Please make sure you have Docker and Conda installed.

Set up a Neo4j database


docker run --rm \
-d \
--publish=7475:7474 --publish=7688:7687 \
--name=neo4j \
--env NEO4J_AUTH=neo4j/test \

For additional information,
see the instructions on Setting up Docker.

Connect with Neo4j Browser

The username and password for the browser are "neo4j" and
"test" respectively.
Find additional instructions on Neo4j Browser here.

Install mako through Conda

Follow the instructions on the installation page: mako installation.

Write data to the Neo4j database

Please follow this link to download the sponge_biomfiles.zip and the sponge_networks.zip files for the Sponges case study.
Unzip these files into two folders, sponge_biomfiles and sponge_networks respectively. In your command-line interface, navigate to the location that contains both folders.

mako neo4biom -u neo4j -p test -a neo4j://localhost:7688 -cf -biom sponge_biomfiles
mako io -cf -net sponge_networks

Find microbial associations of interest

MATCH p=(:Order {name: 'o__Nitrospirales'})--(:Taxon)--(:Edge)--(:Taxon)--(:Order {name: 'o__Cenarchaeales'}) RETURN p LIMIT 25 

You should now have a running Neo4j database that contains a number of networks derived from different taxonomic orders of sponges. This can be used to find associations linked to specific bacterial orders, like in the query above. This query finds all associations between taxa assigned to the orders Nitrospirales and Cenarchaeales, across all networks in the database. It is also possible to ask questions such as ‘Which associations are found in at least three sponge orders?’ or ‘Are there associations that form a motif which are recovered in multiple networks?’. Additionally, you can add extra data to the database, such as sponge LMA or HMA status (low or high microbial abundance) and use this to query associations linked to those statuses. The benefit of using a Neo4j database is that the queries look relatively similar to schematic overviews you might make of the information you are interested in. This makes writing those queries a lot more intuitive.

Visit the Cypher webpages for additional instructions on working with Cypher.