About acowan

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So far acowan has created 13 blog entries.

New published model of the PLC/PKC pathway

July 10th, 2017|News, NRCAM publication, Uncategorized, VCell Posts|

2017-07-10. A new publication in Biophysical Journal by Song 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|CCAM Events, News, Uncategorized, VCell Posts|

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 […]

VCell model of Plant and fungal transporters

May 10th, 2017|News, NRCAM publication|

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|News, NRCAM publication|

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.

New publication describes hybrid deterministic – stochastic spatial solver

December 28th, 2016|News, NRCAM publication|

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|News, VCell Posts|

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 […]

September 15th, 2016|News, NRCAM publication|

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|News|

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|News|

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|News, VCell Posts|

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.