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 |
