

12 investigators traveled to CCAM to work with the VCell team, developing a model relevant to their specific research project.

 

 

New VCell model of blood coagulation factors

June 9th, 2016|Comments Off on New VCell model of blood coagulation factors

2016 -06-09  Hysteresis-like binding of coagulation factors x/xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization (Podoplelova et al. 2016. Biochim Biophys Acta. 1858:1216-1227. PMID 26874201).  Find the public BioModel here.

New VCell Model from the Hille lab

June 9th, 2016|Comments Off on New VCell Model from the Hille lab

VCell models were used to quantitatively analyze FRET measurements were used to demonstrate that voltage-sensing phosphatases (VSPs) have catalytic activity for PIP3 (Keum et al. 2016.  Phosphoinositide 5- and 3-phosphatase activities of a voltage-sensing phosphatase in living cells show identical voltage dependence. Proc Natl Acad Sci U S A. 10.1073/pnas.1606472113, PMID 27222577).  Find the public VCell model here.

New VCell model of G-protein coupled receptors

June 9th, 2016|Comments Off on New VCell model of G-protein coupled receptors

2016-05-03  A new model of pancreatic beta cell G-protein coupled receptors and second messenger interactions was recently published in PLoS One by Fridlyand and Philipson. Go to our Published Models listing to link to the publication and view details of the model.

New published VCell Model of protease-activated receptor 2 signaling.

June 8th, 2016|Comments Off on New published VCell Model of protease-activated receptor 2 signaling.

2016-03-01.   A new publication describes a VCell model that evaluates the contributions of protein kinases and beta-arrestin to termination of protease-activated receptor 2 signaling. Visit the Published Models page for details and links to the publication.

New method for particle-based simulations with excluded volume.

June 8th, 2016|Comments Off on New method for particle-based simulations with excluded volume.

2016-02-02  SpringSaLad (Springs, Sites, and Langevin Dynamics) is a new software that uses a course-grained approach to model biomolecules as a group of linked spherical sites with excluded volumes.  The software user material is available here.  Read about the method and software in  Springsalad: A spatial, particle-based biochemical simulation platform with excluded volume. Michalski, P.J., and L.M. Loew. 2016 Biophys J. 110:523-529. PMID 26840718.

New VCell Model of phosphoinositide signaling

June 8th, 2016|Comments Off on New VCell Model of phosphoinositide signaling

2016-06-08  A new VCell Model from the Hille lab describes the dynamics of phosphoinositide signaling in sympathetic neurons.   Details of the model and links to the publication can be found on our Published Models listing.

New VCell model of PAR2 desensitization

March 15th, 2016|Comments Off on New VCell model of PAR2 desensitization

2016-03-15. A new VCell model  of the mechanisms and kinetics of desensitization of the protease-activated receptor-2 (PAR2), a Gq-PCR, was published by Jung et al. in the Journal of General Physiology.  Visit the Published Models listing to view the model details and link to the publication.

February 2nd, 2016|Comments Off on

2016-02-02 Paul Michalski and Les Loew describe their new Spring SaLaD sofware for spatial, stochastic, particle-based modeling of biochemical systems at the mesoscale. See the publication Michalski and Loew, 2016. SpringSaLaD: A Spatial, Particle-Based Biochemical Simulation Platform with Excluded Volume. Biophysical Journal 110:523-529. PMID 26840718