shjchan / biomassmw

Determining the chemical formulae and molecular weights of macromolecules in genome-scale metabolic models

BiomassMW

(The functions in this repository are already incorporated into the COBRA toolbox since 2018. It is recommended to install COBRA toolbox to use them.)

MATLAB functions for determining the chemical formulae and molecular weights of macromolecules in genome-scale metabolic models.
Please see the following paper for more details:
Siu H. J. Chan, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle, Costas D. Maranas (2017) Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models, Bioinformatics, 33(22), 3603–3609. Link

Main functions:

1. computeMetFormulae two functionalities:

• Compute the chemical formulas of the unknown metabolites given the formulas for a set of known metabolites using a set of reactions.
• Compute the minimum and maximum possible MW of a target metabolite by constraining a minimum level of inconsistency in elemental balance.

Other functions:

1. getElementalComposition
   For converting chemical formulas into a matrix and checking the elemental balance of reactions
2. elementalMatrixToFormulae
   For converting a matrix into chemical formulas

Test script: testComputeMetFormulae.m

Example scripts: example1.m example2.m