VCell News & Events 2019-07-23T18:00:14+00:00



VCell model of RAF1 membrane dynamics published

February 20th, 2019|

2019-02-14. A VCell spatial model created to identify mechanisms regulating membrane abundance of the small Gprotein RAF1 at the plasma membrane has been published in Molecular Biology of the Cell. Visit our published models page for links to the paper and to the VCell Biomodel.

VCell model of voltage-sensisng phosphatase specificity

February 8th, 2019|

2019-02-04. A new publication from the Hille lab uses a VCell model to reveal emergent properties of the behavior of voltage-sensitive phosphatases. Visit our published models page for links to the paper and to the VCell Biomodel.

VCell 7.1 released

November 20th, 2018|

17-11-2018.   Announcing the release of VCell 7.1.  VCell 7.1 adds the ability to explore existing models in the database and VCell functionality without registration. It has an improved model database info panel with model provenance, annotations, direct links to Pubmed and journal websites for models described in publications.  These add to the new features for 2D kinematics to solve simulations with moving boundaries and the ability to use the COMSOL Multiphysics solver already in VCell 7.0.

New publication of VCell model of calcium dynamics in mossy fiber boutons

July 10th, 2018|

2018-07-10. A new Vcell spatial model of calcium influx, buffering and diffusion in mossy fiber boutons  was published by Chamberland and co-authors in PNAS. Visit our published models page for links to the paper.

19th Annual VCell Short Course

June 18th, 2018|

2018-6-18  VCell hosted  its 19th annual VCell Short Course on June 12-14, 2018. Ten scientists traveled to work with the VCell team to construct Virtual Cell models based on their own research interests. It was exciting to see the breadth of cell biological problems to which VCell models were applied.  Thanks to all for a successful time!

VCell 7.0 with kinematics released

March 15th, 2018|

2018-3-15  Announcing the release of VCell 7.0.  VCell 7 includes new 2D kinematics functionality for solving reaction diffusion equations within moving boundaries.  To support models of cell motility and morphogenesis, this allows users to specify velocities of points, surfaces and volumes within the geometry.  Other features in VCell 7.0 are methods for creating simulated fluorescence for direct comparison to microscopy data, the ability to use COMSOL Multiphysics solver (requires a local COMSOL license) and adaptive meshes for simulating with different spatial scales using EBChombo.  VCell 7.0 has also been redesigned with new reusable modules  and a cloud-hosted software development processes supporting external collaboration and extensibility (GitHub, Travis-Cl, DockerHub).    VCell 7.0 also includes reproducible and portable server and solver deployments using container technologies.

The movie shows cell rotations in a model of actomyosin motility using the kinematics algorithm deployed in VCell 7.0; pseudocolors are myosin concentration.  This model also includes cellular mechanics using an algorithm under development for future deployment in VCell.  This work, and details of the model, are described in:

M. Nickaeen et al. (2017) A free-boundary model of a motile cell explains turning behavior. PLOS Computational Biology 13(11): e1005862.

New publication assesses FRAP analysis methods using VCell VirtualFrap tool.

March 13th, 2018|

2018-03-13. A paper by Kinglsey et al assesses the effects of complex geometries on FRAP recovery curves. They develop a computational model of the FRAP processes to assess methods of analyzing FRAP experiments. They determined that the Vcell VirtualFRAP tool provides the best accuracy to measure diffusion coefficients. A link to the paper can be found on our published models page.


Leslie Loew awarded 2018 Biophysical Society Distinguished Service Award

February 21st, 2018|

2018-02-21.  Leslie Loew received the Distinguished Service Award of the Biophysical Society at its 2017 annual meeting February 17-21. The award acknowledged his ongoing commitment to the Society and his dedicated service as Editor-in-Chief of Biophysical Journal. Congratulations to Les for this well-deserved award.

New publication on how cell shape information alters phenotype features VCell model

December 15th, 2017|

2017-12-15.  A new publication from the Iyngar, Hone and He laboratories using Vcell among a number of other modeling strategies to explore how cell shape information can alter cellular phenotype via tension-independent mechansims. A link to the publication is found in our published models list.


SpringSaLaD version 2 released

December 7th, 2017|

11-30-2017. Version 2 of the SpringSaLaD software was released today. The primary new feature is the ability to directly build models from atomic coordinates in pdb files, using an interactive 3D viewer to compare the course-grained linked spheres representation in SpringSaLaD with the PDB structure.

New publication of novel free-boundary model of a moving cell

December 7th, 2017|

11-14-2017. A new publication, Nickaeen et al. 2017, from the VCell team describes a novel free-boundary model of actin -myosin contractility that couples force-balance and myosin transport equations. A previously developed mass-conservation algorithm originally developed for VCell to solve parabolic equations in moving domains with know kinematics was augmented by coupling with the FronTier front-tracking software and a segregated solver.

VCell model used to estimate diffusion coefficient in FRAP experiments.

December 6th, 2017|

2017-12-06. Simulations from a VCell model were used to estimate the diffusion coefficient of myosin II in fission yeast in a new publication from the Pollard laboratory. Visit our published models page for links to the paper and the public model.

New model of SH2 binding to EGFR published

November 25th, 2017|

2017-11-25.  A new VCell model explores the effect of SH2 domain overexpression on the EGFR signaling pathway in a publication by Jadwin et al.   The results suggest that signaling via SH2 domain binding is buffered over a wide range of concentrations. Explore the model from the listing on our Published Models page

Binding kinetics between VASP and Zyxin explored in VCell model

August 27th, 2017|

2017-8-27. In a new publication from Acevedo et al (2017) binding interactions between VASP and the cytoskeletal adapter protein Zyxin were explored using a VCell model to predict the population distribution of different molecular complexes based on different kinetic parameters. Find a link to the publication in our published models list.

New publication from Hille lab uses VCell model of GPCR signaling in neurons

July 30th, 2017|

2017-07-30. A new PNAS publication by Jung et al. is the latest in a series of VCell models published by the Hille lab. This new model explores the role of arrestin in regulating ERK activity during GPCR signaling. View the model structure through our list of published models.

New published model of the PLC/PKC pathway

July 10th, 2017|

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|

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 project involves coupling ImageJ technology with VCell to improve comparison of image data to simulation outputs, and Joe is working on an enhancement to SpringSaLaD, to allow coarse grained molecular models to be derived directly from atomic coordinates. In addition, a high school intern Nathan Schaumburger is helping to update VCell tutorials. We are excited by their excellent progress so far.

New VCell model of blood coagulation pathway

June 30th, 2017|

2017-6-30. A VCell model has been used to investigate activation of the contact pathway for blood coagulation, describing membrane-dependent reactions for activation of Factor XII and Factor XI in the presence of inhibitors. A link to the paper from Chelushkin et al., 2017 is found in our list of Published Models .

18th Annual VCell Short Course

June 15th, 2017|

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|

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|

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|

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|

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|

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 new VCell beta.

September 15th, 2016|

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