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 relevant functionality. So mdl has sub-commands that relate to models while bio has sub-commands that relate to the biochemistry.

Anatomy of mdl commands

$ mdl <command> [model-id] [options]

model-id is optional and specifies which model to run command with. mdl will default to the model selected in your workspace---set your workspace model with ws model [model-id]. You may also pipe in a model from standard input:

$ mseed get model/model-id | mdl <command>

command is required and may be one of:

• info prints general information about the model. By default it prints out information in a more readable format. That may not be suitable for your needs so there are a variety of formatting options:

    -v[erbose]   Print detailed information
    -r[aw]       Print raw JSON (implies -v)
    -t[able]     Print as tab-delimited table
    -h[eader]    Print as tab-delimited table with header row
    -i[d]        Print the current reference id for this model 
    -w[orkspace] Print output to current workspace 
    -f[ile] f    Print output to named file 'f'
  

  So the following two commands will produce the same output:

    $ mdl info -v tutorial/iJR904
    $ mseed get model tutorial/iJR904
  

• genome returns the genome object associated with this model. If no genome is associated with the model, this command returns nothing. Note that this takes the same arguments as $ genome info but by default prints with the [-r] raw output. This makes piping between mdl and genome commands simple:

    $ mdl genome tutorial/iJR904 | genome taxonomyId
    83333
  

• annotations returns the annotations object associated with this model. This behaves like the mdl genome command and may be piped to the ann command.

• biochemistry returns the biochemistry object associated with this model. This behaves like the mdl genome command and may be piped to the bio command.

• mapping returns the mapping object associated with this model. This behaves like the mdl genome command and may be piped to the map command.

• fba starts a flux balance analysis on the model. There are a variety of configuration options for this. These may be supplied in an options-file or as command line parameters. Output from this function behaves like the mdl genome command and may be piped to the fba command for further analysis.

• check-growth

• gapfill starts an algorithm to gapfill the model. Configuration options may be supplied with a configuration-file or as command line parameters.

• fva

• validate

• diff

• patch

• readable converts the model to a human readable format. By default this function prints to standard output. There are options for printing:

    -[t]ype <format>  # specify the format, currently only 'text'
    -[f]ile f         # print output to named file
    -[w]orkspace      # print output to workspace
  

• unreadable converts a model from the human readable format back to the format used in the ModelSeed system.

Command list

Configuring the environment

$ mseed [ -s session ]      # start a ModelSeed session
$ mseed config              # change configuration parameters
$ mseed login <username>    # login as authenticated user
$ mseed logout              

Accessing data

$ mseed list             # list available types

$ mseed list models      # list / query available models
$ mseed list biochem     # list / query available biochemistries
$ mseed list mappings    # list / query available mappings
$ mseed list genomes     # list / query available genomes

$ mseed get model/name   # then get the raw objects

Configuring storage

$ mseed stores -v                   # list available stores
$ mseed stores add <name> ...       # add a store to the set
$ mseed stores remove <name>        # remove a store
$ mseed stores prioritize <name> <name> ...

Model Commands

Basic informational commands:

$ mdl info [id]         # print basic info on model
$ mdl genome [id]       # get raw genome object
$ mdl annotations [id]  # get raw annotation object
$ mdl biochemistry [id] # get raw biochemistry object
$ mdl list reactions    # list model reactions

Model analysis and flux-balance commands:

$ mdl gapfill [id] [config]   # run gapfilling algorithm
$ mdl fba                     # run flux balance analysis
$ mdl fva                     # run flux-variability analysis

$ mdl check-growth  # simply check growth ("mdl fba" wrapper)

Model comparison commands:

$ mdl diff                  # produce human-readable diff
$ mdl diff -p               # produce diff suitable for mdl-patch
$ mdl patch -f patchFile    # apply changes to model

Model human-readable file commands:

$ mdl readable              # convert model to human-readable file
$ mdl unreadable            # convert readable file to model

Biochemistry Commands

Basic informational commands:

$ bio info          # print basic information about biochemistry
$ bio media         # print media refs
$ bio list media    
$ bio list compounds

Biochemistry import and validation:

$ bio import -r <file> -c <file> -m <file>
$ bio validate      # validates biochemistry is suitable

Biochemistry comparison commands:

$ bio diff                       # produce human-readable diff
$ bio diff -p                    # produce diff suitable for bio-patch
$ bio patch -f patchFile         # apply changes to biochemistry 

Biochemistry human-readable file commands:

$ mdl readable
$ mdl unreadable

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)
...