Virtual cell modeling and simulation software.

Abstract

Virtual Cell (VCell, http://vcell.org) is free open-source software for modeling cell biological systems. Biology-based interface is designed for researchers with no programming/scripting experience: they enter reactions and reaction rules in an intuitive graphical way, and VCell automatically creates the math for you. Models and simulations can be accessed from anywhere using the VCell database; models can be shared among collaborators or made publicly available. Simulations can be run locally (on a user's computer) or using our server - a job can be sent to a server and results can be retrieved any time later. VCell provides a variety of simulation frameworks. The same reaction network can be simulated using deterministic (compartmental ODE) and/or stochastic reactions (SSA solvers) simulators. By adding a geometry for compartments and diffusion for species, the same reaction network can be simulated as a reaction-diffusion-advection PDE with support for 2D kinematics and/or using spatial stochastic (reaction-diffusion with Smoldyn, http://smoldyn.org). Geometries from 2D or 3D microscope images or from idealized analytical expressions can be used, and membrane flux, lateral membrane diffusion and electrophysiology could be incorporated. If elements of the model are defined by reaction rules (using a novel graphical user interface for defining, visualizing, and verifying rule-based models), the model can be simulated using BioNetGen (http://bionetgen.org) engine and/or network-free agent-based simulations. The VCell models can be exchanged with other tools using standard formats such as SBML and BNGL, as well as exported as MatLab, SED-ML, and COMBINE archive. The latest developments include better support of SBML features, the possibility to fully annotate the models, view models online, interact with ImageJ, and send simulations to runBiosimulations (https://run.biosimulations.org) service for online simulations and visualization with modified parameters. (Supported by NIGMS grant R24 GM137787)