VCell - a modeling and simulation framework for computational cell biology

The vcell documentation in Markdown format (*.md) is edited in eclipse using the WikiText plugin

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

http://vcell.org which hosts a free VCell Server for cluster computing and shared database.
Prebuilt installers for vcell-client are available for Windows, Mac and Linux.
http://vcell.org/webstart Location of VCell clients web page links to
-----Public installers path naming scheme= {Alpha,Beta,Rel,Test,...}/VCell_{Alpha,Beta,Rel}_{macos,unix,windows-x64,windows}latest{64,32}bit.{dmg,sh.exe}
-----Install4J updates.xml (read remotely by VCell client when starting to determine if a newer version of VCell has been deployed)
-----BioFormats jar (used by running VCell clients when importing image data, can't be shiiped directly with VCell, license issue)

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 and Running VCell Client as a standalone tool

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

# to build vcell client
git clone https://github.com/virtualcell/vcell
cd vcell
mvn clean install dependency:copy-dependencies
# to run vcell client quickly
./vcell.sh

Eclipse Setup for Windows

Requirements: Git, Maven, Eclipse IDE for Java Developers and Java JDK 1.8 or later

• Open CommandPrompt, navigate to the Eclipse workspace folder.
• Clone the VCell client using git:

git clone https://github.com/virtualcell/vcell

• Open Eclipse, Import the project using Maven. Depending on the Eclipse version there'll be small differences with the importing steps.
  • Important! Deselect the ojdbc6 and ucp subprojects, then Finish to start importing.
  • Once importing is finished (it takes a while) there will be errors.
• Open CommandPrompt again, navigate to the ojdbc6 folder and execute the script in the text file. Do the same for the ucp folder.
• Rebuild the project in Eclipse, there should be no more errors.
• Create a Debug configuration as a Java Application.
  • the Main Class is cbit.vcell.client.test.VCellClientTest
  • the Program Arguments is vcellapi-beta.cam.uchc.edu:8080
  • the VM needed arguments are:

    • the installation directory: -Dvcell.installDir=

    • the software version: -Dvcell.softwareVersion=...

      for example: -Dvcell.installDir=G:\dan\jprojects\git\vcell -Dvcell.softwareVersion=DanDev_Version_7.0_build_99

Building and Running VCell Client/Server

service has 1 image and configuration, manages 1 or more containers, container is a running image
All services defined in ./swarm/docker-compose.yml (collection of services,volumes, dependencies,...)

VCell Server Installation General Requirements

• Linux
• 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

0a) Creating certs details
--(TLS/SSL website for (vcellapi.cam.uchc.edu,vcell-api.cam.uchc.edu)
--Microsoft authenticode codesigning (to prevent install4j from being rejected on windows clients)
--Apple codesigning for macos (prevents from mac refusing install4j install))
0b) Understanding VCell services detailed instructions

1. NEW VCell Server Node configuration detailed instructions
   -----1a) Create new Docker swarm with node or Add node to existing Docker swarm detailed instructions
   -----1b) Finish NEW VCell Server Node configuration detailed instructions
2. Building VCell Client/Server Software detailed instructions
   2a) Github/Travis/Appveyor/Dockerhub Details detials
3. Deploying VCell Client/Server software detailed instructions
   3a) VCell System Flow-Control details
4. Server Administration detailed instructions (.e.g restarting VCell services)
5. Debugging detailed instructions (.e.g debug vcell client/server)

serverconfig.sh file must be customized for your configuration (see vcell/docker/swarm/serverconfig-uch.sh).

License

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