Documentation - TreeBASE/treebase GitHub Wiki

Documentation roadmap

Non-technical documentation for users and submitters

The TreeBASE website contains information, from a non-technical user's perspective, on the background of the project, and the people, organizations, and journals involved. The website also describes how to upload data and how doing this can help satisfy data management requirements of funding agencies.

Technical documentation for data re-users

For users that are comfortable writing data mining scripts (e.g. in R or Python), there is introductory documentation on web service interfaces. These interfaces include a REST interface based on the informal PhyloWS pattern, and a OAI-PMH interface. Also of interest for data re-users might be the separate project to develop a NeXML file dump of TreeBASE and pipelines that operate on this, and code derivatives that operate on the database schema directly.

Technical documentation for developers

The TreeBASE websites gives a bird's eye view of the software stack. The code that the project has delivered to build up this stack is stored in a github repository. Instructions are available for building the main artifacts, which are stored in a separate repo for automated provisioning of servers.

Technical documentation for admins

The compiled artifacts are deployed by a provisioning module for Puppet, so that a new server can be bootstrapped and deployed easily. Potentially, an admin might also be interested in setting up a server environment that can be used for loading data files. This functionality was developed for loading Nexus data files such as existed in TreeBASE v.1 and is probably no longer needed: data loading is now done by reading a postgres dump. In any case, the document on data loading describes both procedures.