About acowan

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So far acowan has created 10 blog entries.

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 […]

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.

New VCell models of cAMP domains

July 15th, 2016|News|

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.

New VCell model of PAR2 desensitization

March 15th, 2016|News, VCell Posts|

2016-03-15. A new VCell model  of the mechanisms and kinetics of desensitization of the protease-activated receptor-2 (PAR2), a Gq-PCR, was published by Jung et al. in the Journal of General Physiology.  Visit the Published Models listing to view the model details and link to the publication.

February 2nd, 2016|News, NRCAM publication|

2016-02-02 Paul Michalski and Les Loew describe their new Spring SaLaD sofware for spatial, stochastic, particle-based modeling of biochemical systems at the mesoscale. See the publication Michalski and Loew, 2016. SpringSaLaD: A Spatial, Particle-Based Biochemical Simulation Platform with Excluded Volume. Biophysical Journal 110:523-529. PMID 26840718