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[](https://github.com/biosimulators/Biosimulators_vcell/issues)
---
# Biosimulators_vcell
BioSimulators-compliant command-line interface to the [VCell](http://vcell.org/) simulation program.
## Contents
* [Installation](#installation)
* [Project setup IntelliJ IDEA](#to-setup-the-project-in-intellij-idea)
* [Project setup Eclipse](#to-setup-the-project-in-eclipse)
* [Maven installation](#maven-installation-package)
* [Usage](#local-usage)
* [License](#license)
* [Development team](#development-team)
* [Questions and comments](#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](./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](#local-usage) for more options)
* `Working Directory:` is `<Your-Project-Directory-Path>`
* Select `vcell-cli` as `Use classpath of module:`
8. 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](./README.md) to build python dependencies
4. Run `mvn clean install dependency:copy-dependencies` to build the project
4. Open Eclipse, Import the project using Maven. Depending on the Eclipse version there'll be small differences with the importing steps.
5. 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](LICENSE).
## Development team
This package was developed by the BioSimulators Team of the [Center for Reproducible Biomedical Modeling](https://reproduciblebiomodels.org).
## Questions and comments
Please contact the [BioSimulators Team](mailto:info@biosimulators.org) with any questions or comments.
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