alisalehzadeh-yazdi / biomassmw

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

BiomassMW

MATLAB and Python 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; Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models, Bioinformatics, btx453
Link

MATLAB functions (MatlabCobraToolbox/ Require COBRA Toolbox)
Main functions:

1. computeMetFormulae
   Compute the chemical formulas of the unknown metabolites given the formulas for a set of known metabolites using a set of reactions.
2. computeMetMWrange
   Similar to computeFormulasFillMets but return the minimum and maximum possible MW of the target metabolite.

Other functions:

1. checkEleBalance
   For converting chemical formulas into a matrix and checking the elemental balance of reactions
2. checkSolFeas
   For manually checking the feasibility of CPLEX solutions
3. convertMatrixFormulas
   For converting a matrix into chemical formulas
4. MW
   For calculating molecular weights
5. setCplexParam
   For conveniently setting CPLEX parameters in Matlab

Python functions (PythonCobrapy/ Require Cobrapy)
Main object: MetFormulae in metFormulae/MetFormulae.py.
It is initialized with a cobra model. Use the following two methods to calculate chemical formulae or the range for biomass MW:

• .computeMetForm: Compute the chemical formulas of the unknown metabolites given the formulas for a set of known metabolites using a set of reactions.
• .computeMetRange: Compute the minimum and maximum possible MW of the target metabolite.