Determining the chemical formulae and molecular weights of macromolecules in genome-scale metabolic models
HTML Matlab Python PHP CSS
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
MatlabCobraToolbox
PythonCobrapy
.gitignore
README.md

README.md

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.