VCell Modeling & Analysis Software
Published in Numerical Simulations, Tools.
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.