sybil: Efficient Constrained Based Modelling in R

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.

AuthorC. 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 publication2016-06-06 20:23:29
MaintainerC. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
LicenseGPL-3 | file LICENSE
Version2.0.0
http://www.cs.hhu.de/en/research-groups/bioinformatics/software/sybil.html

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

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