schaff/vcell-mongo

vcell - a modeling and simulation framework for computational cell biology

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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, vcell-api)
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 [***] 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 (http://github.com/jcschaff/vcell-solvers).

Building VCell Client as a standalone tool

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

bash
git clone https://github.com/virtualcell/vcell
cd vcell
mvn clean install dependency:copy-dependencies
./vcell.sh

scripts to run the standalone client will be available soon.

Building VCell Client/Server

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

bash
$ 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).

License

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