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.

   • ChemAxon Marvin: optional to calculate major protonation states
     • Java >= 1.8
   • Git
   • OpenBabel: optional to calculate chemical formulae
   • Pip >= 18.0
   • Python >= 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.

License

The build utilities are released under the MIT license.

Development team

This package was developed by the Karr Lab 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 with any questions or comments.