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:
- a standalone modeling and simulation tool (vcell-client)
- a shared server providing a centralized model database, cluster computing and shared storage (vcell-server, vcell-api)
- simulation solvers written in C++/Fortran/Python and developed as part of the project as well as third party solvers and analysis.
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.
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 (http://github.com/jcschaff/vcell-solvers).
Requirements: Git, Maven, and Java JDK 1.8 or later
git clone https://github.com/virtualcell/vcell
cd vcell
mvn clean install dependency:copy-dependencies
./vcell.sh
Requirements:
- Linux or Macos
- Git, Maven, and Java JDK 1.8 or later to build vcell-client and vcell-server
- Docker (swarm mode)
- Singularity (Linux) or Singularity in a Virtual Machine (Macos needs VirtualBox and Vagrant)
- PostgreSQL or Oracle database
- SLURM service for batch scheduling
- Obtain an Install4J license if creating client installers
$ git clone https://github.com/jcschaff/vcell
$ cd vcell/docker
$ ./build.sh <args>
$ ./serverconfig.sh <args>
$ ./deploy.sh <args>
# see README in vcell/docker
serverconfig.sh file must be customized for your configuration (see vcell/docker/serverconfig-uch.sh).
Virtual Cell software is licensed under the MIT open source license.