|  | |
| [](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. | |