sybil package - RDocumentation

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#sybil - Efficient Constrained Based Modelling in R

The package sybil is a Systems Biology Library for R, implementing 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).

Please consider downloading and installing the package via the R internal package management: install.packages("sybil")

Alternatively you can visit the CRAN pakage website.

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Version

Install

install.packages('sybil')

Monthly Downloads

283

Version

2.0.0

License

GPL-3 | file LICENSE

Maintainer

Claus Jonathan Fritzemeier

Last Published

June 6th, 2016

Functions in sybil (2.0.0)

addCols-methods

Add Columns to an Optimization Problem

Add/Change Reactions in a Model

addColsToProb-methods

Add New Columns (Variables) to an Optimization Problem

addRowsToProb-methods

Add New Rows (Constraints) to an Optimization Problem

addRowsCols-methods

Add Rows and Columns to an Optimization Problem

Add a New Mathematical Programming Solver to sybil

Add a New Algorithm Name to sybil

applyChanges-methods

Generic Function to Apply Changes to Objects of Class sysBiolAlg

Add Exchange Reactions to a Model

addRows-methods

Add Rows to an Optimization Problem

changeColsBndsObjCoefs-methods

Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem

Check and Change the GPR Rules

Change Variable Bounds in a Metabolic Network

Find Blocked Reactions in a Metabolic Network

changeColsBnds-methods

Change Column (Variable) Bounds in the Optimization Problem

Sets/changes the Objective Function

backupProb-methods

Copies a Problem Object to a New Problem Object

changeRowsBnds-methods

Change Row Bounds in the Optimization Problem

changeObjCoefs-methods

Change Column (Variable) Objective Coefficients in the Optimization Problem

changeMatrixRow-methods

Change a Row in the Constraint Matrix of the Optimization Problem

Check Algorithm

Check if a Reaction Id is Valid

deadEndMetabolites-methods

Identify Dead End Metabolites

delProb-methods

Free Memory Associated to the Pointer to the Problem Object

sybil-deprecated

Deprecated Functions and Methods in Package sybil

checkOptSol-methods

Summarized Information About an Object of Class Optsol

checkDefaultMethod

Validate Solver and Method

Structure of the Class "checksol"

checkVersion-methods

checks Version of modelorg

changeUptake-methods

Change Uptake Reactions

fluxDistribution-class

Class "fluxDistribution"

Escherichia coli Core Metabolic Model

Double Gene Deletion Experiment

Identifies Identical Reactions

Flux Variability Analysis

Double Flux Deletion Experiment

Get Gene-Reaction Association

Environment Editor for Metabolic Networks

Find Exchange Reactions

Gene Deletion Experiments

getNumNnz-methods

Retrieve the Number of Non-Zero Elements of the Constraint Matrix

getNumRows-methods

Get Number of Rows (Constraints) of the Optimization Problem

getNumCols-methods

Get Number of Columns (Variables) of the Optimization Problem

getFluxDist-methods

Retrieve Flux Distribution

getColsUppBnds-methods

Get Upper Bounds of the Columns (Variables) of the Optimization Problem

getColsNames-methods

Retrieve Variable Names

getColPrim-methods

Get Primal Value of Variables After Optimization

getObjCoefs-methods

Get Objective Coefficients of the Optimization Problem

getColsLowBnds-methods

Get Lower Bounds of the Columns (Variables) of the Optimization Problem

getObjDir-methods

Get Direction of Optimization.

getRowsLowBnds-methods

Get Lower Bounds of the Rows (Constraints) of the Optimization Problem

getRowsNames-methods

Retrieve Constraint Names

getSolverParm-methods

Retrieve Current Parameter Settings Used By The Optimization Software

Print sybil Environment

getRowsUppBnds-methods

Get Upper Bounds of the Rows (Constraints) of the Optimization Problem

getSolStat-methods

Get Solution Status After Optimization

loadLPprob-methods

Load Data to Optimization Problem

getObjVal-methods

Get Value of the Objective Function After Optimization

initProb-methods

Initialize Problem Object

getRedCosts-methods

Get Reduced Costs of all Variables After Optimization

Structure of Class "modelorg"

Parallel Support for sybil

Write an Instance of Class modelorg to File

Write an Instance of Class modelorg to File in ExPA Format

Produces a Model in Irreversible Format

modelorg_irrev-class

Class for Metabolic Networks in Irreversible Format.

loadQobj-methods

Load Quadratic Part of the Objective Function to the Optimization Problem

Single Flux Deletion Experiment

Class "netFlux"

Constructor Function for Objects of Class optsol_optimizeProb.

optObj_lpSolveAPI-class

Class "optObj_lpSolveAPI"

Class "optObj"

optsol_phpp-class

Class "optsol_phpp"

reactId_Exch-class

Class "reactId_Exch"

optsol_robAna-class

Class "optsol_robAna"

Structure of Class "reactId"

setObjDir-methods

Set Direction of Optimization

setRhsZero-methods

Set Right Hand Side of the Optimization Problem To Zero

sybilError-class

Class "sybilError"

Class "sybilLog"

General Constructor Function For Objects of Class sysBiolAlg

Performs Series of Optimizations

upgradeModelorg

Upgrade modelorg to newer version.

optObj_clpAPI-class

Class "optObj_clpAPI"

optsol_optimizeProb-class

Class "optsol_optimizeProb"

optsol_fluxVar-class

Class "optsol_fluxVar"

Robustness Analysis

scaleProb-methods

Scaling of the Constraint Matrix of an Optimization Problem

solveLp-methods

Optimize Problem Object

summaryOptsol-class

Class "summaryOptsol"

Summarize Objects of Class Optsol

Set and Get sybil Parameters

readProb-methods

Read Problem Object From File

optsol_blockedReact-class

Class "optsol_blockedReact"

General Constructor Function For Objects of Class optObj

Read a Metabolic Network in a TSV (CSV) Format

setRowsNames-methods

Set/Change Constraint Names

setSolverParm-methods

Set Parameters Used By The Optimization Software

Internal sybil Functions

sybil -- Efficient Constrained Based Modelling in R

Single Gene Deletion Experiment

Change the GPR Rules

Check the GPR Rules

optimizeProb-methods

Optimize Problem Object

printMetabolite-methods

Print Rows of the Stoichiometric Matrix

Class "ppProc"

resetChanges-methods

Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg

Remove Reactions From a Model

singletonMetabolites-methods

Identify Singleton Metabolites

sysBiolAlg_fv-class

Class "sysBiolAlg_fv"

shrinkMatrix-methods

Get a Subset of Matrix Like Objects

sysBiolAlg_lmoma-class

Class "sysBiolAlg_lmoma"

sysBiolAlg_moma-class

Class "sysBiolAlg_moma"

sysBiolAlg_mtf-class

Class "sysBiolAlg_mtf"

sysBiolAlg-class

Class "sysBiolAlg"

sysBiolAlg_room-class

Class "sysBiolAlg_room"

optObj_cplexAPI-class

Class "optObj_cplexAPI"

optObj_glpkAPI-class

Class "optObj_glpkAPI"

Phenotypic Phase Plane Analysis

printReaction-methods

Print Columns of the Stoichiometric Matrix

promptSysBiolAlg

Generate A Skeletal Structure of Subclasses of sysBiolAlg

setColsNames-methods

Set/Change Variable Names

sensitivityAnalysis-methods

Sensitivity Analysis

A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality

sysBiolAlg_fba-class

Class "sysBiolAlg_fba"

writeProb-methods

Write Problem Object to File

In Sillico YPD Medium

optsol_genedel-class

Class "optsol_genedel"

optsol_fluxdel-class

Class "optsol_fluxdel"

sysBiolAlg_fbaEasyConstraint-class

Class "sysBiolAlg_fbaEasyConstraint" and Class "sysBiolAlg_mtfEasyConstraint"