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Virtual Cell

VCell - a modeling and simulation framework for computational cell biology

The VCell is a comprehensive framework for modeling and simulating cell biology from biological pathways down to cell biophysics. VCell supports the biochemical network and rule-based modeling and electrophysiology in compartmental modeling 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 kinematics (moving boundary problems).

Contents

• VCell software
• Download VCell
• Building VCell
• Building and Running VCell Client as a standalone tool
• Eclipse Setup for VCell Client on Windows/Mac
• Building and Running VCell Server
• CLI Requirements
• Other Details
• License

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

• VCell which hosts a free VCell Server for cluster computing and shared database.
• Prebuilt installers for vcell-client are available for Windows, Mac and Linux.
• WebStart location of VCell clients web page links to
• Public installers path naming scheme= {Alpha,Beta,Rel}/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 shipped 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 as 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

VCell client Eclipse setup for Windows and Mac

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

• Start Eclipse
• In Eclipse: Project Explorer -> Import -> Projects from Git (smart import) -> Clone URI -> Paste https://github.com/virtualcell/vcell.git, follow all next steps
  • If git is installed, you can install VCell client from a local repository:
    • Open CommandPrompt, navigate to the Eclipse workspace folder.
    • Clone the VCell client using git: git clone https://github.com/virtualcell/vcell
    • During Eclipse setup, use an option -> Existing local repository, follow all next steps
• Make sure the project comes in as a Maven project (letter M on the top of the project, not J), otherwise you need to add it to Maven
• Build the project in Eclipse (should start automatically, may come with several errors due to different build order).
• Errors in individual projects can be fixed by Maven -> Update Project for individual projects that display 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=<your install dir>
    • the software version: -Dvcell.softwareVersion=...

      • for example:

        WINDOWS

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

        MAC:

        -Dvcell.installDir=/Users/mike/eclipse-workspace2/vcell
        -Dvcell.softwareVersion=MikeDev_Version_7.0_build_99           
        

  • Make sure JRE is 1.8 or newer (build-in Eclipse JRE may case problems)

Building and Running VCell Server

1. Service has 1 image and configuration, manages 1 or more containers, container is a running image
2. 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

VCell CLI Requirements

1. Make sure to update the submodules git submodule update --init --recursive
2. VCell-CLI module requires python>3.6 and <=3.8.0

Other Details

1. Creating certs details
   1.1. (TLS/SSL website for (vcellapi.cam.uchc.edu,vcell-api.cam.uchc.edu)
   1.2. Microsoft authenticode codesigning (to prevent install4j from being rejected on windows clients)
   1.3. Apple codesigning for macos (prevents from mac refusing install4j install))
2. Understanding VCell services detailed instructions
3. NEW VCell Server Node configuration detailed instructions
   3.1. Create new Docker swarm with node or Add node to existing Docker swarm detailed instructions
   3.2. Finish NEW VCell Server Node configuration detailed instructions
4. Building VCell Client/Server Software detailed instructions
   4.1. Github/Travis/Appveyor/Dockerhub Instructions
5. Deploying VCell Client/Server software detailed instructions
   5.1. VCell System Flow-Control
6. Server Administration detailed instructions (.e.g restarting VCell services)
7. Debugging detailed instructions (.e.g debug vcell client/server)
8. 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.