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



VCell model of PLC/PKC signaling

April 7th, 2020|

2020-04-07. A new spatial model of the PLC/PKC pahtway created in VCell was used to explore chemotactic sensing in fibroblasts in a new publication by Nosbisch et al from the Haugh lab.   Visit our published models page for links to the paper and the VCell model.

New VCell model of pattern formation system

March 9th, 2020|

2020-03-09. A new VCell model is used to explore how MYB proteins form an activator-inhibitor system that defines the spot pattern in mokeyflower petals.   Visit our published models page for links to the paper and the VCell model.

VCell model of transport in plants

January 30th, 2020|

2020-01-30. A VCell model is used in a new paper by Dreyer and Michard to re-examine the concept of high- and low-affinity nutrient uptade systems in plants.   Visit our published models page for links to the paper.

VCell 7.2 Released

December 10th, 2019|

2019-12-10. VCell 7.2 has been released.  See the Release Notes for a full list of the many new features in VCell 7.2 including new functionality to store identifiers and text annotations for model components, a service linking VCell simulation with ImageJ image analysis functions, rate rules and assignment rules in ODE applications, improved SBML import along with several other improvements.

20th Annual VCell Short Course

June 30th, 2019|

2019-6-18  CCAM hosted a Computational Cell Biology Workshop on June 24-26, 2019, a combined workshop for both VCell and COPASI modeling software. Ten scientists from the US, Netherlands and Germany traveled to work with the VCell and COPASI teams to construct models based on their own research interests. It was exciting to see VCell and COPASI models applied to such interesting cell biology projects.  Thanks to all for a very successful course!

New model of GIV/girdin modulation of cyclic AMP signals

June 13th, 2019|

2019-06-13. A new Molecular Biology of the Cell publication from the Rangamani lab uses VCell and COPASI to develop a model to examine cross-talk between receptor tyrosine kinases and G proteins that regulate cAMP levels.   Visit our published models page for links to the paper and to the VCell Biomodel.

VCell models aid in design of SH2 domain biosensors

June 4th, 2019|

2019-06-04. A new publication in Science Signaling  from the Haugh and Rao labs describes the use of VCell modeling to assist in designing improved SH2 domain biosensors of EGFR phosphorylation.   Visit our published models page for links to the paper and to the VCell Biomodel.

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-sensing 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.

New VCell analysis of FRAP experiments

January 25th, 2019|

2019-01-25. A new publication from Karvinen et al uses VCell models to analyze photobleaching experiments in their characterization of hydrogel properties. Visit our published models page for links to the paper.

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.