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 […]
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 .
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
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 […]
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
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.
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.
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.