Cost Constrained Flux Balance Analysis (ccFBA): MetabOlic Modeling with ENzyme kineTics (MOMENT)

Different techniques of cost constrained flux balance analysis. 1- MetabOlic Modeling with ENzyme kineTics 'MOMENT' which uses enzyme kinetic data and enzyme molecular weights to constrain flux balance analysis(FBA) and it is described in Adadi, R., Volkmer, B., Milo, R., Heinemann, M., & Shlomi, T. (2012). Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters, 8(7). . 2- an improvement of 'MOMENT' that considers multi-functional enzymes 'ccFBA'. Described in Desouki, Abdelmoneim. Algorithms for improving the predictive power of flux balance analysis. PhD dissertation, 2016. FBA is a mathematical technique to find fluxes in metabolic models at steady state. It is described in Orth, J.D., Thiele, I. and Palsson, B.O. What is flux balance analysis? Nat. Biotech. 28, 245-248(2010).


News

sybilccFBA Version History

-------------------------------------------------------

Version 3.0.0 2018-11-11

-------------------------------------------------------

  • Add function getccFBA_mat that gets the model of ccFBA as a matrix and includes protein complex stoichiometry.

  • Add function getGpr1iso that preprocesses the metabolic model to get for any catalysed reaction by set of isoenzymes the one iso enzyme (i.e the smallest Molecular Weight)

  • Add runFVA option to cfba_moment_mr to get flux variability.

  • Add parameter C_mu_coef that is used to have C as a linear function of mu (biomass) : C = RHS + C_mu_coef*Biomass.

  • Add function simulate_EColi to combine different functions and show a test case for them.

  • Add iML1515 data model

  • Add Kcat lists for EColi and molecular weight for iML1515 model

-------------------------------------------------------

Version 2.0.0 2015-04-01

-------------------------------------------------------

  • Add function cfba_moment_mr that included modelling of multi-functional enzymes
  • Adjust documentation of other methods

-------------------------------------------------------

Version 1.0.0 2014-03-31

-------------------------------------------------------

  • initial public release

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("sybilccFBA")

3.0.0 by Abdelmoneim Amer Desouki, a month ago


Browse source code at https://github.com/cran/sybilccFBA


Authors: Abdelmoneim Amer Desouki [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Depends on sybil, Matrix, methods

Suggests glpkAPI, cplexAPI


See at CRAN