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.
Related Software
| Biology Tools | |
|---|---|
| EMBOSS | The European Molecular Biology Open Software Suite |
| NAMD | Parallel, object-oriented molecular dynamics |
| GROMACS | Molecular dynamics simulator, with building and analysis tools |
| VMD | Displays, animates, and analyzes large biomolecular systems 3-D graphics |
| simuPOP | Forward-time population genetics simulation environment |
| MUSCLE | MUltiple Sequence Comparison by Log-Expectation |
| SeaView | Graphical user interface for molecular phyologeny |
| SeqViz | DNA, RNA, and protein sequence viewer |
| TREE-PUZZLE | Reconstruction of phylogenetic trees by maximum likelihood |
| TreeView X | Displays and prints phylogenetic trees |
| CellProfiler | Image analysis application for researchers |
| napari | Python-based image viewer |
| COPASI | Biochemical systems simulator |
| VCell | Modeling and simulation framework |
| NEURON | Build and run biophysically detailed models |
| NEST | Simulator for spiking neural network models |
Read our verdict in the software roundup.
 LinuxLinks helps you discover the best free and open source software for Linux. Explore our extensive collection of recommended applications, including alternatives to popular proprietary software.We also publish software reviews, Linux tutorials, hardware reviews, free programming books and articles covering the wider open source community. Browse our Linux resources to discover more. Know a useful free and open source Linux application we haven't covered? Suggest a program for inclusion. Has your software been featured on LinuxLinks? Display one of our Featured on LinuxLinks badges on your website or GitHub README. |
Please read our Comment Policy before commenting.