VCell Modeling & Analysis Software 2024-06-12T18:51:28+00:00

25th Annual On-site CCB Workshop

July 22 – 24, 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

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.

Employment

Please see the CCAM Employment page for opportunities.

News

For additional posts see News & Events.

Reaction-diffusion modeling with VCell used to study biophysical carbon concentrating mechanisms in land plants

2024-06-10. The team of researchers from Michigan State University used reaction-diffusion modeling with VCell to provide insights into biophysical carbon concentrating mechanisms in land plants.
Kaste, J. A., Walker, B. J., & Shachar-Hill, Y. (2024). Reaction-diffusion modeling provides insights into biophysical […]

A VCell model of endocytic nanoclusters is published in Nature Comm

2024-05-14. The team of researchers from Australia and Johns Hopkins University used VCell to design and simulate a model explaining the formation of endocytic nanoclusters driven by distinct recruitment of Dynamin1 long- and short-tail isoforms.
Jiang, A., Kudo, K., Gormal, R.S., […]

VCell at HARMONY 2024

2024-04-10. Michael Blinov and Ion Moraru presented VCell tutorial at HARMONY 2024 at University College London. Other topics discussed include interoperability of multiple standards like SBML, SED-ML and COMBINE archive supported by VCell.

25th Annual Comp Cell Bio workshop

VCell, COPASI and SpringSalad were taught and used for projects at the  25th Annual Computational Cell Biology (CCB) workshop that took place online February 26-28th.  The invited talks were given by Yulia Timofeeva (University of Warwick), James P Sluka (Indiana University) […]

A model of K+ and pH homeostasis in plant cells.

2024-02-12. Ingo Dreyer (U Talca, Chile) and Kai Konrad (U Wuerzburg, Germany) used VCell to design and simulate a model explaining the properties of transporter networks and the coupling of transport across the PM and VM. They demonstrated fundamental principles […]

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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