2019-6-18 CCAM hosted a Computational Cell Biology Workshop on June 24-26, 2019, a combined workshop for both VCell and COPASI modeling software. Ten scientists from the US, Netherlands and Germany traveled to work with the VCell and COPASI teams to construct models based on their own research interests. It was exciting to see VCell and COPASI models applied to such interesting cell biology projects. Thanks to all for a very successful course!
2018-6-18 VCell hosted its 19th annual VCell Short Course on June 12-14, 2018. Ten scientists traveled to work with the VCell team to construct Virtual Cell models based on their own research interests. It was exciting to see the breadth of cell biological problems to which VCell models were applied. Thanks to all for a successful time!
2018-3-15 Announcing the release of VCell 7.0. VCell 7 includes new 2D kinematics functionality for solving reaction diffusion equations within moving boundaries. To support models of cell motility and morphogenesis, this allows users to specify velocities of points, surfaces and volumes within the geometry. Other features in VCell 7.0 are methods for creating simulated fluorescence for direct comparison to microscopy data, the ability to use COMSOL Multiphysics solver (requires a local COMSOL license) and adaptive meshes for simulating […]
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.
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 […]
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 […]
2016-07-27 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.
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.
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.