Ec_core                 Escherichia coli Core Metabolic Model
SYBIL_SETTINGS          Set and Get sybil Parameters
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,modelorg-method
                        Add/Change Reactions in a Model
addRows-methods         Add Rows to an Optimization Problem
addRowsCols-methods     Add Rows and Columns 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 sysBiolAlg
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 the Optimization Problem
changeGPR               Check and Change the GPR Rules
changeMatrixRow-methods
                        Change a Row in the Constraint Matrix of the
                        Optimization Problem
changeObjCoefs-methods
                        Change Column (Variable) Objective Coefficients
                        in the Optimization Problem
changeObjFunc           Sets/changes the Objective Function
changeRowsBnds-methods
                        Change Row Bounds in the Optimization Problem
changeUptake-methods    Change Uptake Reactions
checkAlgorithm          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
checkVersion-methods    checks Version of modelorg
checksol-class          Structure of the Class "checksol"
deadEndMetabolites-methods
                        Identify Dead End Metabolites
delProb-methods         Free Memory Associated to the Pointer to the
                        Problem Object
doubleFluxDel           Double Flux Deletion Experiment
doubleGeneDel           Double Gene Deletion Experiment
doubleReact             Identifies Identical Reactions
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 Optimization Problem
getColsNames-methods    Retrieve Variable Names
getColsUppBnds-methods
                        Get Upper Bounds of the Columns (Variables) of
                        the Optimization Problem
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 Matrix
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 Optimization Problem
getRowsNames-methods    Retrieve Constraint Names
getRowsUppBnds-methods
                        Get Upper Bounds of the Rows (Constraints) of
                        the Optimization Problem
getSolStat-methods      Get Solution Status After Optimization
getSolverParm-methods   Retrieve Current Parameter Settings Used By The
                        Optimization Software
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 Optimization Problem
makeOptsolMO            Constructor Function for Objects of Class
                        'optsol_optimizeProb'.
mergeReact2Modelorg     Functions to subset and merge modelorg objects.
mod2irrev               Produces a Model in Irreversible Format
modelorg-class          Structure of Class "modelorg"
modelorg2ExPA           Write an Instance of Class modelorg to File in
                        ExPA Format
modelorg2tsv            Write an Instance of Class modelorg to File
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
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"'
optimizeProb-methods    Optimize Problem Object
optimizer               Performs Series of Optimizations
optsol-class            Class optsol
optsol_blockedReact-class
                        Class '"optsol_blockedReact"'
optsol_fluxVar-class    Class '"optsol_fluxVar"'
optsol_fluxdel-class    Class '"optsol_fluxdel"'
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 Class sysBiolAlg
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"'
sybil-deprecated        Deprecated Functions and Methods in Package
                        'sybil'
sybil-package           sybil - Efficient Constrained Based Modelling
                        in R
sybilError-class        Class '"sybilError"'
sybilLog-class          Class '"sybilLog"'
sybilStack              A Data Type Providing Stack (LIFO) And Queue
                        (FIFO) Functionality
sysBiolAlg              General Constructor Function For Objects of
                        Class 'sysBiolAlg'
sysBiolAlg-class        Class '"sysBiolAlg"'
sysBiolAlg_fba-class    Class '"sysBiolAlg_fba"'
sysBiolAlg_fbaEasyConstraint-class
                        Class '"sysBiolAlg_fbaEasyConstraint"' and
                        Class '"sysBiolAlg_mtfEasyConstraint"'
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
