Run Scanner is a service that scans run directories on the file system and serves run metadata via a REST interface. MISO features integration with Run Scanner, allowing MISO to retrieve run data from Run Scanner and automatically create and update runs in MISO.
Documentation for Run Scanner can be found in its GitHub repository.
Pinery is a REST webservice for serving LIMS data, mainly for consumption by other applications. Pinery is used as an abstraction layer to prevent other applications from depending on a specific LIMS' schema. This means that you can write applications to consume Pinery data, and then if you ever want to use a different data source, such as another LIMS, you just need a Pinery implementation for that data source and all of your existing applications will remain compatible.