VCell Modeling & Analysis Software 2022-06-09T19:24:39+00:00

VCell is hiring Application Developers! 

Please visit the CCAM Employment page for more information.

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

SpringSaLaDSpringSaLaD 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 tutorial at ICSB 2022 in Berlin

2022-09-12. The VCell team will give a tutorial at the 21st International Conference on Systems Biology – the premier meeting on systems studies in biology, human evolution disease and planetary health. The meeting will take place in Berlin, Germany on October […]

The 23rd Annual Workshop on Computational Cell Biology

2022-05-25. The 23rd Computational Cell Biology workshop took place at R. D. Berlin Center for Cell Analysis and Modeling (CCAM) on May 23-25th. For 3 days more than 40 online participants learnt how to use VCell, COPASI and SpringSalad software […]

New VCell Model of nutrients transporter network in plants

2022-04-14. A new compartmental VCell Model was used to explore nutrients transporter network in plants. Find links to the paper and BioModel on our published models page.

VCell is used in Nature biosynthesis paper

2022-02-10. VCell was used to analyze structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis in a new Nature paper (available on our published models page).

Teaching with VCell MathModels

2021-12-8. A discussion of how to use a VCell MathModel to teach mathematical modeling in cellular systems has been published by the Carlier lab with contributions from Cowan and Loew. Find links to the paper and public VCell models […]

New VCell Model of Nucleocytoplasmic Actin Dynamics

2021-11-24. A new VCell Model of actin dynamics was used to explore how phsophorylation of cofilin is involved in transmission of signals to the transcriptional machinery by depleting of nuclear G-actin. Find links to the paper on our published […]

VCell Model of LINE-1 RNA lifecycle

2021-10-05. A new publication by Martin et al. describes a VCell model of the lifecyle of LINE-1 RNA elements in order to understand their activation and propagation. Find links to the paper and public VCell models on our published […]

VCell Used to Validate new cAMP Model

2021-10-04. VCell was used to validate a new model for cAMP metabolism used to explore cAMP signaling in pulmonary microvascular endothelial cells. Find links to the paper and on our published models page.

VCell Partners

-VCell acknowledges our collaborative partners that enhance VCell capabilities

-Software Associates

EJ Technologies

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

Funding

NIGMS National and Regional Resources (R24) Program

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