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).

VCell software
Download VCell
Building and running VCell Client as a standalone tool
IntelliJ Setup for VCell Client on Windows/Mac
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.
BioFormats jar (used by running VCell clients when importing image data, can't be shipped directly with VCell, license issue)

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

Building, testing and running VCell on the command line

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.
Requirements: Git, Maven, Poetry, Python 3.10, Java 17

Build Java and Python

mvn clean install -DskipTests

INSTALL_DIR=$(pwd)
cd ${INSTALL_DIR}/pythonCopasiOpt/vcell-opt
poetry env use 3.10
poetry install

cd ${INSTALL_DIR}/docker/swarm/vcell-admin
poetry env use 3.10
poetry install

cd ${INSTALL_DIR}/pythonVtk
poetry env use 3.10
poetry install

cd ${INSTALL_DIR}/vcell-cli-utils
poetry env use 3.10
poetry install

Test Java and Python

mvn test -Dgroups="Fast"

INSTALL_DIR=$(pwd)
cd ${INSTALL_DIR}/pythonCopasiOpt/vcell-opt
poetry run python -m pytest

cd ${INSTALL_DIR}/docker/swarm/vcell-admin
poetry run python -m pytest

cd ${INSTALL_DIR}/pythonVtk
poetry run python -m pytest

cd ${INSTALL_DIR}/vcell-cli-utils
poetry run python -m pytest

cd ${INSTALL_DIR}

Run the VCell client (connects to the VCell servers)

./vcell.sh

VCell client IntelliJ setup for Windows and Mac (follow command line instructions first)

Requirements: IntelliJ, Java 17, Python 3.10 and poetry

Follow the instructions above for building Python packages with poetry

Start IntelliJ

Open Project -> Navigate to vcell folder where VCell was installed and built at the previous step.

Edit Configurations -> "+" Application

Name: VCellClient
-cp -> choose vcell-admin, Java 17 SDK of vcell-admin module
Main class: org.vcell.standalone.VCellClientDevMain
Modify options -> check Add VM options

VM options:

-Dlog4j.configurationFile=${INSTALL_DIR}/vcell-cli/src/main/resources/log4j2.xml
-Dcli.workingDir=${INSTALL_DIR}/vcell-cli-utils
-Dvcell.primarySimdatadir.internal=/path/to/local/simdata
-Dvcell.secondarySimdatadir.internal=/path/to/local/simdata
-Dvcell.server.dbConnectURL=jdbc:postgresql://localhost:5432/postgres
-Dvcell.server.dbDriverName=org.postgresql.Driver
-Dvcell.server.dbPassword=dbpassword
-Dvcell.server.dbUserid=dbuser
-Dvcell.server.id=TEST
-Dvcell.softwareVersion=Dev_Version_7.5_build_00
-Dvcell.mongodb.host=localhost
-Dvcell.mongodb.host.internal=localhost
-Dvcell.mongodb.port.internal=27019
-Dvcell.mongodb.database=TEST
-Dvcell.server.maxJobsPerScan=2

VCell client Eclipse setup for Windows and Mac (follow command line instructions first)

Requirements: Eclipse IDE for Java Developers and Java 17, Python 3.10 and poetry

Follow the instructions above for building Python packages with poetry
Start Eclipse
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 an Application in IntelliJ.

Building and Running VCell 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 17 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

VCell-CLI module requires python 3.10 and poetry

Other Details

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))
Understanding VCell services detailed instructions
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
Building VCell Client/Server Software detailed instructions
4.1. Github/Travis/Appveyor/Dockerhub Instructions
Deploying VCell Client/Server software detailed instructions
5.1. VCell System Flow-Control
Server Administration detailed instructions (.e.g restarting VCell services)
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.

virtualcell / vcell

readme