18th Annual Virtual Cell Short Course
June 12 -14, 2017

Frontpiece landscape_600wide

Download VCell
  • One-stop simulation shopping: deterministic (compartmental ODE or  reaction-diffusion-advection PDE), stochastic reactions (several 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.  Models can be formulated as an explicit network or generated from graphically expressed rules.
  • VCell is free and has automatic installers for Windows, Mac OS and Linux.
  • Inexperienced modelers enter reactions and pathways in a biology-based interface; VCell automatically creates the math for you. Experienced modelers can enter math directly.
  • Simulations can run on our remote servers from any low-cost laptop; optionally simulations can also be run locally without an internet connection.
  • Model geometries may be derived from idealized analytical expressions or from experimental 2D or 3D microscope images.
  • Models and simulations can be accessed from anywhere; models can be shared among collaborators or made publicly available.


SpringSaLaD Update

Update released August 4, 2016. It fixes a minor bug in cluster size statistics. Go to CCAM Software to replace your current version.

New publication describes hybrid deterministic – stochastic spatial solver

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. […]

VCell 6.1 released to beta site

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 […]

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 […]

For additional posts see News & Events.

What Is 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. VCell permits construction of models, application of numerical solvers to perform simulations, and analysis of simulation results, offering the choice of multiple physical approximations and simulation technologies to appropriately model a particular system. The BioModel interface provides an intuitive interface to construct models using either pathway diagrams or rules and from a single model of the physiology allows a choice of compartmental (0 dimensions) or spatial (1,2 or3 dimensions) applications of the physiology that can apply  stochastic, determistic, or hybrid stochastic/deterministic solvers.  Applications are automatically translated into full mathematical descriptions of reaction and diffusion systems and then solved via fully validated numerical methods. A MathModel interface provides a direct interface to develop models using a math description language.  VCell supports multiple biophysical mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion and electrophysiology.

Who Are We?

The Virtual Cell is currently developed and  funded as a National Resource Center, National Resource for Cell Analysis and Modeling (NRCAM), by the National Institute of General Medical Sciences(NIGMS), grant number P41 GM103313. NRCAM 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?

NRCAM, responsible for the development of VCell, resides at The Center for Cell Analysis & Modeling, at UConn Health. CCAM, established in 1994, consists of expertly trained faculty of varying backgrounds. This diverse wealth of knowledge ranges 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.

What Our Users Say!

“Searching through existing software packages, our attention focused on Virtual Cell….For solving differential equations, as well as storing and sharing models, Virtual Cell provides free, remote solvers and storage servers available to a worldwide community of users.”
Baik J, Rosania GR.
2013 Modeling and Simulation of Intracellular Drug Transport and Disposition Pathways with Virtual Cell.
Journal of pharmaceutics & pharmacology:1(1) .
“A key advantage of Virtual Cell is that the math is performed “behind the scenes???, so the user can focus on the biochemical reactions and biology of interest. Virtual Cell was developed … to be a simple yet powerful tool to allow students and biologists with relatively little math background to perform computational modeling.”
Greenwald EC, Polanowska-Grabowska RK, Saucerman JJ. 2014. Integrating fluorescent biosensor data using computational models. Methods in Molecular Biology:1071:227-48.
“An advantage of the compartmentalized models supported by Virtual Cell is the ease of building complex, but well constrained models that are informed by experimental data.”
Hake, J., P.M. Kekenes-Huskey, and A.D. McCulloch. 2014. Computational modeling of subcellular transport and signaling.
Current Opinion in Structural Biology. 25:92-97.
Download Now!

The Virtual Cell is a software modeling environment for quantitative cell biological research.

Users can create simple or complex multi-layered models with a Java web-based interface. Distinct biological and mathematical frameworks exist within a single graphical interface designed for experimental cell biologists or theoretical biophysicists.
Download Now!