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Introduction Version

Draft recon

TASK
Typing name :  TASK.gws_gena.DraftRecon001 Brick :  gws_gena v

Draft network reconstruction

DraftRecon task.

This task performs a draft reconstruction of a metabolic network using a list of EC numbers or taxonomy IDs.

In input, you need to provide at least a resource EC number Table or set the parameter "tax_id". You can also add a Biomass Reaction Table describing the composition of a cell (or organism) biomass.

Input

Table of ec numbers
2d excel like table
Optional
Table
2d excel like table
Optional

Output

Network
Metabolic network

Configuration

unique_name

Optional

The unique name of the network. Required to uniquely identify taxa in microbial communities

Type : stringDefault value : jUqQ

tax_id

Optional

The NCBI taxonomy id. For example: `tax_id = 562` for E. Coli

Type : string

tax_search_method

Optional

If 'bottom_up', the algorithm will to traverse the taxonomy tree to search at higher taxonomy levels until a reaction is found. If `none`, the algorithm will only search at the given taxonomy level given by `tax_id`

Type : stringAllowed values : none  bottom_up  Default value : bottom_up