1. Installation

1.1. 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

1.2. Latest release From PyPI

Run the following command to install the latest release from PyPI. For most environments, the --process-dependency-links option is needed to install some of the dependencies from GitHub:

pip install --process-dependency-links bpforms[all]

1.3. Latest revision from GitHub

Run the following command to install the latest version from GitHub. For most environments, the --process-dependency-links option is needed to install some of the dependencies from GitHub:

pip install --process-dependency-links git+git://github.com/KarrLab/bpforms.git#egg=bpforms[all]