schaff/vcell-batch

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 and Running VCell Client as a standalone tool

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

bash
# 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

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

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
3. Deploying VCell Client/Server software detailed instructions
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).

##Random Info

Reset simulation hasdata status
If VCell client simulation list view says 'hasdata=no' but there is data
-----Find sim id (click 'i' button when sim is selected) -> theSimID
-----log into vcell-node1 (or any node not in DMZ, not vcellapi or vcellapi-beta)
-----Check data exists, give cmd " ls /share/apps/vcell3/users/boris/SimID_theSimID* "
-----open oracle db tool (toad,sql,squirrel), log into *** and do query " select * from vc_simulationjob where simref=theSimID; "
-----If the query column 'hasdata' is blank then do update " update vc_simulationJob set hasdata='Y' where simref=theSimID; " and " commit; "
-----log into vcellapi(Rel) or vcellapi-beta(Alpha)
-----Restart VCell docker scheduler service with cmd " sudo docker service update --force --detach=false vcell{rel,alpha}_sched "

Rel restart, login vcellapi
sudo docker service update --force --detach=false vcellrel_activemqint
sudo docker service update --force --detach=false vcellrel_activemqsim
sudo docker service update --force --detach=false vcellrel_mongodb
sudo docker service update --force --detach=false vcellrel_db
sudo docker service update --force --detach=false vcellrel_data
sudo docker service update --force --detach=false vcellrel_sched
sudo docker service update --force --detach=false vcellrel_submit
sudo docker service update --force --detach=false vcellrel_api
​

Alpha restart, login vcellapi-beta
sudo docker service update --force --detach=false vcellalpha_activemqint
sudo docker service update --force --detach=false vcellalpha_activemqsim
sudo docker service update --force --detach=false vcellalpha_mongodb
sudo docker service update --force --detach=false vcellalpha_db
sudo docker service update --force --detach=false vcellalpha_data
sudo docker service update --force --detach=false vcellalpha_sched
sudo docker service update --force --detach=false vcellalpha_submit
sudo docker service update --force --detach=false vcellalpha_api ​

Build quickrun linux solvers
do this in a pristine checkout (cloned).
git clone https://github.com/virtualcell/vcell-solvers.git
cd vcell-solvers

sudo docker build --tag=frm/vcell-solvers:latest -f Dockerfile-local .
sudo docker run -it --rm -v /Users/schaff/.vcell/simdata/temp:/vcelldata frm/vcell-solvers:latest SundialsSolverStandalone_x64 /vcelldata/SimID_0.cvodeInput /vcelldata/SimID_0.ida
-----where /Users/schaff/.vcell/simdata/temp is the simulation data directory (input file) mapped to /vcelldata inside the Docker container.

License

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