data/README_BioSim.md

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Biosimulators_vcell

BioSimulators-compliant command-line interface to the VCell simulation program.

Contents

• Installation
  • Project setup IntelliJ IDEA
  • Project setup Eclipse
  • Maven installation
• Usage
• License
• Development team
• Questions and comments

Installation

To set up the project in IntelliJ IDEA

• Requirements: Git, Maven, Python 3.10, Poetry, Jetbrains IntelliJ IDEA and Java JDK 17

1. Clone the repo
2. Open the project as new project in IntelliJ
3. Go to Files > Project Structure... > Modules and select all modules and then click apply.
4. follow instructions in README.md to build python dependencies
5. Run mvn clean install dependency:copy-dependencies to build the project
6. For creating Run/Debug Configurations:
   • Go to Run/Debug Configurations > + > select Application
   • Name it VCell-CLI
   • Now setup the configuration
     • Add org.vcell.cli.CLIStandalone for Main class:
     • For VM options:

       -Dvcell.installDir=<Your-Project-Directory-Path>
       -Dvcell.softwareVersion="frm_VCell_7.2"
       

     • eg for <Your-Project-Directory-Path>: /Users/akhil/projects/Biosimulators_vcell
     • Add -h for Program arguments: (refer Local Usage for more options)
     • Working Directory: is <Your-Project-Directory-Path>
     • Select vcell-cli as Use classpath of module:
7. Click apply and build

To setup the project in Eclipse

• Requirements: Git, Maven, Python 3.10, Poetry, Eclipse IDE and Java JDK 17

1. Open terminal, navigate to the Eclipse workspace folder.
2. Clone the repo
3. follow instructions in README.md to build python dependencies
4. Run mvn clean install dependency:copy-dependencies to build the project
5. Open Eclipse, Import the project using Maven. Depending on the Eclipse version there'll be small differences with the importing steps.
6. Create a Debug configuration as a Java Application.
   • the Main Class is org.vcell.cli.CLIStandalone
   • Leave the 'Program Arguments' blank.
   • The VM needed arguments are:

      -Dvcell.installDir=<Your-Project-Directory-Path>
      -Dvcell.softwareVersion="VCell_7.3.0.0"
     

Program arguments for both Eclipse and IntelliJ

1. For running a simulation from OMEX and VCML files as an input: -i "/PATH/TO/OMEX/OR/VCML" -o "/PATH/TO/SAVE"
2. For converting a VCML to OMEX file: convert -i "/PATH/TO/VCML" -o "/PATH/TO/SAVE/OMEX"

Maven installation package

Install Docker image

docker pull ghcr.io/biosimulators/vcell

Local usage

usage: vcell [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the VCELL simulation program <http://vcell.org>.

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -i ARCHIVE, --archive ARCHIVE
                        Path to OMEX file which contains one or more SED-ML-
                        encoded simulation experiments or VCML file
  -o OUT_DIR, --out-dir OUT_DIR
                        Directory to save outputs
  -v, --version         show program's version number and exit

Usage through Docker container

docker run \
  --tty \
  --rm \
  --mount type=bind,source="$(pwd)"/tests/fixtures,target=/root/in,readonly \
  --mount type=bind,source="$(pwd)"/tests/results,target=/root/out \
  ghcr.io/biosimulators/vcell:latest \
    -i /root/in/BIOMD0000000297.omex \
    -o /root/out

License

This package is released under the MIT license.

Development team

This package was developed by the BioSimulators Team of the Center for Reproducible Biomedical Modeling.

Questions and comments

Please contact the BioSimulators Team with any questions or comments.