sybil

Escherichia coli Core Metabolic Model

Set and Get sybil Parameters

Add a New Algorithm Name to sybil

Add Columns to an Optimization Problem

Add New Columns (Variables) to an Optimization Problem

Add Exchange Reactions to a Model

Add/Change Reactions in a Model

Add Rows to an Optimization Problem

Add Rows and Columns to an Optimization Problem

Add New Rows (Constraints) to an Optimization Problem

Add a New Mathematical Programming Solver to sybil

Generic Function to Apply Changes to Objects of Class sysBiolAlg

Copies a Problem Object to a New Problem Object

Find Blocked Reactions in a Metabolic Network

Change Variable Bounds in a Metabolic Network

Change Column (Variable) Bounds in the Optimization Problem

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

Check and Change the GPR Rules

Change a Row in the Constraint Matrix of the Optimization Problem

Change Column (Variable) Objective Coefficients in the Optimization Problem

Sets/changes the Objective Function

Change Row Bounds in the Optimization Problem

Change Uptake Reactions

Check Algorithm

Validate Solver and Method

Summarized Information About an Object of Class Optsol

Check if a Reaction Id is Valid

checks Version of modelorg

Structure of the Class "checksol"

Identify Dead End Metabolites

Free Memory Associated to the Pointer to the Problem Object

Deprecated Functions and Methods in Package sybil

Double Flux Deletion Experiment

Double Gene Deletion Experiment

Identifies Identical Reactions

Environment Editor for Metabolic Networks

Find Exchange Reactions

Class "fluxDistribution"

Flux Variability Analysis

Get Gene-Reaction Association

Gene Deletion Experiments

Get Primal Value of Variables After Optimization

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

Retrieve Variable Names

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

Retrieve Flux Distribution

Get Number of Columns (Variables) of the Optimization Problem

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

Get Number of Rows (Constraints) of the Optimization Problem

Get Objective Coefficients of the Optimization Problem

Get Direction of Optimization.

Get Value of the Objective Function After Optimization

Get Reduced Costs of all Variables After Optimization

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

Retrieve Constraint Names

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

Get Solution Status After Optimization

Retrieve Current Parameter Settings Used By The Optimization Software

Print sybil Environment

Initialize Problem Object

Load Data to Optimization Problem

Load Quadratic Part of the Objective Function to the Optimization Problem

Constructor Function for Objects of Class optsol_optimizeProb.

Functions to subset and merge modelorg objects.

Produces a Model in Irreversible Format

Structure of Class "modelorg"

Write an Instance of Class modelorg to File in ExPA Format

Write an Instance of Class modelorg to File

Class for Metabolic Networks in Irreversible Format.

Parallel Support for sybil

Class "netFlux"

Single Flux Deletion Experiment

Single Gene Deletion Experiment

Change the GPR Rules

Check the GPR Rules

General Constructor Function For Objects of Class optObj

Class "optObj"

Class "optObj_clpAPI"

Class "optObj_cplexAPI"

Class "optObj_glpkAPI"

Class "optObj_lpSolveAPI"

Optimize Problem Object

Performs Series of Optimizations

Class optsol

Class "optsol_blockedReact"

Class "optsol_fluxVar"

Class "optsol_fluxdel"

Class "optsol_genedel"

Class "optsol_optimizeProb"

Class "optsol_phpp"

Class "optsol_robAna"

Phenotypic Phase Plane Analysis

Class "ppProc"

Print Rows of the Stoichiometric Matrix

Print Columns of the Stoichiometric Matrix

Generate A Skeletal Structure of Subclasses of sysBiolAlg

Structure of Class "reactId"

Class "reactId_Exch"

Read Problem Object From File

Read a Metabolic Network in a TSV (CSV) Format

Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg

Remove Reactions From a Model

Robustness Analysis

Scaling of the Constraint Matrix of an Optimization Problem

Sensitivity Analysis

Set/Change Variable Names

Set Direction of Optimization

Set Right Hand Side of the Optimization Problem To Zero

Set/Change Constraint Names

Set Parameters Used By The Optimization Software

Get a Subset of Matrix Like Objects

Identify Singleton Metabolites

Optimize Problem Object

Summarize Objects of Class Optsol

Class "summaryOptsol"

Internal sybil Functions

sybil – Efficient Constrained Based Modelling in R

Class "sybilError"

Class "sybilLog"

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

General Constructor Function For Objects of Class sysBiolAlg

Class "sysBiolAlg"

Class "sysBiolAlg_fba"

Class "sysBiolAlg_fbaEasyConstraint" and Class "sysBiolAlg_mtfEasyConstraint"

Class "sysBiolAlg_fv"

Class "sysBiolAlg_lmoma"

Class "sysBiolAlg_moma"

Class "sysBiolAlg_mtf"

Class "sysBiolAlg_room"

Upgrade modelorg to newer version.

Write Problem Object to File

In Sillico YPD Medium