Skip to content
master
Go to file
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

README.md

PyPI package Documentation Test results Test coverage Code analysis License Analytics

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.

  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.

About

Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others

Resources

License

Packages

No packages published
You can’t perform that action at this time.