VCell is hiring Application Developers!
Please visit the CCAM Employment page for more information.
24th Annual CCB Workshop Online Format
February 26 – 28, 2024
VCell
VCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a web application.
- One-stop simulation shopping: deterministic (compartmental ODE or reaction-diffusion-advection PDE with support for 2D kinematics), stochastic reactions (SSA solvers), spatial stochastic (reaction-diffusion with Smoldyn), hybrid deterministic/stochastic and network-free agent based simulations. Support for membrane flux, lateral membrane diffusion and electrophysiology.
- Explicit network or graphically expressed rules can be used to model
- Free with automatic installers for Windows, Mac OS and Linux.
- Biology-based interface for inexperienced modelers; enter reactions and pathways and VCell automatically creates the math for you. Experienced modelers can enter math directly.
- Our remote servers can run complex simulations from any low-cost laptop
- Geometries from 2D or 3D microscope images or from idealized analytical expressions.
- Access models and simulations from anywhere using the VCell database; models can be shared among collaborators or made publicly available.
SpringSaLaD
SpringSaLaD is a stand-alone software tool to explicitly model binding events and state changes among multivalent molecules. It is one of the first algorithms to account for crowding effects within multimolecular clusters. Spring SaLaD models proteins as sets of reactive sites (spheres) connected by stiff springs. The impenetrable spheres capture excluded volume and steric hindrance effects. Langevin dynamics are used to model diffusion of each reaction site, and binding reactions are governed by probability based on diffusion coefficients of the sites, the site radii and the macroscopic on rate. Go here to download the software or read more about the about Spring SaLaD.
Computational Cell Biology
CompCellBio.org is designed to provide a central site for access to software, model repositories, quantitative repositories and educational resources for computational cell biology research. Developed under the NIGMS National and Regional Resources funding that maintains COPASI and Virtual Cell (VCell), two of the most powerful modeling environments for computational cell biology, the website provides the broader community with information and resources to aid in the development of computational models of cell biology.
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Who Are We?
The Virtual Cell was developed with funding from the National Institute of General Medical Sciences (NIGMS) as a Biomedical Technology Research Resource at the Center for Cell Analysis and Modeling (CCAM), and is currently funded by R24 GM137787. CCAM continues to develop new technologies for mathematical models of cell and systems biology through development of new physical formulations of biological mechanisms, developing the numerical methods for mathematically simulating these mechanisms, and bulding software infrastructure to deliver these tools for different types of modeling applications including large reaction network applications, spatial applications and detailed molecular interactions. Meet the VCell Team.
Where Are We?
VCell is developed at The Center for Cell Analysis & Modeling, at UConn Health. Established in 1994, CCAM consists of faculty trained in diverse backgrounds from chemistry, physics, and experimental cell biology to software engineering. Research at CCAM focuses on the development of new approaches for in vivo measurements and manipulation of molecular events within the cell, as well as new computational approaches to organize such data into quantitative models. CCAM is home to the Microscopy Facility, housing numerous extensive fluorescent imaging microscopes, and the High Performance Computing facility.
Please acknowledge the VCell Resource in all publications. VCell is supported by NIH Grant Number R24 GM137787 from the National Institute for General Medical Sciences. And please reference the appropriate citations.
News
For additional posts see News & Events.
VCell at ICSB 2023
VCell was highlighted at the 22nd International Conference on Systems Biology (ICSB) that took place in Hartford October 8-12, 2023. The meeting was organized by CCAM faculty and co-chaired by Pedro Mendes and Ion Moraru. VCell team presented two […]
A model of the cadherin-11 and PDGFR pathways crosstalk
2023-09-22. VCell collaborator Aurélie Carlier from Maastricht University published a manuscript where a computational model in VCell was used to represent the experimentally proven interactions between cadherin-11 and the two PDGFRs. The authors demonstrated the existence of a crosstalk between β-catenin […]
19 new VCell models on G-actin diffusion are published by Haugh group
2023-08-28. VCell collaborator Jason Haugh from North Carolina State University published a manuscript where experiments and VCell modeling demonstrated that G-actin diffusion is insufficient to achieve F-actin assembly in fast-treadmilling protrusions.
Appalabhotla, R., Butler, M.T., Bear, J.E. and Haugh, J.M. G-actin diffusion […]
Biophysical Modeling of the Cell special interests group at ASCB
Prof Margaret Johnson from John Hopkins University and Michael Blinov are hosting the Special Interest Subgroup session on Biophysical Modeling of the Cell at Cell Bio 2023 – an ASCB/EMBO (https://www.ascb.org/cellbio2023/) meeting in Boston, MA, December 2-6. […]
24th Annual Computational Cell Biology (CCB) workshop
2023-06-28. The 24th Annual Computational Cell Biology (CCB) workshop took place at the Center for Cell Analysis and Modeling (CCAM) on June 26-28th. 11 participants from all over the US (from Maryland to Illinois) came to Farmington to work on […]
VCell Partners
-VCell acknowledges our collaborative partners that enhance VCell capabilities
-Software Associates

VCell uses Install4J, a multi-platform installer builder to create our executables.