Transformer Biomass Reaction

Typing name : TASK.gws_gena.TransformerBiomassReactionTable

Brick : gws_gena

Task to transform table into Biomass Reaction table

TransformerBiomassReactionTable class

Allows to transform a Table with the right columns names to create a Biomass Reaction Table. The Biomass Reaction Table is a stoichiometry table describing the composition of a cell (or organism) biomass.

A stoichiometry resource table describing the composition of the biomass.

The first column is the compound name (offical or user-defined name) [required]
The next columns are:
- chebi_id: the chebi ids of componds of they are known (each chebi id must be prefixed by the keyword CHEBI:). [required]
- biomass: the biomass reaction data (described like a stoichiometric matrix) [required]
- other colums: these columns describe the reaction of the intermediate biomass constituents (described like a stoichiometric matrix) [optional]

For example:

component	chebi_id	biomass	protein
biomass		1
protein		-0.3176	1
DNA		-0.0503
RNA		-0.0259
Cofactors		-0.0216
Cell wall		-0.115
Carbohydrates		-0.2021
Phospholipids		-0.1542
L-alanine zwitterion	CHEBI:57972		-0.5875
L-argininium(1+)	CHEBI:32682		-0.1040
L-asparagine zwitterion	CHEBI:58048		-0.4755
L-aspartate(1-)	CHEBI:29991		-0.6109
L-cysteine zwitterion	CHEBI:35235		-0.4755

Input

Initial table

2d excel like table

Table

Output

Table

2d excel like table

Table

Configuration

entity_column

Optional

The name of the entity column

Type : string

Default value : entity

chebi_id_column

Optional

The name of the column of ChEBI ID

Type : string

Default value : chebi_id

biomass_column

Optional

The name of the biomass column

Type : string

Default value : biomass

Input

Output

Configuration

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