sybil: Efficient Constrained Based Modelling in R

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This Systems Biology Library for R implements algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). Most of the current LP/MILP solvers are supported via additional packages.

Author
C. Jonathan Fritzemeier [cre, ctb], Gabriel Gelius-Dietrich [aut], Rajen Piernikarczyk [ctb], Marc Andre Daxer [ctb], Benjamin Braasch [ctb], Abdelmoneim Desouki [ctb], Martin J. Lercher [ctb]
Date of publication
2016-06-06 20:23:29
Maintainer
C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
License
GPL-3 | file LICENSE
Version
2.0.0
URLs

View on CRAN

Man pages

addAlgorithm
Add a New Algorithm Name to sybil
addCols-methods
Add Columns to an Optimization Problem
addColsToProb-methods
Add New Columns (Variables) to an Optimization Problem
addExchReact
Add Exchange Reactions to a Model
addReact
Add/Change Reactions in a Model
addRowsCols-methods
Add Rows and Columns to an Optimization Problem
addRows-methods
Add Rows to an Optimization Problem
addRowsToProb-methods
Add New Rows (Constraints) to an Optimization Problem
addSolver
Add a New Mathematical Programming Solver to sybil
applyChanges-methods
Generic Function to Apply Changes to Objects of Class...
backupProb-methods
Copies a Problem Object to a New Problem Object
blockedReact
Find Blocked Reactions in a Metabolic Network
changeBounds
Change Variable Bounds in a Metabolic Network
changeColsBnds-methods
Change Column (Variable) Bounds in the Optimization Problem
changeColsBndsObjCoefs-methods
Change Column (Variable) Bounds and Objective Coefficients in...
changeGPR
Check and Change the GPR Rules
changeMatrixRow-methods
Change a Row in the Constraint Matrix of the Optimization...
changeObjCoefs-methods
Change Column (Variable) Objective Coefficients in the...
changeObjFunc
Sets/changes the Objective Function
changeRowsBnds-methods
Change Row Bounds in the Optimization Problem
changeUptake-methods
Change Uptake Reactions
checkAkgorithm
Check Algorithm
checkDefaultMethod
Validate Solver and Method
checkOptSol-methods
Summarized Information About an Object of Class Optsol
checkReactId
Check if a Reaction Id is Valid
checksol-class
Structure of the Class "checksol"
checkVersion-methods
checks Version of modelorg
deadEndMetabolites-methods
Identify Dead End Metabolites
delProb-methods
Free Memory Associated to the Pointer to the Problem Object
deprecated
Deprecated Functions and Methods in Package 'sybil'
doubleFluxDel
Double Flux Deletion Experiment
doubleGeneDel
Double Gene Deletion Experiment
doubleReact
Identifies Identical Reactions
Ec_core
Escherichia coli Core Metabolic Model
editEnvir
Environment Editor for Metabolic Networks
findExchReact
Find Exchange Reactions
fluxDistribution-class
Class '"fluxDistribution"'
fluxVar
Flux Variability Analysis
geneDel
Get Gene-Reaction Association
geneDeletion
Gene Deletion Experiments
getColPrim-methods
Get Primal Value of Variables After Optimization
getColsLowBnds-methods
Get Lower Bounds of the Columns (Variables) of the...
getColsNames-methods
Retrieve Variable Names
getColsUppBnds-methods
Get Upper Bounds of the Columns (Variables) of the...
getFluxDist-methods
Retrieve Flux Distribution
getNumCols-methods
Get Number of Columns (Variables) of the Optimization Problem
getNumNnz-methods
Retrieve the Number of Non-Zero Elements of the Constraint...
getNumRows-methods
Get Number of Rows (Constraints) of the Optimization Problem
getObjCoefs-methods
Get Objective Coefficients of the Optimization Problem
getObjDir-methods
Get Direction of Optimization.
getObjVal-methods
Get Value of the Objective Function After Optimization
getRedCosts-methods
Get Reduced Costs of all Variables After Optimization
getRowsLowBnds-methods
Get Lower Bounds of the Rows (Constraints) of the...
getRowsNames-methods
Retrieve Constraint Names
getRowsUppBnds-methods
Get Upper Bounds of the Rows (Constraints) of the...
getSolStat-methods
Get Solution Status After Optimization
getSolverParm-methods
Retrieve Current Parameter Settings Used By The Optimization...
getsybilenv
Print sybil Environment
initProb-methods
Initialize Problem Object
loadLPprob-methods
Load Data to Optimization Problem
loadQobj-methods
Load Quadratic Part of the Objective Function to the...
makeOptsolMO
Constructor Function for Objects of Class...
mod2irrev
Produces a Model in Irreversible Format
modelorg2ExPA
Write an Instance of Class modelorg to File in ExPA Format
modelorg2tsv
Write an Instance of Class modelorg to File
modelorg-class
Structure of Class "modelorg"
modelorg_irrev-class
Class for Metabolic Networks in Irreversible Format.
multiDel
Parallel Support for sybil
netFlux-class
Class '"netFlux"'
oneFluxDel
Single Flux Deletion Experiment
oneGeneDel
Single Gene Deletion Experiment
onlyChangeGPR
Change the GPR Rules
onlyCheckGPR
Check the GPR Rules
optimizeProb-methods
Optimize Problem Object
optimizer
Performs Series of Optimizations
optObj
General Constructor Function For Objects of Class 'optObj'
optObj-class
Class '"optObj"'
optObj_clpAPI-class
Class '"optObj_clpAPI"'
optObj_cplexAPI-class
Class '"optObj_cplexAPI"'
optObj_glpkAPI-class
Class '"optObj_glpkAPI"'
optObj_lpSolveAPI-class
Class '"optObj_lpSolveAPI"'
optsol_blockedReact-class
Class '"optsol_blockedReact"'
optsol-class
Class optsol
optsol_fluxdel-class
Class '"optsol_fluxdel"'
optsol_fluxVar-class
Class '"optsol_fluxVar"'
optsol_genedel-class
Class '"optsol_genedel"'
optsol_optimizeProb-class
Class '"optsol_optimizeProb"'
optsol_phpp-class
Class '"optsol_phpp"'
optsol_robAna-class
Class '"optsol_robAna"'
phpp
Phenotypic Phase Plane Analysis
ppProc-class
Class '"ppProc"'
printMetabolite-methods
Print Rows of the Stoichiometric Matrix
printReaction-methods
Print Columns of the Stoichiometric Matrix
promptSysBiolAlg
Generate A Skeletal Structure of Subclasses of sysBiolAlg
reactId-class
Structure of Class "reactId"
reactId_Exch-class
Class '"reactId_Exch"'
readProb-methods
Read Problem Object From File
readTSVmod
Read a Metabolic Network in a TSV (CSV) Format
resetChanges-methods
Generic Function to Reset Temporary Changes in Objects of...
rmReact
Remove Reactions From a Model
robAna
Robustness Analysis
scaleProb-methods
Scaling of the Constraint Matrix of an Optimization Problem
sensitivityAnalysis-methods
Sensitivity Analysis
setColsNames-methods
Set/Change Variable Names
setObjDir-methods
Set Direction of Optimization
setRhsZero-methods
Set Right Hand Side of the Optimization Problem To Zero
setRowsNames-methods
Set/Change Constraint Names
setSolverParm-methods
Set Parameters Used By The Optimization Software
shrinkMatrix-methods
Get a Subset of Matrix Like Objects
singletonMetabolites-methods
Identify Singleton Metabolites
solveLp-methods
Optimize Problem Object
summaryOptsol
Summarize Objects of Class Optsol
summaryOptsol-class
Class '"summaryOptsol"'
sybilError-class
Class '"sybilError"'
sybil-internal
Internal sybil Functions
sybilLog-class
Class '"sybilLog"'
sybil-package
sybil - Efficient Constrained Based Modelling in R
SYBIL_SETTINGS
Set and Get sybil Parameters
sybilStack
A Data Type Providing Stack (LIFO) And Queue (FIFO)...
sysBiolAlg
General Constructor Function For Objects of Class...
sysBiolAlg-class
Class '"sysBiolAlg"'
sysBiolAlg_fba-class
Class '"sysBiolAlg_fba"'
sysBiolAlg_fbaEasyConstraint-class
Class '"sysBiolAlg_fbaEasyConstraint"' and Class...
sysBiolAlg_fv-class
Class '"sysBiolAlg_fv"'
sysBiolAlg_lmoma-class
Class '"sysBiolAlg_lmoma"'
sysBiolAlg_moma-class
Class '"sysBiolAlg_moma"'
sysBiolAlg_mtf-class
Class '"sysBiolAlg_mtf"'
sysBiolAlg_room-class
Class '"sysBiolAlg_room"'
upgradeModelorg
Upgrade modelorg to newer version.
writeProb-methods
Write Problem Object to File
ypd
In Sillico YPD Medium

Files in this package

sybil
sybil/inst
sybil/inst/CITATION
sybil/inst/NEWS.Rd
sybil/inst/extdata
sybil/inst/extdata/Ec_core_desc.tsv
sybil/inst/extdata/Ec_core_react.tsv
sybil/inst/extdata/Ec_core_met.tsv
sybil/inst/doc
sybil/inst/doc/sybil.R
sybil/inst/doc/sybil.Rnw
sybil/inst/doc/sybil.pdf
sybil/NAMESPACE
sybil/data
sybil/data/Ec_core.RData
sybil/R
sybil/R/validsysBiolAlg.R
sybil/R/upgradeModelorg.R
sybil/R/optObj_lpSolveAPIClass.R
sybil/R/checkDefaultMethod.R
sybil/R/deadEndMetabolite.R
sybil/R/generateFluxdels.R
sybil/R/makeLPcompatible.R
sybil/R/readTSVmod.R
sybil/R/doubleGeneDel.R
sybil/R/sybilErrorClass.R
sybil/R/optObj_lpSolveAPIcompat.R
sybil/R/optsol_optimizeProbClass.R
sybil/R/sysBiolAlgClass.R
sybil/R/phpp.R
sybil/R/sybilStack.R
sybil/R/optsol_genedelClass.R
sybil/R/checkEmptyField.R
sybil/R/ppProcessing.R
sybil/R/changeObjFunc.R
sybil/R/sysBiolAlg_momaClass.R
sybil/R/sysBiolAlg_lmomaClass.R
sybil/R/parseBoolean.R
sybil/R/changeBounds.R
sybil/R/ceilValues.R
sybil/R/validreactId_Exch.R
sybil/R/sybilLogClass.R
sybil/R/onlyChangeGPR.R
sybil/R/createReactionString.R
sybil/R/rmReact.R
sybil/R/optObj_pointer.R
sybil/R/mod2irrev.R
sybil/R/modelorg_irrevClass.R
sybil/R/validoptsol.R
sybil/R/promptSysBiolAlg.R
sybil/R/sysBiolAlg_fvClass.R
sybil/R/robAna.R
sybil/R/prepareSubSysMatrix.R
sybil/R/generateModKey.R
sybil/R/optObj_clpAPIClass.R
sybil/R/singletonMetabolite.R
sybil/R/reactId_ExchClass.R
sybil/R/ypd.R
sybil/R/addSolver.R
sybil/R/modelorg2text.R
sybil/R/generics.R
sybil/R/checkAlgorithm.R
sybil/R/reactIdClass.R
sybil/R/optsol_fluxVarClass.R
sybil/R/ppProcClass.R
sybil/R/optsolClass.R
sybil/R/optsol_blockedReactClass.R
sybil/R/addExchReact.R
sybil/R/geneDeletion.R
sybil/R/progress.R
sybil/R/optsol_robAnaClass.R
sybil/R/checkReactId.R
sybil/R/optsol_phppClass.R
sybil/R/editEnvir.R
sybil/R/blockedReact.R
sybil/R/sysBiolAlg_mtfClass.R
sybil/R/optObj_glpkAPIClass.R
sybil/R/recodeMatrix.R
sybil/R/netFluxClass.R
sybil/R/settings.R
sybil/R/floorValues.R
sybil/R/addAlgorithm.R
sybil/R/changeGPR.R
sybil/R/doInRound.R
sybil/R/oneFluxDel.R
sybil/R/getsybilenv.R
sybil/R/geneDel.R
sybil/R/optObj_basicfunc.R
sybil/R/summaryOptsolClass.R
sybil/R/validmodelorg.R
sybil/R/optObj_cplexAPIClass.R
sybil/R/oneGeneDel.R
sybil/R/modelorg2tsv.R
sybil/R/optimizer.R
sybil/R/doubleFluxDel.R
sybil/R/sysBiolAlg_fbaEasyConstraintClass.R
sybil/R/optsol_fluxdelClass.R
sybil/R/sysBiolAlg_fbaClass.R
sybil/R/fluxDistributionClass.R
sybil/R/optObjClass.R
sybil/R/sysBiolAlg_roomClass.R
sybil/R/fluxVar.R
sybil/R/modelorg2ExPA.R
sybil/R/reassignFwBwMatch.R
sybil/R/validreactId.R
sybil/R/multiDel.R
sybil/R/sysBiolAlg_mtfEasyConstraintClass.R
sybil/R/check_brackets.R
sybil/R/modelorgClass.R
sybil/R/generateWT.R
sybil/R/findExchReact.R
sybil/R/printNamedList.R
sybil/R/bracket_pairs.R
sybil/R/zzz.R
sybil/R/onlyCheckGPR.R
sybil/R/checksolClass.R
sybil/R/printLogComment.R
sybil/R/doubleReact.R
sybil/R/readTEXTmod.R
sybil/R/addReact.R
sybil/vignettes
sybil/vignettes/sysBiolAlg-class.pdf
sybil/vignettes/optObj-class.pdf
sybil/vignettes/sybil.bib
sybil/vignettes/optsol-class.pdf
sybil/vignettes/sysBiolAlg-const.pdf
sybil/vignettes/net-crop.pdf
sybil/vignettes/sysBiolAlg-init.pdf
sybil/vignettes/sybil.Rnw
sybil/vignettes/optObj-const.pdf
sybil/README.md
sybil/MD5
sybil/build
sybil/build/vignette.rds
sybil/DESCRIPTION
sybil/man
sybil/man/optsol_genedel-class.Rd
sybil/man/doubleGeneDel.Rd
sybil/man/getsybilenv.Rd
sybil/man/deadEndMetabolites-methods.Rd
sybil/man/getNumCols-methods.Rd
sybil/man/sysBiolAlg_fba-class.Rd
sybil/man/robAna.Rd
sybil/man/changeUptake-methods.Rd
sybil/man/addExchReact.Rd
sybil/man/getRowsUppBnds-methods.Rd
sybil/man/addRowsToProb-methods.Rd
sybil/man/resetChanges-methods.Rd
sybil/man/solveLp-methods.Rd
sybil/man/findExchReact.Rd
sybil/man/addAlgorithm.Rd
sybil/man/reactId_Exch-class.Rd
sybil/man/changeRowsBnds-methods.Rd
sybil/man/oneFluxDel.Rd
sybil/man/deprecated.Rd
sybil/man/optObj_lpSolveAPI-class.Rd
sybil/man/optimizer.Rd
sybil/man/promptSysBiolAlg.Rd
sybil/man/changeMatrixRow-methods.Rd
sybil/man/addRowsCols-methods.Rd
sybil/man/checkDefaultMethod.Rd
sybil/man/summaryOptsol-class.Rd
sybil/man/geneDel.Rd
sybil/man/blockedReact.Rd
sybil/man/changeColsBnds-methods.Rd
sybil/man/setObjDir-methods.Rd
sybil/man/doubleReact.Rd
sybil/man/changeGPR.Rd
sybil/man/getRedCosts-methods.Rd
sybil/man/optimizeProb-methods.Rd
sybil/man/upgradeModelorg.Rd
sybil/man/optsol_robAna-class.Rd
sybil/man/printMetabolite-methods.Rd
sybil/man/getFluxDist-methods.Rd
sybil/man/getColPrim-methods.Rd
sybil/man/loadQobj-methods.Rd
sybil/man/getColsLowBnds-methods.Rd
sybil/man/optObj_clpAPI-class.Rd
sybil/man/phpp.Rd
sybil/man/reactId-class.Rd
sybil/man/changeBounds.Rd
sybil/man/checkOptSol-methods.Rd
sybil/man/fluxVar.Rd
sybil/man/printReaction-methods.Rd
sybil/man/netFlux-class.Rd
sybil/man/getRowsNames-methods.Rd
sybil/man/getObjCoefs-methods.Rd
sybil/man/rmReact.Rd
sybil/man/delProb-methods.Rd
sybil/man/sybilStack.Rd
sybil/man/setRowsNames-methods.Rd
sybil/man/sysBiolAlg_moma-class.Rd
sybil/man/onlyChangeGPR.Rd
sybil/man/optsol_fluxdel-class.Rd
sybil/man/changeColsBndsObjCoefs-methods.Rd
sybil/man/optsol_phpp-class.Rd
sybil/man/loadLPprob-methods.Rd
sybil/man/sysBiolAlg_fbaEasyConstraint-class.Rd
sybil/man/singletonMetabolites-methods.Rd
sybil/man/optsol_blockedReact-class.Rd
sybil/man/Ec_core.Rd
sybil/man/sybilError-class.Rd
sybil/man/getSolverParm-methods.Rd
sybil/man/summaryOptsol.Rd
sybil/man/readTSVmod.Rd
sybil/man/modelorg2ExPA.Rd
sybil/man/sybil-internal.Rd
sybil/man/changeObjCoefs-methods.Rd
sybil/man/geneDeletion.Rd
sybil/man/addColsToProb-methods.Rd
sybil/man/getNumRows-methods.Rd
sybil/man/sybil-package.Rd
sybil/man/sysBiolAlg_fv-class.Rd
sybil/man/sysBiolAlg-class.Rd
sybil/man/optObj_glpkAPI-class.Rd
sybil/man/onlyCheckGPR.Rd
sybil/man/addSolver.Rd
sybil/man/scaleProb-methods.Rd
sybil/man/ppProc-class.Rd
sybil/man/readProb-methods.Rd
sybil/man/getColsNames-methods.Rd
sybil/man/getColsUppBnds-methods.Rd
sybil/man/applyChanges-methods.Rd
sybil/man/addCols-methods.Rd
sybil/man/checkAkgorithm.Rd
sybil/man/sysBiolAlg.Rd
sybil/man/optObj_cplexAPI-class.Rd
sybil/man/initProb-methods.Rd
sybil/man/sysBiolAlg_mtf-class.Rd
sybil/man/getSolStat-methods.Rd
sybil/man/sensitivityAnalysis-methods.Rd
sybil/man/checkVersion-methods.Rd
sybil/man/sysBiolAlg_room-class.Rd
sybil/man/optsol_fluxVar-class.Rd
sybil/man/optsol_optimizeProb-class.Rd
sybil/man/checkReactId.Rd
sybil/man/optObj-class.Rd
sybil/man/makeOptsolMO.Rd
sybil/man/backupProb-methods.Rd
sybil/man/getObjVal-methods.Rd
sybil/man/addReact.Rd
sybil/man/editEnvir.Rd
sybil/man/getObjDir-methods.Rd
sybil/man/addRows-methods.Rd
sybil/man/modelorg-class.Rd
sybil/man/changeObjFunc.Rd
sybil/man/fluxDistribution-class.Rd
sybil/man/modelorg2tsv.Rd
sybil/man/writeProb-methods.Rd
sybil/man/checksol-class.Rd
sybil/man/oneGeneDel.Rd
sybil/man/doubleFluxDel.Rd
sybil/man/optsol-class.Rd
sybil/man/mod2irrev.Rd
sybil/man/sybilLog-class.Rd
sybil/man/getRowsLowBnds-methods.Rd
sybil/man/setColsNames-methods.Rd
sybil/man/shrinkMatrix-methods.Rd
sybil/man/SYBIL_SETTINGS.Rd
sybil/man/setRhsZero-methods.Rd
sybil/man/ypd.Rd
sybil/man/getNumNnz-methods.Rd
sybil/man/optObj.Rd
sybil/man/modelorg_irrev-class.Rd
sybil/man/sysBiolAlg_lmoma-class.Rd
sybil/man/multiDel.Rd
sybil/man/setSolverParm-methods.Rd
sybil/LICENSE