vcell - a modeling and simulation framework for computational cell biology

The VCell is a comprehensive framework for modeling and simulation of cell biology from biological pathways down to cell biophysics. VCell supports biochemical network and rule-based modeling and electrophysiology in compartmental modeing and within cellular geometry.

Simulation capabilities include ODEs, Reaction-Diffusion equations within cellular geometry, Gillespie and Hybrid stochastic solvers, Particle based spatial simulations, network free simulations and cell kinetimatics (moving boundary problems).

The VCell software consists of:

1. a standalone modeling and simulation tool (vcell-client)
2. a shared server providing a centralized model database, cluster computing and shared storage (vcell-server)
3. simulation solvers written in C++/Fortran/Python and developed as part of the project as well as third party solvers and analysis.

Download VCell

Prebuilt installers for vcell-client are available for Windows, Mac and Linux at http://vcell.org which hosts a free VCell Server for cluster computing and shared database.

Building VCell

This VCell github project includes all Java/Python source code required to build both the VCell client and the VCell Server.
The simulation solver source code is available as a separate project, but the executables currently bundled within this repository for your convenience, but are separately available in the vcell-solvers project (http://github.com/jcschaff/vcell-solvers).

Building VCell Client as a standalone tool

Requirements: Git, Maven, and Java JDK 1.8 or later

git clone https://github.com/virtualcell/vcell cd vcell mvn clean verify

scripts to run the standalone client will be available soon.

Building VCell Client/Server

Requirements:

• Git, Maven, and Java JDK 1.8 or later to build vcell-client and vcell-server

• PostgreSQL or Oracle database

• ActiveMQ messaging service

• MongoDB nosql database (for distributed logging)

• SLURM service for batch scheduling

• Install4J, VirtualBox, Vagrant to build platform installers for Windows, Mac, Linux. ** Install VirtualBox for your platform ** Install Vagrant for your platform (using the VirtualBox provider. ** Obtain an Install4J license if creating client installers

• $ git clone https://github.com/jcschaff/vcell

• $ cd vcell

• $ cd deploy

• $ ./deploy.sh server-config.include

server-config.include file must be customized for your configuration (see examples in /deploy directory).

a Vagrant box virtual machine will act as a reference implementation for a VCell Server

License

Virtual Cell software is licensed under the MIT open source license.