nutrient_types

A subset of exchange reactions annotated to indicate typical availability

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

nutrient_types function

A data frame with 25 rows and 2 columns:<dl class="dl-horizontal">
 <dt>abbreviation</dt><dd>an exchange reaction id</dd>
 <dt>nutrient_type</dt><dd>the nutrient availability, one of 'micro', 'macro' or 'substrate'</dd>
</dl>

Format

A subset of exchange reactions annotated to indicate typical availability — nutrient_types

A data frame with 25 rows and 2 columns:<dl class='dl-horizontal'>
 <dt>abbreviation</dt><dd>an exchange reaction id</dd>
 <dt>nutrient_type</dt><dd>the nutrient availability, one of 'micro', 'macro' or 'substrate'</dd>
</dl>

nutrient_types: A subset of exchange reactions annotated to indicate typical availability

Description

Usage

Arguments

Format