To use mako to store biological data, it needs to be able to access a Neo4j database. There are multiple ways to run one; in this guide, several strategies for using Neo4j will be addressed, with relevant links to Neo4j sources included. Two editions of Neo4j are available: Neo4j Community and Neo4j Enterprise. Neo4j Community is open source and freely available, while Neo4j Enterprise requires a licence. Many of the advanced features available to Enterprise are not necessary for simpler biology applications, and therefore will not be discussed in this guide. For a full overview of features available to Neo4j Community and Neo4j Enterprise editions, please take a look at the Neo4j web page.

In this guide, three options for accessing Neo4j database will be discussed: via Docker, via Neo4j Desktop and via a server.