This manual describes how mako can be installed and how its interfaces work. Mako includes an application programming interface (API), command line interface (CLI) and graphical user interface (GUI) for converting files to the database, or for extracting relevant files and exporting these as a text file or to Cytoscape. Each of the commands of the CLI will be discussed in detail. For the API, we will address the structure of the drivers and key commands that can be used to run custom Python scripts.

For the latest version of mako, please install directly from Github. Otherwise, conda installations can be used to get access to the mako CLI without needing to handle dependencies.