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 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|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

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

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.

VCell 3-day course June 20-22, 2016

June 9th, 2016|News, VCell Posts|

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

 

 

New VCell model of blood coagulation factors

June 9th, 2016|News, VCell Posts|

2016 -06-09  Hysteresis-like binding of coagulation factors x/xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization (Podoplelova et al. 2016. Biochim Biophys Acta. 1858:1216-1227. PMID 26874201).  Find the public BioModel here.

New VCell Model from the Hille lab

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 VCell model of G-protein coupled receptors

June 9th, 2016|News, VCell Posts|

2016-05-03  A new model of pancreatic beta cell G-protein coupled receptors and second messenger interactions was recently published in PLoS One by Fridlyand and Philipson. Go to our Published Models listing to link to the publication and view details of the model.

New published VCell Model of protease-activated receptor 2 signaling.

June 8th, 2016|News, VCell Posts|

2016-03-01.   A new publication describes a VCell model that evaluates the contributions of protein kinases and beta-arrestin to termination of protease-activated receptor 2 signaling. Visit the Published Models page for details and links to the publication.

New method for particle-based simulations with excluded volume.

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.