sybilccFBA: Cost Constrained FLux Balance Analysis: MetabOlic Modeling with ENzyme kineTics (MOMENT)
Version 2.0.0

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).

AuthorAbdelmoneim Amer Desouki [aut, cre]
Date of publication2015-04-02 17:52:06
MaintainerAbdelmoneim Amer Desouki <abdelmoneim.amer@uni-duesseldorf.de>
LicenseGPL-3
Version2.0.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sybilccFBA")

Getting started

Package overview

Popular man pages

addGlcTrns: add Glucose Transport constraint
cfba_moment_pw: Function: cfba_moment_pw: implement MOMENT method
getRevFlux: getRevFlux
iMM904: Saccharomyces cerevisiae Metabolic Model
kcat: Escherichia coli KCAT values used in MOMENT method
mw: Escherichia coli molecular weight values used in MOMENT...
sybilccFBA-package: Cost Constrained Flux Balance Analysis(ccFBA)
See all...

All man pages Function index File listing

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...

Functions

addGlcTrns Man page Source code
calc_MW Man page Source code
cfba_moment Man page Source code
cfba_moment_mr Man page Source code
cfba_moment_pw Man page Source code
getRevFlux Man page Source code
iAF1260 Man page
iJO1366 Man page
iMM904 Man page
kcat Man page
mw Man page
readmodel Man page Source code
sybilccFBA Man page
sybilccFBA-package Man page
yst_kcat Man page
yst_mw Man page

Files

inst
inst/extdata
inst/extdata/mat.csv
inst/extdata/mets.csv
inst/extdata/aa.txt
inst/extdata/cbnds.csv
inst/extdata/ALL_PTT.TSV
inst/extdata/rxns.csv
inst/extdata/rbnds.csv
inst/extdata/NC_000913.faa
inst/extdata/test2.ptt
NAMESPACE
NEWS
data
data/yst_kcat.RData
data/iAF1260.RData
data/kcat.RData
data/yst_mw.RData
data/iJO1366.RData
data/iMM904.RData
data/mw.RData
R
R/cfba_moment.R
R/calc_MW.R
R/addGlcTrns.R
R/readmodel.R
R/getRevFlux.R
R/cfba_moment_pw.R
R/cfba_moment_mr.R
MD5
DESCRIPTION
man
man/yst_mw.Rd
man/mw.Rd
man/readmodel.Rd
man/kcat.Rd
man/cfba_moment_mr.Rd
man/sybilccFBA-package.Rd
man/getRevFlux.Rd
man/yst_kcat.Rd
man/calc_MW.Rd
man/cfba_moment_pw.Rd
man/cfba_moment.Rd
man/iJO1366.Rd
man/iAF1260.Rd
man/iMM904.Rd
man/addGlcTrns.Rd
sybilccFBA documentation built on May 19, 2017, 1:05 p.m.

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