Summer Research Projects

2017-12-01T20:49:22+00:00 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 6.1 released to beta site

2016-11-07T19:15:17+00:00 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 […]

New VCell models of chemotactic networks

2016-11-07T20:00:07+00:00 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 Model from the Hille lab

2016-09-13T16:15:57+00:00 June 9th, 2016|News, VCell Posts|

VCell models were used to quantitatively analyze FRET measurements were used to demonstrate that voltage-sensing phosphatases (VSPs) have catalytic activity for PIP3 (Keum et al. 2016.  Phosphoinositide 5- and 3-phosphatase activities of a voltage-sensing phosphatase in living cells show identical voltage dependence. Proc Natl Acad Sci U S A. 10.1073/pnas.1606472113, PMID 27222577).  Find the public VCell model here.

New method for particle-based simulations with excluded volume.

2016-11-07T20:24:43+00:00 June 8th, 2016|News, VCell Posts|

2016-02-02  SpringSaLad (Springs, Sites, and Langevin Dynamics) is a new software that uses a course-grained approach to model biomolecules as a group of linked spherical sites with excluded volumes.  The software user material is available here.  Read about the method and software in  Springsalad: A spatial, particle-based biochemical simulation platform with excluded volume. Michalski, P.J., and L.M. Loew. 2016 Biophys J. 110:523-529. PMID 26840718.