Usage

This page shows how to quickly access functionalities from the refineGEMs toolbox. For more detailed examples see About different applications.

Access points

via command line/terminal

The main functionalities of refineGEMs can be accessed directly from the command line after a successful installation.

For more information, call the following in your command line or terminal:

refinegems --help

or refer to the following section: Command Line access points.

from inside Python

Alternatively, refineGEMs can be directly imported into Python or a python script for full access of all modules, classes and more.

import refinegems as rg

Or, e.g.:

from refinegems.analysis.growth import growth_analysis

The media database

The media database can be accessed via a multitude of different routes.

Hint

For more information about the database and its contents, refer to Media & Subsets.

Direct access via SQL

One way to inspect the database is to download it from the GitHub page and open it with an IDE with an SQL-extension (e.g. VSCode) or with a graphical SQL interface like SQLite.

Access via the command line

The refineGEMs command line tool provides limited access to some of the basic functionalities concerning the media database, including downloading a configuration (config) file and retrieving a list of all available media:

refinegems media --help

For more information, see section refinegems media.

Access via Python

To access the media from inside a Python script, the module medium provides classes and functions.

For example, to extract the medium LB run:

from refinegems.classes.medium import load_medium_from_db

lb = load_medium_from_db('LB')

Access the database via a config.yaml

If the idea is to load a list of media - from the database or external, with or without modifications - it might be useful to use the media configuration file. There, different media names with options for modifications can be listed and subsequently loaded using load_media() or used as input for other entry points that require a list of media or the config itself.