Bac-class

Structure of the S4 class <code>Bac</code> inheriting from class <code><a rd-options="" href="/link/Organism-class?package=BacArena&version=1.8.2" data-mini-rdoc="BacArena::Organism-class">Organism-class</a></code> representing bacterial cells.

Can be used for simulation of organisms living in
communities (Bauer and Zimmermann (2017) <doi:10.1371/journal.pcbi.1005544>).
Each organism is represented individually and genome scale
metabolic models determine the uptake and release of compounds. Biological
processes such as movement, diffusion, chemotaxis and kinetics are available
along with data analysis techniques.

Johannes Zimmermann

BacArena

Modeling Framework for Cellular Communities in their
Environments

Eugen Bauer

Bac-class function

<dl class="dl-horizontal">
<dt><code>deathrate</code></dt><dd>A numeric value giving the factor by which the biomass should be reduced in every iteration if no growth is possible (default (E.coli): 0.21 pg)</dd></dl><dt><code>minweight</code></dt><dd>A numeric value giving the growth limit at which the organism dies. (default (E.coli): 0.083 pg)</dd><dt><code>cellarea</code></dt><dd>A numeric value indicating the surface that one organism occupies (default (E.coli): 4.42 mu_m^2)</dd><dt><code>maxweight</code></dt><dd>A numeric value giving the maximal dry weight of single organism (default (E.coli): 1.172 pg)</dd><dt><code>chem</code></dt><dd>A character vector indicating name of substance which is the chemotaxis attractant. Empty character vector if no chemotaxis.</dd>

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Structure of the S4 class <code>Bac</code> inheriting from class <code><a rd-options='' href='Organism-class'>Organism-class</a></code> representing bacterial cells.

Bac-class: Structure of the S4 class "Bac"

Description

Arguments

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