Utilities for whole-cell modeling
Project description
Whole-cell modeling utilities
This package contains utilities that are useful to multiple whole-cell (WC) software components.
Installation
Install the third-party dependencies listed below. Detailed installation instructions are available in An Introduction to Whole-Cell Modeling.
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
To use Marvin to calculate major protonation states, add Marvin to the Java class path export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar
Install this package
Install the latest release from PyPI pip install wc_utils[all]
Install the latest revision from GitHub pip install git+git://github.com/KarrLab/wc_utils#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.
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