2. Installation

2.1. Prerequisites

First, install the third-party packages listed below. Detailed installation instructions are available in An Introduction to Whole-Cell Modeling.

To use ChemAxon Marvin to calculate major protonation and tautomerization states, set JAVA_HOME to the path to your Java virtual machine (JVM) and add Marvin to the Java class path:

export JAVA_HOME=/usr/lib/jvm/default-java
export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar

2.2. Latest release From PyPI

Run the following command to install the latest release from PyPI.:

pip install bpforms[all]

2.3. Latest revision from GitHub

Run the following command to install the latest version from GitHub.:

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