export_pbtk_sbml

This function exports the multiple compartment PBTK model to an sbml file.

Export

Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predictions for chemicals
where in vivo data do exist. The models are systems of ordinary
differential equations that are developed in MCSim and solved
using compiled (C-based) code for speed. A Monte Carlo sampler is
included for simulating human biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and propagating parameter uncertainty
(Wambaugh et al., 2019 <doi:10.1093/toxsci/kfz205>).
Empirically calibrated methods are included for predicting
tissue:plasma partition coefficients and volume of distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for using IVIVE to
convert concentrations from high-throughput screening experiments
(for example, Tox21, ToxCast) to real-world exposures via reverse
dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).

John Wambaugh

httk

High-Throughput Toxicokinetics

Sarah Davidson-Fritz

Robert Pearce

Caroline Ring

Greg Honda

Mark Sfeir

Matt Linakis

Dustin Kapraun

Kimberly Truong

Colin Thomson

Meredith Scherer

Annabel Meade

Celia Schacht

Leonie Lautz

Todor Antonijevic

Miyuki Breen

Shannon Bell

Xiaoqing Chang

Jimena Davis

Elaina Kenyon

Gilberto Padilla Mercado

Katie Paul Friedman

Nathan Pollesch

Noelle Sinski

Nisha Sipes

James Sluka

Caroline Stevens

Barbara Wetmore

Lily Whipple

Woodrow Setzer

export_pbtk_sbml function

<dl><dt>initial.amounts</dt>
<dd>Must specify initial amounts in units of choice.</dd>
<dt>filename</dt>
<dd>The name of the jarnac file containing the model.</dd>
<dt>folder</dt>
<dd>The folder on the file system containing the output file. Defaults to <code><a href="/link/tempdir?package=httk&version=2.7.2" data-mini-rdoc="httk::tempdir">tempdir</a></code>.</dd>
<dt>digits</dt>
<dd>Desired number of decimal places to round the parameters.</dd>
<dt>...</dt>
<dd>Arguments to <code>parameterize_pbtk</code> such as chem.name, chem.cas, dtxsid, species.</dd></dl>

Arguments

Author

Export model to sbml. — export_pbtk_sbml

<dl>

<dt>initial.amounts</dt>
<dd>Must specify initial amounts in units of choice.</dd>


<dt>filename</dt>
<dd>The name of the jarnac file containing the model.</dd>


<dt>folder</dt>
<dd>The folder on the file system containing the output file. Defaults to <code><a href='https://rdrr.io/r/base/tempfile.html'>tempdir</a></code>.</dd>


<dt>digits</dt>
<dd>Desired number of decimal places to round the parameters.</dd>


<dt>...</dt>
<dd>Arguments to <code>parameterize_pbtk</code> such as chem.name, chem.cas, dtxsid, species.</dd>

</dl>

Export model to sbml.

export_pbtk_sbml: Export model to sbml.

Description

Usage

Value

Arguments

Author

Details

Examples