VCell is a modeling and simulation framework for computational cell biology.
It lets researchers build and analyze cell biological systems ranging from biochemical reaction networks to spatial models that use cellular geometry, combining a standalone client, server components, a shared model database, and simulation tools for deterministic, stochastic, hybrid, and particle-based workflows.
This is free and open source software.
Key Features
- Build and simulate biochemical network, rule-based, electrophysiology, and spatial cell biology models.
- Run deterministic ODE and reaction-diffusion simulations, Gillespie and hybrid stochastic simulations, particle-based spatial simulations, network-free simulations, and moving-boundary cell kinematics.
- Use a standalone VCell client with server components for centralized model storage, cluster computing, and shared simulation data.
- Work with cellular geometries derived from microscopy images or analytical expressions.
- Build the Java and Python components from source using Maven, Poetry, Python 3.10, and Java 17.
Website: github.com/virtualcell/vcell
Support:
Developer: Center for Cell Analysis & Modeling, UConn Health
License: MIT License
VCell is written in Java. Learn Java with our recommended free books and free tutorials.
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