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sybil (version 1.1.1)

sybil - Efficient Constrained Based Modelling in R

Description

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).

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Version

Install

install.packages('sybil')

Monthly Downloads

99

Version

1.1.1

License

GPL-3

Maintainer

Gabriel Gelius-Dietrich

Last Published

October 8th, 2012

Functions in sybil (1.1.1)

initProb-methods

Initialize Problem Object

Check and Change the GPR Rules

getNumNnz-methods

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

changeColsBnds-methods

Change Column (Variable) Bounds in the Optimization Problem

getObjDir-methods

Get Direction of Optimization.

Strukture of Class "modelorg"

changeMatrixRow-methods

Change a Row in the Constraint Matrix of the Optimization Problem

Escherichia coli Core Metabolic Model

changeColsBndsObjCoefs-methods

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

In Sillico YPD Medium

Structure of the Class "checksol"

Add Exchange Reactions to a Model

Add a New Mathematical Programming Solver to sybil

checkDefaultMethod

Validate Solver and Method

getFluxDist-methods

Retrieve Flux Distribution

getNumCols-methods

Get Number of Columns (Variables) of the Optimization Problem

Interprets an Object of Class Optsol

addRowsCols-methods

Add Rows and Columns to an Optimization Problem

addColsToProb-methods

Add New Columns (Variables) to an Optimization Problem

addCols-methods

Add Columns to an Optimization Problem

Strukture of Class "reactId"

Check if a Reaction Id is Valid

changeRowsBnds-methods

Change Row Bounds in the Optimization Problem

addRowsToProb-methods

Add New Rows (Constraints) to an Optimization Problem

optsol_genedel-class

Class "optsol_genedel"

Check Algorithm

One Flux Deletion Experiment

Prints a Human Readable Objective Function

getSolStat-methods

Get Solution Status After Optimization

optObj_cplexAPI-class

Class "optObj_cplexAPI"

Simulate N Gene Deletion Experiments

Performs Optimizations for the Gene/Flux Deletion Experiments

Get Gene-Reaction Association

modelorg_irrev-class

Class for Metabolic Networks in Irreversible Format.

delProb-methods

Free Memory Associated to the Pointer to the Problem Object

General Constructor Function For Objects of Class optObj

getNumRows-methods

Get Number of Rows (Constraints) of the Optimization Problem

Find Exchange Reactions

Add/Change Reactions in a Model

addRows-methods

Add Rows to an Optimization Problem

getColPrim-methods

Get Primal Value of Variables After Optimization

General Constructor Function For Objects of Class sysBiolAlg

Identifies Identical Reactions

fluxDistribution-class

Class "fluxDistribution"

getObjVal-methods

Get Value of the Objective Function After Optimization

optsol_fluxdel-class

Class "optsol_fluxdel"

optsol_fluxVar-class

Class "optsol_fluxVar"

Sets/changes the Objective Function

Print sybil Environment

backupProb-methods

Copies a Problem Object to a New Problem Object

getRedCosts-methods

Get Reduced Costs of all Variables After Optimization

writeProb-methods

Write Problem Object to File

Write an Instance of Class modelorg to File in ExPA Format

getColsLowBnds-methods

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

getSolverParm-methods

Retrieve Current Parameter Settings Used By The Optimization Software

Find Blocked Reactions in a Metabolic Network

optObj_lpSolveAPI-class

Class "optObj_lpSolveAPI"

getColsUppBnds-methods

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

Write an Instance of Class modelorg to File

Change the GPR Rules

loadQobj-methods

Load Quadratic Part of the Objective Function to the Optimization Problem

sysBiolAlg_lmoma-class

Class "sysBiolAlg_lmoma"

getRowsLowBnds-methods

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

solveLp-methods

Optimize Problem Object

setObjDir-methods

Set Direction of Optimization

setRhsZero-methods

Set Right Hand Side of the Optimization Problem To Zero

getObjCoefs-methods

Get Objective Coefficients of the Optimization Problem

changeObjCoefs-methods

Change Column (Variable) Objective Coefficients in the Optimization Problem

getRowsUppBnds-methods

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

Creates an Instance of Class "optObj"

Robustness Analysis

sysBiolAlg_moma-class

Class "sysBiolAlg_moma"

Add a New Algorithm Name to sybil

scaleProb-methods

Scaling of the Constraint Matrix of an Optimization Problem

Set and Get sybil Parameters

Produces a Model in Irreversible Format

loadLPprob-methods

Load Data to Optimization Problem

sybil -- Efficient Constrained Based Modelling in R

Double Flux Deletion Experiment

Flux Variability Analysis

Flux Balance Analysis with a Given Model

Parallel (Multicore) Support for sybil

optObj_clpAPI-class

Class "optObj_clpAPI"

Internal sybil Functions

sysBiolAlg-class

Class "sysBiolAlg"

promptSysBiolAlg

Generate A Skeletal Structure of Subclasses of sysBiolAlg

sysBiolAlg_fv-class

Class "sysBiolAlg_fv"

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

optsol_blockedReact-class

Class "optsol_blockedReact"

Class "sybilLog"

Check the GPR Rules

Class "netFlux"

Class "optObj"

sysBiolAlg_room-class

Class "sysBiolAlg_room"

Environment Editor for Metabolic Networks

Class "ppProc"

optsol_optimizeProb-class

Class "optsol_optimizeProb"

sysBiolAlg_mtf-class

Class "sysBiolAlg_mtf"

Constructor Function for Objects of Class optsol_optimizeProb.

optsol_robAna-class

Class "optsol_robAna"

Change Variable Bounds in a Metabolic Network

sysBiolAlg_fba-class

Class "sysBiolAlg_fba"

setSolverParm-methods

Set Parameters Used By The Optimization Software

printReaction-methods

Print Columns of the Stoichiometric Matrix

sensitivityAnalysis-methods

Sensitivity Analysis

sybil-deprecated

Deprecated Functions and Methods in Package sybil

readProb-methods

Read Problem Object From File

Read a Metabolic Network in a TSV (CSV) Format

checkOptSol-methods

Summarized Information About an Object of Class Optsol

optimizeProb-methods

Optimize Problem Object

Double Gene Deletion Experiment

Single Gene Deletion Experiment

reactId_Exch-class

Class "reactId_Exch"

applyChanges-methods

Generic Function to Apply Changes to Objects of Class sysBiolAlg

Summarize Objects of Class Optsol

shrinkMatrix-methods

Get a Subset of Matrix Like Objects

Remove Reactions From a Model

optObj_glpkAPI-class

Class "optObj_glpkAPI"

sybilError-class

Class "sybilError"

summaryOptsol-class

Class "summaryOptsol"

printMetabolite-methods

Print Rows of the Stoichiometric Matrix

resetChanges-methods

Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg