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sybil (version 1.1.2)

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

150

Version

1.1.2

License

GPL-3

Maintainer

Gabriel Gelius-Dietrich

Last Published

October 10th, 2012

Functions in sybil (1.1.2)

solveLp-methods

Optimize Problem Object

getSolverParm-methods

Retrieve Current Parameter Settings Used By The Optimization Software

changeMatrixRow-methods

Change a Row in the Constraint Matrix of the Optimization Problem

sybil-deprecated

Deprecated Functions and Methods in Package sybil

addCols-methods

Add Columns to an Optimization Problem

addRows-methods

Add Rows to an Optimization Problem

Double Flux Deletion Experiment

Add/Change Reactions in a Model

Write an Instance of Class modelorg to File in ExPA Format

Add a New Algorithm Name to sybil

getObjVal-methods

Get Value of the Objective Function After Optimization

getRedCosts-methods

Get Reduced Costs of all Variables After Optimization

Add a New Mathematical Programming Solver to sybil

optsol_fluxVar-class

Class "optsol_fluxVar"

Double Gene Deletion Experiment

Flux Variability Analysis

Sets/changes the Objective Function

getColsUppBnds-methods

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

optsol_fluxdel-class

Class "optsol_fluxdel"

optsol_genedel-class

Class "optsol_genedel"

initProb-methods

Initialize Problem Object

One Flux Deletion Experiment

changeColsBnds-methods

Change Column (Variable) Bounds in the Optimization Problem

Produces a Model in Irreversible Format

Parallel (Multicore) Support for sybil

Strukture of Class "reactId"

changeObjCoefs-methods

Change Column (Variable) Objective Coefficients in the Optimization Problem

checkDefaultMethod

Validate Solver and Method

Structure of the Class "checksol"

optimizeProb-methods

Optimize Problem Object

addColsToProb-methods

Add New Columns (Variables) to an Optimization Problem

Escherichia coli Core Metabolic Model

sysBiolAlg_mtf-class

Class "sysBiolAlg_mtf"

getRowsUppBnds-methods

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

getFluxDist-methods

Retrieve Flux Distribution

Check if a Reaction Id is Valid

delProb-methods

Free Memory Associated to the Pointer to the Problem Object

Internal sybil Functions

Check the GPR Rules

addRowsCols-methods

Add Rows and Columns to an Optimization Problem

getColPrim-methods

Get Primal Value of Variables After Optimization

Check and Change the GPR Rules

setRhsZero-methods

Set Right Hand Side of the Optimization Problem To Zero

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

sybil -- Efficient Constrained Based Modelling in R

Change Variable Bounds in a Metabolic Network

fluxDistribution-class

Class "fluxDistribution"

Add Exchange Reactions to a Model

Find Exchange Reactions

Interprets an Object of Class Optsol

sysBiolAlg-class

Class "sysBiolAlg"

Strukture of Class "modelorg"

Simulate N Gene Deletion Experiments

Remove Reactions From a Model

optObj_glpkAPI-class

Class "optObj_glpkAPI"

Flux Balance Analysis with a Given Model

Class "ppProc"

sensitivityAnalysis-methods

Sensitivity Analysis

General Constructor Function For Objects of Class optObj

optsol_simpleFBA-class

Class "optsol_simpleFBA"

loadQobj-methods

Load Quadratic Part of the Objective Function to the Optimization Problem

Identifies Identical Reactions

optObj_cplexAPI-class

Class "optObj_cplexAPI"

setObjDir-methods

Set Direction of Optimization

getColsLowBnds-methods

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

Print sybil Environment

optsol_blockedReact-class

Class "optsol_blockedReact"

modelorg_irrev-class

Class for Metabolic Networks in Irreversible Format.

optsol_optimizeProb-class

Class "optsol_optimizeProb"

getRowsLowBnds-methods

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

General Constructor Function For Objects of Class sysBiolAlg

setSolverParm-methods

Set Parameters Used By The Optimization Software

Class "sybilLog"

scaleProb-methods

Scaling of the Constraint Matrix of an Optimization Problem

Creates an Instance of Class "optObj"

changeRowsBnds-methods

Change Row Bounds in the Optimization Problem

getObjCoefs-methods

Get Objective Coefficients of the Optimization Problem

sysBiolAlg_lmoma-class

Class "sysBiolAlg_lmoma"

loadLPprob-methods

Load Data to Optimization Problem

getNumNnz-methods

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

getSolStat-methods

Get Solution Status After Optimization

sysBiolAlg_fv-class

Class "sysBiolAlg_fv"

In Sillico YPD Medium

sysBiolAlg_fba-class

Class "sysBiolAlg_fba"

backupProb-methods

Copies a Problem Object to a New Problem Object

sysBiolAlg_moma-class

Class "sysBiolAlg_moma"

optsol_robAna-class

Class "optsol_robAna"

One Gene Deletion Experiment

Prints a Human Readable Objective Function

promptSysBiolAlg

Generate A Skeletal Structure of Subclasses of sysBiolAlg

Read a Metabolic Network in a TSV (CSV) Format

getNumRows-methods

Get Number of Rows (Constraints) of the Optimization Problem

Performs Optimizations for the Gene/Flux Deletion Experiments

Class "optObj"

Robustness Analysis

getNumCols-methods

Get Number of Columns (Variables) of the Optimization Problem

Get Gene-Reaction Association

Write an Instance of Class modelorg to File

Change the GPR Rules

Find Blocked Reactions in a Metabolic Network

optObj_lpSolveAPI-class

Class "optObj_lpSolveAPI"

sysBiolAlg_room-class

Class "sysBiolAlg_room"

writeProb-methods

Write Problem Object to File

getObjDir-methods

Get Direction of Optimization.

changeColsBndsObjCoefs-methods

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

Set and Get sybil Parameters

addRowsToProb-methods

Add New Rows (Constraints) to an Optimization Problem

Check Algorithm

optObj_clpAPI-class

Class "optObj_clpAPI"

sybilError-class

Class "sybilError"