sybilccFBA: Cost Constrained FLux Balance Analysis: MetabOlic Modeling with ENzyme kineTics (MOMENT)

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An implementation of a cost constrained flux balance analysis technique (i.e. MetabOlic Modeling with ENzyme kineTics (MOMENT)). MOMENT 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). doi:10.1371/journal.pcbi.1002575. This package also implements an improvement of MOMENT that considers multi-functional enzymes. 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).

Author
Abdelmoneim Amer Desouki [aut, cre]
Date of publication
2015-04-02 17:52:06
Maintainer
Abdelmoneim Amer Desouki <abdelmoneim.amer@uni-duesseldorf.de>
License
GPL-3
Version
2.0.0

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Man pages

addGlcTrns
add Glucose Transport constraint
calc_MW
Calculate molecular weights
cfba_moment
Function: cfba_moment: implement MOMENT method
cfba_moment_mr
Function: cfba_moment_mr: implement MOMENT method taking into...
cfba_moment_pw
Function: cfba_moment_pw: implement MOMENT method
getRevFlux
getRevFlux
iAF1260
Escherichia coli Metabolic Model iAF1260
iJO1366
Escherichia coli Metabolic Model iJO1366
iMM904
Saccharomyces cerevisiae Metabolic Model
kcat
Escherichia coli KCAT values used in MOMENT method
mw
Escherichia coli molecular weight values used in MOMENT...
readmodel
read MOMENT model
sybilccFBA-package
Cost Constrained Flux Balance Analysis(ccFBA)
yst_kcat
Saccharomyces cerevisiae KCAT values used in MOMENT method
yst_mw
Saccharomyces cerevisiae molecular weight values used in...

Files in this package

sybilccFBA
sybilccFBA/inst
sybilccFBA/inst/extdata
sybilccFBA/inst/extdata/mat.csv
sybilccFBA/inst/extdata/mets.csv
sybilccFBA/inst/extdata/aa.txt
sybilccFBA/inst/extdata/cbnds.csv
sybilccFBA/inst/extdata/ALL_PTT.TSV
sybilccFBA/inst/extdata/rxns.csv
sybilccFBA/inst/extdata/rbnds.csv
sybilccFBA/inst/extdata/NC_000913.faa
sybilccFBA/inst/extdata/test2.ptt
sybilccFBA/NAMESPACE
sybilccFBA/NEWS
sybilccFBA/data
sybilccFBA/data/yst_kcat.RData
sybilccFBA/data/iAF1260.RData
sybilccFBA/data/kcat.RData
sybilccFBA/data/yst_mw.RData
sybilccFBA/data/iJO1366.RData
sybilccFBA/data/iMM904.RData
sybilccFBA/data/mw.RData
sybilccFBA/R
sybilccFBA/R/cfba_moment.R
sybilccFBA/R/calc_MW.R
sybilccFBA/R/addGlcTrns.R
sybilccFBA/R/readmodel.R
sybilccFBA/R/getRevFlux.R
sybilccFBA/R/cfba_moment_pw.R
sybilccFBA/R/cfba_moment_mr.R
sybilccFBA/MD5
sybilccFBA/DESCRIPTION
sybilccFBA/man
sybilccFBA/man/yst_mw.Rd
sybilccFBA/man/mw.Rd
sybilccFBA/man/readmodel.Rd
sybilccFBA/man/kcat.Rd
sybilccFBA/man/cfba_moment_mr.Rd
sybilccFBA/man/sybilccFBA-package.Rd
sybilccFBA/man/getRevFlux.Rd
sybilccFBA/man/yst_kcat.Rd
sybilccFBA/man/calc_MW.Rd
sybilccFBA/man/cfba_moment_pw.Rd
sybilccFBA/man/cfba_moment.Rd
sybilccFBA/man/iJO1366.Rd
sybilccFBA/man/iAF1260.Rd
sybilccFBA/man/iMM904.Rd
sybilccFBA/man/addGlcTrns.Rd