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 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.
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.
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.