VCell News & Events 2018-02-26T20:32:04+00:00

Events

News

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 VCell developers and administrators 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

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

New VCell model of PDE role in AMPAR trafficking

September 10th, 2016|

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|

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|

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|

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|

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