https://github.com/karrlab/wc_utils

Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others
https://github.com/karrlab/wc_utils

Last synced: 8 months ago
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Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others

• Host: GitHub
• URL: https://github.com/karrlab/wc_utils
• Owner: KarrLab
• License: mit
• Created: 2016-09-26T20:26:02.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2022-04-29T03:07:52.000Z (almost 4 years ago)
• Last Synced: 2025-05-29T19:49:51.033Z (9 months ago)
• Language: Python
• Homepage:
• Size: 1.02 MB
• Stars: 1
• Watchers: 6
• Forks: 1
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# Whole-cell modeling utilities

This package contains utilities that are useful to multiple whole-cell (WC) software components.

## Installation

1. Install the third-party dependencies listed below. Detailed installation instructions are available in [An Introduction to Whole-Cell Modeling](http://docs.karrlab.org/intro_to_wc_modeling/master/0.0.1/installation.html).

        

    * [ChemAxon Marvin](https://chemaxon.com/products/marvin): optional to calculate major protonation states

      * [Java](https://www.java.com) >= 1.8

    * [Git](https://git-scm.com/)

    * [OpenBabel](http://openbabel.org): optional to calculate chemical formulae

    * [Pip](https://pip.pypa.io) >= 18.0

    * [Python](https://www.python.org) >= 3.6

2. To use Marvin to calculate major protonation states, set ``JAVA_HOME`` to the path to your Java virtual machine (JVM)

   ```

   export JAVA_HOME=/usr/lib/jvm/default-java

   ```

3. To use Marvin to calculate major protonation states, add Marvin to the Java class path

   ```

   export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar

   ```

4. Install this package 

    * Install the latest release from PyPI

      ```

      pip install wc_utils[all]

      ```

    * Install the latest revision from GitHub

      ```

      pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils[all]

      pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all]

      ```

## Example usage

## Documentation

Please see the [API documentation](http://docs.karrlab.org/wc_utils).

## License

The build utilities are released under the [MIT license](LICENSE).

## Development team

This package was developed by the [Karr Lab](http://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York, USA.

* Arthur Goldberg

* Jonathan Karr

## Questions and comments

Please contact the [Karr Lab](http://www.karrlab.org) with any questions or comments.