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

Events

News

VCell model of Axon Initial Segment

April 5th, 2021|

2021-4-05. A VCell model was used to assess the role of casein kinase 2 and ankyrin-G on sodium channel recruitment to the axon initial segment. Find links the citation on our published models page.

VCell 7.4 released

March 23rd, 2021|

2021-03-23.VCell 7.4 has been released.  New in VCell 7.4 is the ability to preview geometries from the VCell database, vastly accelerated multiple trajectory stochastic simulations using the Gibson-Bruck solver, extension of unit display and automatic conversion to rate and assignment rules, support for external access to containerized versions of some VCell solvers with command line execution, as well as numerous additional improvements and bug fixes.

New VCell model of Ras signaling

March 18th, 2021|

2021-3-18. A new paper by Kerbai Eroume in the Carlier lab published in PLOS One explores how cell shape affects the signaling mechanisms that determine cell polarization. Find links to the model and citation on our published models page.

VCell 7.3 released

November 30th, 2020|

2020-11-30. Announcing the release of VCell 7.3!  VCell 7.3 adds capabilities for multiple trajectories for non-spatial stochastic simulationss, interchange with the Open Modeling EXchange format (.omex), and automatic assignment of catalysts in the reaction diagram as well as numerous additional improvements and bug fixes.

VCell model of Ca-cAMP-PKA

November 17th, 2020|

2020-11-17. A VCell model was used to explore Ca2+-cAMP-PKA signalling circuits in a new publication from the Rangamani and Zhang laboratories. Find links to the model and citation on our published models page.

VCell model of agonist-induced signaling

November 16th, 2020|

2020-11-16. A new publication from the Lambert lab investigates the mechanisms that set the dynamic range of agonist-induced signaling using fluorescence imaging coupled with VCell modeling.   Visit our published models page for links to the paper and to access the VCell model.

New VCell model of Ras signaling copy

November 3rd, 2020|

2020-9-3. A new VCell model created incollaboration between the McCulloch and Zhang labs helped to demonstrate that a second phase of RhoA activation is required to maintain RhoA-mediated transcription after receptor signalling ends. Find links to the model and paper by Zhang et al. on our published models page.

VCell model of Ca2+ signaling in vascular smooth muscle

October 20th, 2020|

2020-10-20. A new publication from the Rangamani and Iyengar labs using VCell modeling to explore how cell shape affects calcium dynamics in vascular smooth muscle cells.   Visit our published models page for links to the paper.

2020 CompCellBio Workshop

August 6th, 2020|

2020-08-05. The 2020 Computational Cell Biology Workshop was held as an online event Aug 3-5.  Find videos of the key presentations here.  Over 70 individuals participated overall; 16 individuals created models with VCell, COPASI and SpringSaLaD with help from CCAM team members in breakout rooms.  A screen shot of one the opening day presentations serves in place of our traditional group photo this year.

VCell model of diffusion in axon initial segment

July 10th, 2020|

2020-07-10. A new publication analyzes fluorescence photobleaching experiments using VCell numerical simulations to explore mechanisms of for differentiating somatodendritic and axonal compartments.   Visit our published models page for links to the paper.

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.

VCell model of cAMP signaling

October 28th, 2019|

2019-11-28. VCell was used to create a 2D spatial model of cAMP intracellular signaling in a new publication by Stone and colleagues.     Visit our published models page for links to the paper.

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. https://doi.org/10.1371/journal.pcbi.1005862