Man pages for sybil
Efficient Constrained Based Modelling

addAlgorithmAdd a New Algorithm Name to sybil
addCols-methodsAdd Columns to an Optimization Problem
addColsToProb-methodsAdd New Columns (Variables) to an Optimization Problem
addExchReactAdd Exchange Reactions to a Model
addReactAdd/Change Reactions in a Model
addRowsCols-methodsAdd Rows and Columns to an Optimization Problem
addRows-methodsAdd Rows to an Optimization Problem
addRowsToProb-methodsAdd New Rows (Constraints) to an Optimization Problem
addSolverAdd a New Mathematical Programming Solver to sybil
applyChanges-methodsGeneric Function to Apply Changes to Objects of Class...
backupProb-methodsCopies a Problem Object to a New Problem Object
blockedReactFind Blocked Reactions in a Metabolic Network
changeBoundsChange Variable Bounds in a Metabolic Network
changeColsBnds-methodsChange Column (Variable) Bounds in the Optimization Problem
changeColsBndsObjCoefs-methodsChange Column (Variable) Bounds and Objective Coefficients in...
changeGPRCheck and Change the GPR Rules
changeMatrixRow-methodsChange a Row in the Constraint Matrix of the Optimization...
changeObjCoefs-methodsChange Column (Variable) Objective Coefficients in the...
changeObjFuncSets/changes the Objective Function
changeRowsBnds-methodsChange Row Bounds in the Optimization Problem
changeUptake-methodsChange Uptake Reactions
checkAkgorithmCheck Algorithm
checkDefaultMethodValidate Solver and Method
checkOptSol-methodsSummarized Information About an Object of Class Optsol
checkReactIdCheck if a Reaction Id is Valid
checksol-classStructure of the Class "checksol"
checkVersion-methodschecks Version of modelorg
deadEndMetabolites-methodsIdentify Dead End Metabolites
delProb-methodsFree Memory Associated to the Pointer to the Problem Object
deprecatedDeprecated Functions and Methods in Package 'sybil'
doubleFluxDelDouble Flux Deletion Experiment
doubleGeneDelDouble Gene Deletion Experiment
doubleReactIdentifies Identical Reactions
Ec_coreEscherichia coli Core Metabolic Model
editEnvirEnvironment Editor for Metabolic Networks
findExchReactFind Exchange Reactions
fluxDistribution-classClass '"fluxDistribution"'
fluxVarFlux Variability Analysis
geneDelGet Gene-Reaction Association
geneDeletionGene Deletion Experiments
getColPrim-methodsGet Primal Value of Variables After Optimization
getColsLowBnds-methodsGet Lower Bounds of the Columns (Variables) of the...
getColsNames-methodsRetrieve Variable Names
getColsUppBnds-methodsGet Upper Bounds of the Columns (Variables) of the...
getFluxDist-methodsRetrieve Flux Distribution
getNumCols-methodsGet Number of Columns (Variables) of the Optimization Problem
getNumNnz-methodsRetrieve the Number of Non-Zero Elements of the Constraint...
getNumRows-methodsGet Number of Rows (Constraints) of the Optimization Problem
getObjCoefs-methodsGet Objective Coefficients of the Optimization Problem
getObjDir-methodsGet Direction of Optimization.
getObjVal-methodsGet Value of the Objective Function After Optimization
getRedCosts-methodsGet Reduced Costs of all Variables After Optimization
getRowsLowBnds-methodsGet Lower Bounds of the Rows (Constraints) of the...
getRowsNames-methodsRetrieve Constraint Names
getRowsUppBnds-methodsGet Upper Bounds of the Rows (Constraints) of the...
getSolStat-methodsGet Solution Status After Optimization
getSolverParm-methodsRetrieve Current Parameter Settings Used By The Optimization...
getsybilenvPrint sybil Environment
initProb-methodsInitialize Problem Object
loadLPprob-methodsLoad Data to Optimization Problem
loadQobj-methodsLoad Quadratic Part of the Objective Function to the...
makeOptsolMOConstructor Function for Objects of Class...
mergeReact2ModelorgFunctions to subset and merge modelorg objects.
mod2irrevProduces a Model in Irreversible Format
modelorg2ExPAWrite an Instance of Class modelorg to File in ExPA Format
modelorg2tsvWrite an Instance of Class modelorg to File
modelorg-classStructure of Class "modelorg"
modelorg_irrev-classClass for Metabolic Networks in Irreversible Format.
multiDelParallel Support for sybil
netFlux-classClass '"netFlux"'
oneFluxDelSingle Flux Deletion Experiment
oneGeneDelSingle Gene Deletion Experiment
onlyChangeGPRChange the GPR Rules
onlyCheckGPRCheck the GPR Rules
optimizeProb-methodsOptimize Problem Object
optimizerPerforms Series of Optimizations
optObjGeneral Constructor Function For Objects of Class 'optObj'
optObj-classClass '"optObj"'
optObj_clpAPI-classClass '"optObj_clpAPI"'
optObj_cplexAPI-classClass '"optObj_cplexAPI"'
optObj_glpkAPI-classClass '"optObj_glpkAPI"'
optObj_lpSolveAPI-classClass '"optObj_lpSolveAPI"'
optsol_blockedReact-classClass '"optsol_blockedReact"'
optsol-classClass optsol
optsol_fluxdel-classClass '"optsol_fluxdel"'
optsol_fluxVar-classClass '"optsol_fluxVar"'
optsol_genedel-classClass '"optsol_genedel"'
optsol_optimizeProb-classClass '"optsol_optimizeProb"'
optsol_phpp-classClass '"optsol_phpp"'
optsol_robAna-classClass '"optsol_robAna"'
phppPhenotypic Phase Plane Analysis
ppProc-classClass '"ppProc"'
printMetabolite-methodsPrint Rows of the Stoichiometric Matrix
printReaction-methodsPrint Columns of the Stoichiometric Matrix
promptSysBiolAlgGenerate A Skeletal Structure of Subclasses of sysBiolAlg
reactId-classStructure of Class "reactId"
reactId_Exch-classClass '"reactId_Exch"'
readProb-methodsRead Problem Object From File
readTSVmodRead a Metabolic Network in a TSV (CSV) Format
resetChanges-methodsGeneric Function to Reset Temporary Changes in Objects of...
rmReactRemove Reactions From a Model
robAnaRobustness Analysis
scaleProb-methodsScaling of the Constraint Matrix of an Optimization Problem
sensitivityAnalysis-methodsSensitivity Analysis
setColsNames-methodsSet/Change Variable Names
setObjDir-methodsSet Direction of Optimization
setRhsZero-methodsSet Right Hand Side of the Optimization Problem To Zero
setRowsNames-methodsSet/Change Constraint Names
setSolverParm-methodsSet Parameters Used By The Optimization Software
shrinkMatrix-methodsGet a Subset of Matrix Like Objects
singletonMetabolites-methodsIdentify Singleton Metabolites
solveLp-methodsOptimize Problem Object
summaryOptsolSummarize Objects of Class Optsol
summaryOptsol-classClass '"summaryOptsol"'
sybilError-classClass '"sybilError"'
sybil-internalInternal sybil Functions
sybilLog-classClass '"sybilLog"'
sybil-packagesybil - Efficient Constrained Based Modelling in R
SYBIL_SETTINGSSet and Get sybil Parameters
sybilStackA Data Type Providing Stack (LIFO) And Queue (FIFO)...
sysBiolAlgGeneral Constructor Function For Objects of Class...
sysBiolAlg-classClass '"sysBiolAlg"'
sysBiolAlg_fba-classClass '"sysBiolAlg_fba"'
sysBiolAlg_fbaEasyConstraint-classClass '"sysBiolAlg_fbaEasyConstraint"' and Class...
sysBiolAlg_fv-classClass '"sysBiolAlg_fv"'
sysBiolAlg_lmoma-classClass '"sysBiolAlg_lmoma"'
sysBiolAlg_moma-classClass '"sysBiolAlg_moma"'
sysBiolAlg_mtf-classClass '"sysBiolAlg_mtf"'
sysBiolAlg_room-classClass '"sysBiolAlg_room"'
upgradeModelorgUpgrade modelorg to newer version.
writeProb-methodsWrite Problem Object to File
ypdIn Sillico YPD Medium
sybil documentation built on May 31, 2021, 5:08 p.m.