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.

Install the latest version of this package by entering the following in R:
install.packages("sybil")
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

Functions

addAlgorithm Man page
addCols Man page
addCols-methods Man page
addCols,optObj_clpAPI,numeric-method Man page
addCols,optObj_cplexAPI,numeric-method Man page
addCols,optObj_glpkAPI,numeric-method Man page
addCols,optObj_lpSolveAPI,numeric-method Man page
addColsToProb Man page
addColsToProb-methods Man page
addColsToProb,optObj_clpAPI-method Man page
addColsToProb,optObj_cplexAPI-method Man page
addColsToProb,optObj_glpkAPI-method Man page
addColsToProb,optObj_lpSolveAPI-method Man page
addExchReact Man page
addReact Man page
addRows Man page
addRowsCols Man page
addRowsCols-methods Man page
addRowsCols,optObj_clpAPI,numeric,numeric-method Man page
addRowsCols,optObj_cplexAPI,numeric,numeric-method Man page
addRowsCols,optObj_glpkAPI,numeric,numeric-method Man page
addRowsCols,optObj_lpSolveAPI,numeric,numeric-method Man page
addRows-methods Man page
addRows,optObj_clpAPI,numeric-method Man page
addRows,optObj_cplexAPI,numeric-method Man page
addRows,optObj_glpkAPI,numeric-method Man page
addRows,optObj_lpSolveAPI,numeric-method Man page
addRowsToProb Man page
addRowsToProb-methods Man page
addRowsToProb,optObj_clpAPI-method Man page
addRowsToProb,optObj_cplexAPI-method Man page
addRowsToProb,optObj_glpkAPI-method Man page
addRowsToProb,optObj_lpSolveAPI-method Man page
addSolver Man page
algorithm Man page
algorithm<- Man page
ALGORITHM Man page
algorithm<-,optsol-method Man page
algorithm,optsol-method Man page
algorithm<-,sysBiolAlg-method Man page
algorithm,sysBiolAlg-method Man page
alg_par Man page
alg_par<- Man page
alg_par<-,optsol-method Man page
alg_par,optsol-method Man page
alg_par<-,sysBiolAlg-method Man page
alg_par,sysBiolAlg-method Man page
allGenes Man page
allGenes<- Man page
allGenes<-,modelorg-method Man page
allGenes,modelorg-method Man page
applyChanges Man page
applyChanges-methods Man page
applyChanges,sysBiolAlg-method Man page
applyChanges,sysBiolAlg_room-method Man page
backupProb Man page
backupProb-methods Man page
backupProb,optObj_clpAPI-method Man page
backupProb,optObj_cplexAPI-method Man page
backupProb,optObj_glpkAPI-method Man page
backupProb,optObj_lpSolveAPI-method Man page
blocked Man page
blocked<- Man page
blocked<-,optsol_blockedReact-method Man page
blocked,optsol_blockedReact-method Man page
blockedReact Man page
blReact Man page
blReact,optsol_fluxVar-method Man page
changeBounds Man page
changeColsBnds Man page
changeColsBnds-methods Man page
changeColsBndsObjCoefs Man page
changeColsBndsObjCoefs-methods Man page
changeColsBndsObjCoefs,optObj_clpAPI-method Man page
changeColsBndsObjCoefs,optObj_cplexAPI-method Man page
changeColsBndsObjCoefs,optObj_glpkAPI-method Man page
changeColsBndsObjCoefs,optObj_lpSolveAPI-method Man page
changeColsBnds,optObj_clpAPI-method Man page
changeColsBnds,optObj_cplexAPI-method Man page
changeColsBnds,optObj_glpkAPI-method Man page
changeColsBnds,optObj_lpSolveAPI-method Man page
changeGPR Man page
changeMatrixRow Man page
changeMatrixRow-methods Man page
changeMatrixRow,optObj_cplexAPI-method Man page
changeMatrixRow,optObj_glpkAPI-method Man page
changeMatrixRow,optObj_lpSolveAPI-method Man page
changeMaxObj Man page
changeMaxObj,sysBiolAlg_mtf-method Man page
changeObjCoefs Man page
changeObjCoefs-methods Man page
changeObjCoefs,optObj_clpAPI-method Man page
changeObjCoefs,optObj_cplexAPI-method Man page
changeObjCoefs,optObj_glpkAPI-method Man page
changeObjCoefs,optObj_lpSolveAPI-method Man page
changeObjFunc Man page
changeRowsBnds Man page
changeRowsBnds-methods Man page
changeRowsBnds,optObj_clpAPI-method Man page
changeRowsBnds,optObj_cplexAPI-method Man page
changeRowsBnds,optObj_glpkAPI-method Man page
changeRowsBnds,optObj_lpSolveAPI-method Man page
changeUptake Man page
changeUptake-methods Man page
changeUptake,modelorg-method Man page
checkAlgorithm Man page
checkDefaultMethod Man page
checkOptSol Man page
checkOptSol-methods Man page
checkOptSol,optsol-method Man page
checkReactId Man page
checksol Man page
checksol-class Man page
checkSolStat Man page
checkStat Man page
checkStat,optsol-method Man page
checkVersion Man page
checkVersion-methods Man page
checkVersion,modelorg Man page
checkVersion,modelorg-method Man page
chlb Man page
chlb<- Man page
chlb<-,optsol_fluxdel-method Man page
chlb,optsol_fluxdel-method Man page
chub Man page
chub<- Man page
chub<-,optsol_fluxdel-method Man page
chub,optsol_fluxdel-method Man page
clpPtr-class Man page
cmd Man page
cmd<- Man page
cmd<-,ppProc-method Man page
cmd,ppProc-method Man page
comp_attr Man page
comp_attr<- Man page
comp_attr<-,modelorg-method Man page
comp_attr,modelorg-method Man page
cplexPointer-class Man page
cplexPtr-class Man page
cpsol Man page
cpsol,optsol_genedel-method Man page
ctrlfl Man page
ctrlfl<- Man page
ctrlfl<-,optsol_phpp-method Man page
ctrlfl,optsol_phpp-method Man page
ctrlfl<-,optsol_robAna-method Man page
ctrlfl,optsol_robAna-method Man page
ctrlr Man page
ctrlr<- Man page
ctrlr<-,optsol_robAna-method Man page
ctrlr,optsol_robAna-method Man page
deadEndMetabolites Man page
deadEndMetabolites-methods Man page
deadEndMetabolites,modelorg-method Man page
deleted Man page
deleted,optsol_fluxdel-method Man page
deleted,optsol_genedel-method Man page
delProb Man page
delProb-methods Man page
delProb,optObj_clpAPI-method Man page
delProb,optObj_cplexAPI-method Man page
delProb,optObj_glpkAPI-method Man page
delProb,optObj_lpSolveAPI-method Man page
dels Man page
dels<- Man page
dels<-,optsol_fluxdel-method Man page
dels,optsol_fluxdel-method Man page
didFoot Man page
didFoot<- Man page
didFoot<-,sybilLog-method Man page
didFoot,sybilLog-method Man page
dim,modelorg-method Man page
dim,optObj-method Man page
doubleFluxDel Man page
doubleGeneDel Man page
doubleReact Man page
EasyConstraint Man page
Ec_core Man page
editEnvir Man page
emsg Man page
emsg<- Man page
emsg<-,sybilError-method Man page
emsg,sybilError-method Man page
enum Man page
enum<- Man page
enum<-,sybilError-method Man page
enum,sybilError-method Man page
exit_code Man page
exit_code<- Man page
exit_code<-,checksol-method Man page
exit_code,checksol-method Man page
exit_meaning Man page
exit_meaning<- Man page
exit_meaning<-,checksol-method Man page
exit_meaning,checksol-method Man page
exit_num Man page
exit_num<- Man page
exit_num<-,checksol-method Man page
exit_num,checksol-method Man page
ex_met Man page
ex_met,summaryOptsol-method Man page
ex_val Man page
ex_val,summaryOptsol-method Man page
fba Man page
fbaEasyConstraint Man page
fenc Man page
fenc<- Man page
fenc<-,sybilLog-method Man page
fenc,sybilLog-method Man page
fh Man page
fh<- Man page
fh<-,sybilLog-method Man page
fh,sybilLog-method Man page
file-class Man page
findExchReact Man page
fldind Man page
fldind<- Man page
fldind<-,optsol-method Man page
fldind,optsol-method Man page
fldind<-,sysBiolAlg-method Man page
fldind,sysBiolAlg-method Man page
fluxdels Man page
fluxdels<- Man page
fluxdels<-,optsol_genedel-method Man page
fluxdels,optsol_genedel-method Man page
fluxdist Man page
fluxdist<- Man page
fluxdist<-,optsol-method Man page
fluxdist,optsol-method Man page
fluxDistribution Man page
[,fluxDistribution,ANY,ANY,ANY-method Man page
fluxDistribution-class Man page
fluxes Man page
fluxes<- Man page
fluxes<-,fluxDistribution-method Man page
fluxes,fluxDistribution-method Man page
fluxes<-,optsol-method Man page
fluxes,optsol-method Man page
fluxVar Man page
fname Man page
fname<- Man page
fname<-,sybilLog-method Man page
fname,sybilLog-method Man page
fpath Man page
fpath<- Man page
fpath<-,sybilLog-method Man page
fpath,sybilLog-method Man page
fv Man page
geneDel Man page
geneDeletion Man page
genes Man page
genes<- Man page
genes<-,modelorg-method Man page
genes,modelorg-method Man page
getColPrim Man page
getColPrim-methods Man page
getColPrim,optObj_clpAPI,numeric-method Man page
getColPrim,optObj_cplexAPI,numeric-method Man page
getColPrim,optObj_glpkAPI,numeric-method Man page
getColPrim,optObj_lpSolveAPI,numeric-method Man page
getColsLowBnds Man page
getColsLowBnds-methods Man page
getColsLowBnds,optObj_clpAPI,numeric-method Man page
getColsLowBnds,optObj_cplexAPI,numeric-method Man page
getColsLowBnds,optObj_glpkAPI,numeric-method Man page
getColsLowBnds,optObj_lpSolveAPI,numeric-method Man page
getColsNames Man page
getColsNames-methods Man page
getColsNames,optObj_cplexAPI,numeric-method Man page
getColsNames,optObj_glpkAPI,numeric-method Man page
getColsNames,optObj_lpSolveAPI,numeric-method Man page
getColsUppBnds Man page
getColsUppBnds-methods Man page
getColsUppBnds,optObj_clpAPI,numeric-method Man page
getColsUppBnds,optObj_cplexAPI,numeric-method Man page
getColsUppBnds,optObj_glpkAPI,numeric-method Man page
getColsUppBnds,optObj_lpSolveAPI,numeric-method Man page
getFluxDist Man page
getFluxDist-methods Man page
getFluxDist,optObj_clpAPI-method Man page
getFluxDist,optObj_cplexAPI-method Man page
getFluxDist,optObj_glpkAPI-method Man page
getFluxDist,optObj_lpSolveAPI-method Man page
getFluxDist,optsol-method Man page
getMeanReturn Man page
getMeanStatus Man page
getNetFlux Man page
getNumCols Man page
getNumCols-methods Man page
getNumCols,optObj_clpAPI-method Man page
getNumCols,optObj_cplexAPI-method Man page
getNumCols,optObj_glpkAPI-method Man page
getNumCols,optObj_lpSolveAPI-method Man page
getNumNnz Man page
getNumNnz-methods Man page
getNumNnz,optObj_clpAPI-method Man page
getNumNnz,optObj_cplexAPI-method Man page
getNumNnz,optObj_glpkAPI-method Man page
getNumRows Man page
getNumRows-methods Man page
getNumRows,optObj_clpAPI-method Man page
getNumRows,optObj_cplexAPI-method Man page
getNumRows,optObj_glpkAPI-method Man page
getNumRows,optObj_lpSolveAPI-method Man page
getObjCoefs Man page
getObjCoefs-methods Man page
getObjCoefs,optObj_clpAPI,numeric-method Man page
getObjCoefs,optObj_cplexAPI,numeric-method Man page
getObjCoefs,optObj_glpkAPI,numeric-method Man page
getObjCoefs,optObj_lpSolveAPI,numeric-method Man page
getObjDir Man page
getObjDir-methods Man page
getObjDir,optObj_clpAPI-method Man page
getObjDir,optObj_cplexAPI-method Man page
getObjDir,optObj_glpkAPI-method Man page
getObjDir,optObj_lpSolveAPI-method Man page
getObjVal Man page
getObjVal-methods Man page
getObjVal,optObj_clpAPI-method Man page
getObjVal,optObj_cplexAPI-method Man page
getObjVal,optObj_glpkAPI-method Man page
getObjVal,optObj_lpSolveAPI-method Man page
getRedCosts Man page
getRedCosts-methods Man page
getRedCosts,optObj_clpAPI-method Man page
getRedCosts,optObj_cplexAPI-method Man page
getRedCosts,optObj_glpkAPI-method Man page
getRedCosts,optObj_lpSolveAPI-method Man page
getRedCosts,optsol_phpp-method Man page
getRowsLowBnds Man page
getRowsLowBnds-methods Man page
getRowsLowBnds,optObj_clpAPI,numeric-method Man page
getRowsLowBnds,optObj_cplexAPI,numeric-method Man page
getRowsLowBnds,optObj_glpkAPI,numeric-method Man page
getRowsLowBnds,optObj_lpSolveAPI,numeric-method Man page
getRowsNames Man page
getRowsNames-methods Man page
getRowsNames,optObj_cplexAPI,numeric-method Man page
getRowsNames,optObj_glpkAPI,numeric-method Man page
getRowsNames,optObj_lpSolveAPI,numeric-method Man page
getRowsUppBnds Man page
getRowsUppBnds-methods Man page
getRowsUppBnds,optObj_clpAPI,numeric-method Man page
getRowsUppBnds,optObj_cplexAPI,numeric-method Man page
getRowsUppBnds,optObj_glpkAPI,numeric-method Man page
getRowsUppBnds,optObj_lpSolveAPI,numeric-method Man page
getSolStat Man page
getSolStat-methods Man page
getSolStat,optObj_clpAPI-method Man page
getSolStat,optObj_cplexAPI-method Man page
getSolStat,optObj_glpkAPI-method Man page
getSolStat,optObj_lpSolveAPI-method Man page
getSolverParm Man page
getSolverParm-methods Man page
getSolverParm,optObj_clpAPI-method Man page
getSolverParm,optObj_cplexAPI-method Man page
getSolverParm,optObj_glpkAPI-method Man page
getSolverParm,optObj_lpSolveAPI-method Man page
getsybilenv Man page
glpkPtr-class Man page
gpr Man page
gpr<- Man page
gpr<-,modelorg-method Man page
gpr,modelorg-method Man page
gprRules Man page
gprRules<- Man page
gprRules<-,modelorg-method Man page
gprRules,modelorg-method Man page
hasEffect Man page
hasEffect<- Man page
hasEffect<-,optsol_genedel-method Man page
hasEffect,optsol_genedel-method Man page
image,summaryOptsol-method Man page
ind Man page
ind<- Man page
ind2id Man page
ind2id,optsol_fluxdel-method Man page
ind2id,optsol_genedel-method Man page
ind<-,ppProc-method Man page
ind,ppProc-method Man page
initProb Man page
initProb-methods Man page
initProb,optObj_clpAPI-method Man page
initProb,optObj_cplexAPI-method Man page
initProb,optObj_glpkAPI-method Man page
initProb,optObj_lpSolveAPI-method Man page
irrev Man page
irrev<- Man page
irrev2rev Man page
irrev2rev<- Man page
irrev2rev<-,modelorg_irrev-method Man page
irrev2rev,modelorg_irrev-method Man page
irrev<-,modelorg_irrev-method Man page
irrev,modelorg_irrev-method Man page
length,netFlux-method Man page
length,optsol-method Man page
length,reactId-method Man page
lethal Man page
lethal,optsol_fluxdel-method Man page
lmoma Man page
loadLPprob Man page
loadLPprob-methods Man page
loadLPprob,optObj_clpAPI-method Man page
loadLPprob,optObj_cplexAPI-method Man page
loadLPprob,optObj_glpkAPI-method Man page
loadLPprob,optObj_lpSolveAPI-method Man page
loadMatrixPerColumnLPSOLVE Man page
loadQobj Man page
loadQobj-methods Man page
loadQobj,optObj_cplexAPI,Matrix-method Man page
loadQobj,optObj_cplexAPI,numeric-method Man page
logCall Man page
logCall,sybilLog-method Man page
logClose<- Man page
logClose<-,sybilLog-method Man page
logComment Man page
logComment,sybilLog-method Man page
logError Man page
logError,sybilLog,ANY,ANY-method Man page
logError,sybilLog,ANY,numeric-method Man page
logError,sybilLog-method Man page
logFH Man page
logFH,sybilLog-method Man page
logFileFH Man page
logFoot<- Man page
logFoot<-,sybilLog-method Man page
logHead Man page
logHead,sybilLog-method Man page
loglevel Man page
loglevel<- Man page
loglevel<-,sybilLog-method Man page
loglevel,sybilLog-method Man page
logMessage Man page
logMessage,sybilLog-method Man page
logOptimization Man page
logOptimization,sybilLog-method Man page
logOptimizationTH Man page
logOptimizationTH,sybilLog-method Man page
logStep<- Man page
logStep<-,sybilLog-method Man page
logWarning Man page
logWarning,sybilLog-method Man page
lowbnd Man page
lowbnd<- Man page
lowbnd<-,modelorg-method Man page
lowbnd,modelorg-method Man page
lowbnd<-,reactId_Exch-method Man page
lowbnd,reactId_Exch-method Man page
lp_dir Man page
lp_dir<- Man page
lp_dir<-,optsol,character-method Man page
lp_dir<-,optsol,factor-method Man page
lp_dir,optsol-method Man page
lp_dir<-,optsol,numeric-method Man page
lpExtPtr-class Man page
lp_num_cols Man page
lp_num_cols<- Man page
lp_num_cols<-,optsol-method Man page
lp_num_cols,optsol-method Man page
lp_num_rows Man page
lp_num_rows<- Man page
lp_num_rows<-,optsol-method Man page
lp_num_rows,optsol-method Man page
lp_obj Man page
lp_obj<- Man page
lp_obj<-,optsol-method Man page
lp_obj,optsol-method Man page
lp_ok Man page
lp_ok<- Man page
lp_ok<-,optsol-method Man page
lp_ok,optsol-method Man page
lp_stat Man page
lp_stat<- Man page
lp_stat<-,optsol-method Man page
lp_stat,optsol-method Man page
lstname Man page
lstname,sybilLog-method Man page
makeOptsolMO Man page
matchrev Man page
matchrev<- Man page
matchrev<-,modelorg_irrev-method Man page
matchrev,modelorg_irrev-method Man page
MAXIMUM Man page
maxSol Man page
maxSol,optsol_blockedReact-method Man page
maxSol,optsol_fluxVar-method Man page
met_attr Man page
met_attr<- Man page
met_attr<-,modelorg-method Man page
met_attr,modelorg-method Man page
met_comp Man page
met_comp<- Man page
met_comp<-,modelorg-method Man page
met_comp,modelorg-method Man page
met_de Man page
met_de<- Man page
met_de<-,modelorg-method Man page
met_de,modelorg-method Man page
method Man page
method<- Man page
METHOD Man page
method,optObj-method Man page
method<-,optsol-method Man page
method,optsol-method Man page
met_id Man page
met_id<- Man page
met_id<-,modelorg-method Man page
met_id,modelorg-method Man page
met_id<-,reactId_Exch-method Man page
met_id,reactId_Exch-method Man page
met_name Man page
met_name<- Man page
met_name<-,modelorg-method Man page
met_name,modelorg-method Man page
met_num Man page
met_num<- Man page
met_num<-,modelorg-method Man page
met_num,modelorg-method Man page
met_pos Man page
met_pos<- Man page
met_pos<-,reactId_Exch-method Man page
met_pos,reactId_Exch-method Man page
met_single Man page
met_single<- Man page
met_single<-,modelorg-method Man page
met_single,modelorg-method Man page
minSol Man page
minSol,optsol_blockedReact-method Man page
minSol,optsol_fluxVar-method Man page
mod2irrev Man page
mod_attr Man page
mod_attr<- Man page
mod_attr<-,modelorg-method Man page
mod_attr,modelorg-method Man page
mod_compart Man page
mod_compart<- Man page
mod_compart<-,modelorg-method Man page
mod_compart,modelorg-method Man page
mod_desc Man page
mod_desc<- Man page
mod_desc<-,modelorg-method Man page
mod_desc,modelorg-method Man page
modelorg Man page
modelorg2ExPA Man page
modelorg2text Man page
modelorg2tsv Man page
modelorg-class Man page
modelorg_irrev Man page
modelorg_irrev-class Man page
mod_id Man page
mod_id<- Man page
mod_id<-,modelorg-method Man page
mod_id,modelorg-method Man page
mod_id<-,optsol-method Man page
mod_id,optsol-method Man page
mod_id<-,reactId-method Man page
mod_id,reactId-method Man page
mod_id<-,summaryOptsol-method Man page
mod_id,summaryOptsol-method Man page
mod_key Man page
mod_key<- Man page
mod_key<-,modelorg-method Man page
mod_key,modelorg-method Man page
mod_key<-,optsol-method Man page
mod_key,optsol-method Man page
mod_key<-,reactId-method Man page
mod_key,reactId-method Man page
mod_key<-,summaryOptsol-method Man page
mod_key,summaryOptsol-method Man page
mod_name Man page
mod_name<- Man page
mod_name<-,modelorg-method Man page
mod_name,modelorg-method Man page
mod_obj Man page
mod_obj<- Man page
mod_obj,optsol-method Man page
mod_obj<-,summaryOptsol-method Man page
mod_obj,summaryOptsol-method Man page
moma Man page
mtf Man page
mtfEasyConstraint Man page
multiDel Man page
nc Man page
nc<- Man page
nc<-,sysBiolAlg-method Man page
nc,sysBiolAlg-method Man page
netFlux Man page
netFlux-class Man page
nfluxes Man page
nfluxes,optsol-method Man page
nnzero,fluxDistribution-method Man page
nnzero,summaryOptsol-method Man page
nr Man page
nr<- Man page
nr<-,sysBiolAlg-method Man page
nr,sysBiolAlg-method Man page
num_of_fluxes Man page
num_of_fluxes,fluxDistribution-method Man page
num_of_prob Man page
num_of_prob<- Man page
num_of_prob<-,checksol-method Man page
num_of_prob,checksol-method Man page
num_of_prob<-,optsol-method Man page
num_of_prob,optsol-method Man page
nvar Man page
nvar,fluxDistribution-method Man page
nzeros Man page
nzeros,summaryOptsol-method Man page
obj_coef Man page
obj_coef<- Man page
obj_coef<-,modelorg-method Man page
obj_coef,modelorg-method Man page
obj_coef<-,optsol-method Man page
obj_coef,optsol-method Man page
object Man page
obj_func Man page
obj_func<- Man page
obj_func<-,optsol-method Man page
obj_func,optsol-method Man page
oneFluxDel Man page
oneGeneDel Man page
onlyChangeGPR Man page
onlyCheckGPR Man page
OPT_DIRECTION Man page
optimizeProb Man page
optimizeProb-methods Man page
optimizeProb,modelorg-method Man page
optimizeProb,sysBiolAlg-method Man page
optimizer Man page
optObj Man page
optObj-class Man page
optObj_clpAPI-class Man page
optObj_cplexAPI-class Man page
optObj_glpkAPI-class Man page
optObj_lpSolveAPI-class Man page
optsol Man page
optsol_blockedReact-class Man page
optsol-class Man page
[,optsol_fluxdel,ANY,ANY,ANY-method Man page
optsol_fluxdel-class Man page
optsol_fluxVar-class Man page
optsol_genedel-class Man page
optsol_optimizeProb-class Man page
optsol_phpp-class Man page
optsol_robAna-class Man page
pa Man page
pa<- Man page
pa<-,ppProc-method Man page
pa,ppProc-method Man page
PATH_TO_MODEL Man page
phpp Man page
plot,fluxDistribution,missing-method Man page
plot,optsol_fluxVar,missing-method Man page
plot,optsol,missing-method Man page
plot,optsol_phpp,character-method Man page
plot,optsol_phpp,missing-method Man page
plot,optsol_robAna,missing-method Man page
plotRangeVar Man page
plotRangeVar,optsol_fluxVar-method Man page
plot,summaryOptsol,missing-method Man page
pointerToProb Man page
pointerToProb-class Man page
postProc Man page
postProc<- Man page
postProc<-,optsol_optimizeProb-method Man page
postProc,optsol_optimizeProb-method Man page
ppProc Man page
ppProc-class Man page
preProc Man page
preProc<- Man page
preProc<-,optsol_optimizeProb-method Man page
preProc,optsol_optimizeProb-method Man page
printExchange Man page
printExchange,summaryOptsol-method Man page
printMetabolite Man page
printMetabolite-methods Man page
printMetabolite,modelorg-method Man page
printObjFunc Man page
printObjFunc,modelorg-method Man page
printReaction Man page
printReaction-methods Man page
printReaction,modelorg,ANY-method Man page
printReaction,summaryOptsol,modelorg-method Man page
problem Man page
problem,sysBiolAlg-method Man page
probType Man page
probType,optObj-method Man page
promptSysBiolAlg Man page
rate Man page
rate,netFlux-method Man page
react Man page
react<- Man page
react_attr Man page
react_attr<- Man page
react_attr<-,modelorg-method Man page
react_attr,modelorg-method Man page
react_de Man page
react_de<- Man page
react_de<-,modelorg-method Man page
react_de,modelorg-method Man page
react_id Man page
react_id<- Man page
reactId Man page
[,reactId,ANY,ANY,ANY-method Man page
reactId-class Man page
reactId_Exch Man page
[,reactId_Exch,ANY,ANY,ANY-method Man page
reactId_Exch-class Man page
react_id<-,modelorg-method Man page
react_id,modelorg-method Man page
react_id<-,netFlux-method Man page
react_id,netFlux-method Man page
react_id<-,optsol-method Man page
react_id,optsol-method Man page
react_id<-,reactId-method Man page
react_id,reactId-method Man page
react_name Man page
react_name<- Man page
react_name<-,modelorg-method Man page
react_name,modelorg-method Man page
react_num Man page
react_num<- Man page
react_num<-,modelorg-method Man page
react_num,modelorg-method Man page
react<-,optsol_blockedReact-method Man page
react,optsol_blockedReact-method Man page
react<-,optsol_fluxVar-method Man page
react,optsol_fluxVar-method Man page
react_pos Man page
react_pos<- Man page
react_pos<-,reactId-method Man page
react_pos,reactId-method Man page
react_rev Man page
react_rev<- Man page
react_rev<-,modelorg-method Man page
react_rev,modelorg-method Man page
react_single Man page
react_single<- Man page
react_single<-,modelorg-method Man page
react_single,modelorg-method Man page
readModel Man page
readProb Man page
readProb-methods Man page
readProb,optObj_clpAPI,character-method Man page
readProb,optObj_cplexAPI,character-method Man page
readProb,optObj_glpkAPI,character-method Man page
readProb,optObj_lpSolveAPI,character-method Man page
readTEXTmod Man page
readTSVmod Man page
resetChanges Man page
resetChanges-methods Man page
resetChanges,sysBiolAlg-method Man page
resetChanges,sysBiolAlg_room-method Man page
return_codeLPSOLVE Man page
rev2irrev Man page
rev2irrev<- Man page
rev2irrev<-,modelorg_irrev-method Man page
rev2irrev,modelorg_irrev-method Man page
rmReact Man page
robAna Man page
room Man page
rxnGeneMat Man page
rxnGeneMat<- Man page
rxnGeneMat<-,modelorg-method Man page
rxnGeneMat,modelorg-method Man page
S Man page
S<- Man page
scaleProb Man page
scaleProb-methods Man page
scaleProb,optObj_clpAPI-method Man page
scaleProb,optObj_cplexAPI-method Man page
scaleProb,optObj_glpkAPI-method Man page
scaleProb,optObj_lpSolveAPI-method Man page
sensitivityAnalysis Man page
sensitivityAnalysis-methods Man page
sensitivityAnalysis,optObj_cplexAPI-method Man page
sensitivityAnalysis,optObj_glpkAPI-method Man page
setColsNames Man page
setColsNames-methods Man page
setColsNames,optObj_clpAPI,numeric,character-method Man page
setColsNames,optObj_cplexAPI,numeric,character-method Man page
setColsNames,optObj_glpkAPI,numeric,character-method Man page
setColsNames,optObj_lpSolveAPI,numeric,character-method Man page
setObjDir Man page
setObjDir-methods Man page
setObjDir,optObj_clpAPI,character-method Man page
setObjDir,optObj_clpAPI,numeric-method Man page
setObjDir,optObj_cplexAPI,character-method Man page
setObjDir,optObj_cplexAPI,integer-method Man page
setObjDir,optObj_cplexAPI,numeric-method Man page
setObjDir,optObj_glpkAPI,character-method Man page
setObjDir,optObj_glpkAPI,integer-method Man page
setObjDir,optObj_glpkAPI,numeric-method Man page
setObjDir,optObj_lpSolveAPI,character-method Man page
setObjDir,optObj_lpSolveAPI,numeric-method Man page
setRhsZero Man page
setRhsZero-methods Man page
setRhsZero,optObj_clpAPI-method Man page
setRhsZero,optObj_cplexAPI-method Man page
setRhsZero,optObj_glpkAPI-method Man page
setRhsZero,optObj_lpSolveAPI-method Man page
setRowsNames Man page
setRowsNames-methods Man page
setRowsNames,optObj_clpAPI,numeric,character-method Man page
setRowsNames,optObj_cplexAPI,numeric,character-method Man page
setRowsNames,optObj_glpkAPI,numeric,character-method Man page
setRowsNames,optObj_lpSolveAPI,numeric,character-method Man page
setSolverParm Man page
setSolverParm-methods Man page
setSolverParm,optObj_clpAPI-method Man page
setSolverParm,optObj_cplexAPI-method Man page
setSolverParm,optObj_glpkAPI-method Man page
setSolverParm,optObj_lpSolveAPI-method Man page
show,checksol-method Man page
show,modelorg-method Man page
show,optsol-method Man page
shrinkMatrix Man page
shrinkMatrix-methods Man page
shrinkMatrix,modelorg-method Man page
singletonMetabolites Man page
singletonMetabolites-methods Man page
singletonMetabolites,modelorg-method Man page
S<-,modelorg-method Man page
S,modelorg-method Man page
Snnz Man page
Snnz,modelorg-method Man page
solveLp Man page
solveLp-methods Man page
solveLp,optObj_clpAPI-method Man page
solveLp,optObj_cplexAPI-method Man page
solveLp,optObj_glpkAPI-method Man page
solveLp,optObj_lpSolveAPI-method Man page
solver Man page
solver<- Man page
SOLVER Man page
SOLVER_CTRL_PARM Man page
solver,optObj-method Man page
solver<-,optsol-method Man page
solver,optsol-method Man page
status_code Man page
status_code<- Man page
status_code<-,checksol-method Man page
status_code,checksol-method Man page
status_meaning Man page
status_meaning<- Man page
status_meaning<-,checksol-method Man page
status_meaning,checksol-method Man page
status_num Man page
status_num<- Man page
status_num<-,checksol-method Man page
status_num,checksol-method Man page
stclear Man page
stexists Man page
stfirst Man page
stinit Man page
stlength Man page
stlist Man page
stpop Man page
stpush Man page
stseek Man page
stshift Man page
stunshift Man page
subSys Man page
subSys<- Man page
subSys<-,modelorg-method Man page
subSys,modelorg-method Man page
summaryOptsol Man page
summaryOptsol-class Man page
sybil Man page
sybil-deprecated Man page
sybilError Man page
sybilError-class Man page
sybilLog Man page
sybilLog-class Man page
sybil-package Man page
SYBIL_SETTINGS Man page
sybilStack Man page
sysBiolAlg Man page
sysBiolAlg-class Man page
sysBiolAlg_fba Man page
sysBiolAlg_fba-class Man page
sysBiolAlg_fbaEasyConstraint Man page
sysBiolAlg_fbaEasyConstraint-class Man page
sysBiolAlg_fv Man page
sysBiolAlg_fv-class Man page
sysBiolAlg_lmoma Man page
sysBiolAlg_lmoma-class Man page
sysBiolAlg_moma Man page
sysBiolAlg_moma-class Man page
sysBiolAlg_mtf Man page
sysBiolAlg_mtf-class Man page
sysBiolAlg_mtfEasyConstraint Man page
sysBiolAlg_mtfEasyConstraint-class Man page
sysBiolAlg_room Man page
sysBiolAlg_room-class Man page
TOLERANCE Man page
upgradeModelorg Man page
uppbnd Man page
uppbnd<- Man page
uppbnd<-,modelorg-method Man page
uppbnd,modelorg-method Man page
uppbnd<-,reactId_Exch-method Man page
uppbnd,reactId_Exch-method Man page
uptake Man page
uptake<- Man page
uptake<-,reactId_Exch-method Man page
uptake,reactId_Exch-method Man page
uptMet Man page
uptMet,reactId_Exch-method Man page
uptReact Man page
uptReact,reactId_Exch-method Man page
USE_NAMES Man page
verblevel Man page
verblevel<- Man page
verblevel<-,sybilLog-method Man page
verblevel,sybilLog-method Man page
version Man page
version<- Man page
version<-,modelorg-method Man page
version,modelorg-method Man page
writeProb Man page
writeProb-methods Man page
writeProb,optObj_clpAPI,character-method Man page
writeProb,optObj_cplexAPI,character-method Man page
writeProb,optObj_glpkAPI,character-method Man page
writeProb,optObj_lpSolveAPI,character-method Man page
wrong_solver_msg Man page
wrong_type_msg Man page
ypd Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.