Command Line Interface

For the ModelSeed's command line interface, there are four major commands that are available:

• mseed for configuring the system and accessing data objects.
• mdl for interacting with model objects.
• bio for interacting with biochemistry objects.
• fba for interacting with the output of flux balance / variability analysis runs.

These commands are called with sub-commands that group together relavant functionality. So mdl has sub-commands that relate to models while bio has sub-commands that relate to the biochemistry.

Commands:

1. mseed list

   -v: option for "verbose mode" where a table is printed instead of ids

Examples:

List all top level object types in Model SEED:

>> mseed list
biochems (3)
models (10)
mappings (1)
annotations (8)

List all models:

>> mseed list models
chenry/Seed83333.1
public/iJR904
...

List all media in the biochemistry currently selected in the environment:

>> mseed list biochem/media
biochem/chenry/main/media/LB
biochem/chenry/main/media/GlucoseMinimal
biochem/chenry/main/media/NMS
...

List all media in the specific biochemistry "chenry/main":

>> mseed list biochem/chenry/main/media
biochem/chenry/main/media/LB
biochem/chenry/main/media/GlucoseMinimal
biochem/chenry/main/media/NMS
...

List all sub-entities of the biochemistry entity:

>> mseed list biochem/
media (200)
reactions (10,134)
compounds (12,439)
compartments (10)
...