Introduction
For presenting mako, we constructed a curated database of 60 data sets and 60 networks which were collected from Qiita (Gonzalez et al., 2018). There are two ways to access this data: one is to load a databasume dump, the other is through Code Ocean. Both methods are explained here.
In addition to working with the Code Ocean code capsule directly, you can download files from the capsule and run the commands locally. This allows you to maintain a persistent database. Some of the files in the capsule are also used for other case studies.