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sybil (version 1.0.1)

SyBiL - Systems Biology Library

Description

A systems biology library for the analysis of metabolic networks.

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Version

Install

install.packages('sybil')

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Version

1.0.1

License

GPL-3

Maintainer

Gabriel Gelius-Dietrich

Last Published

March 16th, 2012

Functions in sybil (1.0.1)

checkOptSol

Interprets an Object of Class Optsol

oneGeneDel

One Gene Deletion Experiment

geneDel

Get Gene-Reaction Association

checksol-class

Structure of the Class "checksol"

optimizer

Performs Optimizations for the Gene/Flux Deletion Experiments

optObj_clp-class

Class "optObj_clp"

SYBIL_SETTINGS

Set and Get SyBiL Parameters

printObjFunc

Prints a Human Readable Objective Function

changeObjFunc

Sets/changes the Objective Function

fluxDistribution-class

Class "fluxDistribution"

optsol_robAna-class

Class "optsol_robAna"

sybil-internal

Internal SyBiL Functions

changeGPR

Check and Change the GPR Rules

oneFluxDel

One Flux Deletion Experiment

optsol_blockedReact-class

Class "optsol_blockedReact"

checkReactId

Check if a Reaction Id is Valid

mod2irrev

Produces a Model in Irreversible Format

Double Gene Deletion Experiment

sybilStack

A Data Type Providing Stack And Queue Functionality

optsol_genedel-class

Class "optsol_genedel"

optsol_fluxdel-class

Class "optsol_fluxdel"

readTSVmod

Read a Metabolic Network in a TSV (CSV) Format

optObj-class

Strukture of Class "optObj"

blockedReact

Find Blocked Reactions in a Metabolic Network

optsol-class

Class optsol

checkDefaultMethod

Validate Solver and Method

geneDeletion

Simulate N Gene Deletion Experiments

sybil-package

Systems Biology Library

optsol_doublegenedel-class

Class "optsol_doublegenedel"

prepProbObj

Creates an Instance of Class "optObj"

sybilError-class

Class "sybilError"

doubleReact

Identifies Identical Reactions

findExchReact

Find Exchange Reactions

ppProc-class

Class "ppProc"

Ec_core

Escherichia coli Core Metabolic Model

fluxVar

Flux Variability Analysis

reactId-class

Strukture of Class "reactId"

changeBounds

Change Variable Bounds in a Metabolic Network

modelorg-class

Strukture of Class "modelorg"

optsol_simpleFBA-class

Class "optsol_simpleFBA"

multiDel

Parallel (Multicore) Support for SyBiL

sybilLog-class

Class "sybilLog"

modelorg_irrev-class

Class for Metabolic Networks in Irreversible Format.

optObj_lpSolveAPI-class

Class "optObj_lpSolveAPI"

rmReact

Removes Reactions From a Model

onlyCheckGPR

Check the GPR Rules

optObj_cplex-class

Class "optObj_cplex"

simpleFBA

Flux Balance Analysis with a Given Model

optObj_glpk-class

Class "optObj_glpk"

optsol_doublefluxdel-class

Class "optsol_doublefluxdel"

modelorg2tsv

Write an Instance of Class modelorg to File

doubleFluxDel

Double Flux Deletion Experiment

optsol_fluxVar-class

Class "optsol_fluxVar"

ypd

In Sillico YPD Medium