ecoli_core

A small E. coli model, created from a number of sources.

datasets

A toolkit for Flux Balance Analysis and related
metabolic modeling techniques. Functions are provided for: parsing
models in tabular format, converting parsed metabolic models to input
formats for common linear programming solvers, and
evaluating and applying gene-protein-reaction mappings. In addition, there
are wrappers to parse a model, select a solver, find the metabolic fluxes,
and return the results applied to the original model. Compared to other
packages in this field, this package puts a much heavier focus on
providing reusable components that can be used in the design of new
implementation of new techniques, in particular those that involve large
parameter sweeps. For a background on the theory, see What is Flux Balance
Analysis <doi:10.1038/nbt.1614>.

Max Conway

fbar

An Extensible Approach to Flux Balance Analysis

ecoli_core function

A data frame with 95 rows and 7 columns:<dl class="dl-horizontal">
 <dt>abbreviation</dt><dd>an abbreviated reaction name, acts as the reaction id</dd>
 <dt>lowbnd</dt><dd>lower bound on the reaction rate</dd>
 <dt>uppbnd</dt><dd>upper bound on the reaction rate</dd>
 <dt>obj_coef</dt><dd>identifies a reaction (or reactions) for which the maximum possible rate should be found</dd>
 <dt>equation</dt><dd>reaction equation</dd>
 <dt>officialName</dt><dd>full reaction name</dd>
 <dt>geneAssociation</dt><dd>A boolean combination of genes which control the reaction</dd>
 <dt>subsystem</dt><dd>an indicator of reaction function</dd>
</dl>

Format

A small E. coli model, created from a number of sources. — ecoli_core

A data frame with 95 rows and 7 columns:<dl class='dl-horizontal'>
 <dt>abbreviation</dt><dd>an abbreviated reaction name, acts as the reaction id</dd>
 <dt>lowbnd</dt><dd>lower bound on the reaction rate</dd>
 <dt>uppbnd</dt><dd>upper bound on the reaction rate</dd>
 <dt>obj_coef</dt><dd>identifies a reaction (or reactions) for which the maximum possible rate should be found</dd>
 <dt>equation</dt><dd>reaction equation</dd>
 <dt>officialName</dt><dd>full reaction name</dd>
 <dt>geneAssociation</dt><dd>A boolean combination of genes which control the reaction</dd>
 <dt>subsystem</dt><dd>an indicator of reaction function</dd>
</dl>

ecoli_core: A small E. coli model, created from a number of sources.

Description

Usage

Arguments

Format