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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<div class="container-fluid">
<!-- CONTENT -->
<div class="row">
<div class="col-lg-12">
<h1 class="page-header"><i class="fa fa-fw fa-file-text"></i> Publications</h1>
<h2>How to cite?</h2>
<ul>
<li>
<dl>
<dt>
<strong>Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N.</strong>
</dt>
<dd>
<div class="pubtitle">Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.</div>
</dd>
<dd>
<div class="pubjournal"><em>BMC Syst Biol. 2011 Dec 15;5:198.</em></div>
</dd>
<dd>
<a href="https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-198">https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-198</a>
</dd>
<dd>
<a href="https://www.ncbi.nlm.nih.gov/pubmed/22172142">PMID:22172142</a>
</dd>
</dl>
</li>
</ul>
<h2>Presentations</h2>
<table class="table table-responsive">
<thead>
<tr>
<th></th>
<th>Date</th>
<th>Author</th>
<th>Title</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<a href="presentations/JWS_Peters2016.pdf" target="_blank">
<img alt="pdf" src="images/pdf.png" height="50"/></a>
</td>
<td>2016</td>
<td>Martin Peters, Jacky Snoep, Dagmar Waltemath</td>
<td>SED-ML support in JWS Online - Using SED-ML and COMBINE archives to reproduce simulation results</td>
</tr>
<tr>
<td>
<a href="presentations/SED-ML_Nickerson2014.pdf" target="_blank">
<img alt="pdf" src="images/pdf.png" height="50"/></a>
</td>
<td>2014</td>
<td>David Nickerson</td>
<td>Introduction to SED-ML</td>
</tr>
<tr>
<td>
<a href="presentations/SED-ML_Bergmann2010b.pdf" target="_blank">
<img alt="pdf" src="images/pdf.png" height="50"/></a>
</td>
<td>2010</td>
<td>Frank Bergmann, Dagmar Waltemath</td>
<td>The Simulation Experiment Description Language (SED-ML)</td>
</tr>
<tr>
<td>
<a href="presentations/SED-ML_Bergmann2010.pdf" target="_blank">
<img alt="pdf" src="images/pdf.png" height="50"/></a>
</td>
<td>2010</td>
<td>Frank Bergmann</td>
<td>SED-ML</td>
</tr>
<tr>
<td>
<a href="presentations/Biomodel.Meta-Information.and.SED-ML_Waltemath2010.pdf" target="_blank">
<img alt="pdf" src="images/pdf.png" height="50"/></a>
</td>
<td>2010</td>
<td>Dagmar Waltemath</td>
<td>Biomodels Meta Information and SED-ML</td>
</tr>
</tbody>
</table>
<h2>Publications that report contributions to SED-ML ecosystem</h2>
<ul>
<li>
<dl>
<dt>
<strong>Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König</strong>
</dt>
<dd>
<div class="pubtitle">The simulation experiment description markup language (SED-ML): language specification for level 1 version 4</div>
</dd>
<dd>
<div class="pubjournal"><em>Journal of Integrative Bioinformatics, vol. , no. , 2021, pp. 20210021. https://doi.org/10.1515/jib-2021-0021</em></div>
</dd>
<!--
<dd>
<a href="https://doi.org/10.1515/jib-2021-0021">https://doi.org/10.1515/jib-2021-0021</a>
</dd>
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<dd>
DOI: <a href="https://doi.org/10.1515/jib-2021-002">10.1515/jib-2021-002</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Shaikh B, Marupilla G, Blinov ML, Moraru II, Karr JR</strong>
</dt>
<dd>
<div class="pubtitle">RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats</div>
</dd>
<dd>
<div class="pubjournal"><em>bioRxiv. 2021.03.05.433787v1.</em></div>
</dd>
<!--
<dd>
<a href="https://www.biorxiv.org/content/10.1101/2021.03.05.433787v1">https://www.biorxiv.org/content/10.1101/2021.03.05.433787v1</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.1101/2021.03.05.433787">10.1101/2021.03.05.433787</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Bergmann FT, Cooper J, König M, Moraru I, Nickerson D, Le Novère N, Olivier BG, Sahle S, Smith L, Waltemath D</strong>
</dt>
<dd>
<div class="pubtitle">Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)</div>
</dd>
<dd>
<div class="pubjournal"><em>Integr Bioinform. 2018;15(1):20170086.</em></div>
</dd>
<!--
<dd>
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6167040/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6167040/</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.1515/jib-2017-0086">10.1515/jib-2017-0086</a>
</dd>
<dd>
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29550789">29550789</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Bergmann FT, Nickerson D, Waltemath D, Scharm M.</strong>
</dt>
<dd>
<div class="pubtitle">SED-ML web tools: generate, modify and export standard-compliant simulation studies.</div>
</dd>
<dd>
<div class="pubjournal"><em>Bioinformatics. 2017 Apr 15;33(8):1253-1254.</em></div>
</dd>
<!--
<dd>
<a href="https://academic.oup.com/bioinformatics/article-abstract/33/8/1253/2881437/">https://academic.oup.com/bioinformatics/article-abstract/33/8/1253/2881437/</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.1093/bioinformatics/btw812">10.1093/bioinformatics/btw812</a>
</dd>
<dd>
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28049131">28049131</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Scharm M, Waltemath D.</strong>
</dt>
<dd>
<div class="pubtitle">A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos</div>
</dd>
<dd>
<div class="pubjournal"><em>F1000Research 2016, 5:2421</em></div>
</dd>
<!--
<dd>
<a href="https://f1000research.com/articles/5-2421/v1">https://f1000research.com/articles/5-2421/v1</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.12688/f1000research.9379.1">10.12688/f1000research.9379.1</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Choi K, Smith LP, Medley JK, Sauro HM.</strong>
</dt>
<dd>
<div class="pubtitle">phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.</div>
</dd>
<dd>
<div class="pubjournal"><em>J Bioinform Comput Biol. 2016 Dec;14(6):1650035.</em></div>
</dd>
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<dd>
<a href="http://www.worldscinet.com/doi/abs/10.1142/S0219720016500359?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed">http://www.worldscinet.com/doi/abs/10.1142/S0219720016500359?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed</a>
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<dd>
DOI: <a href="https://doi.org/10.1142/S0219720016500359">10.1142/S0219720016500359</a>
</dd>
<dd>
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27774871">27774871</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Henkel R, Wolkenhauer O, Waltemath D</strong>
</dt>
<dd>
<div class="pubtitle">Combining computational models, semantic annotations and simulation experiments in a graph database.</div>
</dd>
<dd>
<div class="pubjournal"><em>Database (Oxford). 2015 Mar 8;2015. pii: bau130.</em></div>
</dd>
<!--
<dd>
<a href="https://academic.oup.com/database/article-lookup/doi/10.1093/database/bau130">https://academic.oup.com/database/article-lookup/doi/10.1093/database/bau130</a>
</dd>
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<dd>
DOI: <a href="https://doi.org/10.1093/database/bau130">10.1093/database/bau130</a>
</dd>
<dd>
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25754863">25754863</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Bergmann FT, Cooper J, Le Novère N, Nickerson D, Waltemath D.</strong>
</dt>
<dd>
<div class="pubtitle">Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.</div>
</dd>
<dd>
<div class="pubjournal"><em>J Integr Bioinform. 2015 Sep 4;12(2):262.</em></div>
</dd>
<!--
<dd>
<a href="https://www.degruyter.com/view/j/jib.2015.12.issue-2/biecoll-jib-2015-262/biecoll-jib-2015-262.xml">https://www.degruyter.com/view/j/jib.2015.12.issue-2/biecoll-jib-2015-262/biecoll-jib-2015-262.xml</a>
</dd>
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<dd>
DOI: <a href="https://doi.org/10.2390/biecoll-jib-2015-262">10.2390/biecoll-jib-2015-262</a>
</dd>
<dd>
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26528560">26528560</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Adams RR.</strong>
</dt>
<dd>
<div class="pubtitle">SED-ED, a workflow editor for computational biology experiments written in SED-ML.</div>
</dd>
<dd>
<div class="pubjournal"><em>Bioinformatics. 2012 Apr 15;28(8):1180-1.</em></div>
</dd>
<!--
<dd>
<a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts101">https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts101</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.1093/bioinformatics/bts101">10.1093/bioinformatics/bts101</a>
</dd>
<dd>
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22368254">22368254</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Miller AK, Britten RD, Nielsen PM.</strong>
</dt>
<dd>
<div class="pubtitle">Declarative representation of uncertainty in mathematical models.</div>
</dd>
<dd>
<div class="pubjournal"><em>PLoS One. 2012;7(7):e39721.</em></div>
</dd>
<!--
<dd>
<a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039721">http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039721</a>
</dd>
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<dd>
DOI: <a href="https://doi.org/10.1371/journal.pone.0039721">10.1371/journal.pone.0039721</a>
</dd>
<dd>
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22802941">22802941</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N.</strong>
</dt>
<dd>
<div class="pubtitle">Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.</div>
</dd>
<dd>
<div class="pubjournal"><em>BMC Syst Biol. 2011 Dec 15;5:198.</em></div>
</dd>
<!--
<dd>
<a href="https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-198">https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-198</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.1186/1752-0509-5-198">10.1186/1752-0509-5-198</a>
</dd>
<dd>
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22172142">22172142</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Waltemath D, Bergmann FT, Adams R, LeNovère N</strong>
</dt>
<dd>
<div class="pubtitle">Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1</div>
</dd>
<dd>
<div class="pubjournal"><em>Nature Precedings.</em></div>
</dd>
<!--
<dd>
<a href="http://precedings.nature.com/documents/5846/version/1">http://precedings.nature.com/documents/5846/version/1</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.1038/npre.2011.5846.1">10.1038/npre.2011.5846.1</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N.</strong>
</dt>
<dd>
<div class="pubtitle">Minimum Information About a Simulation Experiment (MIASE).</div>
</dd>
<dd>
<div class="pubjournal"><em>PLoS Comput Biol. 2011 Apr;7(4):e1001122.</em></div>
</dd>
<!--
<dd>
<a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001122">http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001122</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.1371/journal.pcbi.1001122">10.1371/journal.pcbi.1001122</a>
</dd>
<dd>
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21552546">21552546</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Bergmann FT.</strong>
</dt>
<dd>
<div class="pubtitle">A simple nested simulation for SED-ML.</div>
</dd>
<dd>
<div class="pubjournal"><em>Nature Precedings (2010): 1-1.</em></div>
</dd>
<!--
<dd>
<a href="https://www.nature.com/articles/npre.2010.4257.1">https://www.nature.com/articles/npre.2010.4257.1</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.1038/npre.2010.4257.1">10.1038/npre.2010.4257.1</a>
</dd>
</dl>
</li>
<li>
<dl>
<dt>
<strong>Dagmar Köhn, Nicolas Le Novère</strong>
</dt>
<dd>
<div class="pubtitle">SED-ML – An XML Format for the Implementation of the MIASE Guidelines.</div>
</dd>
<dd>
<div class="pubjournal"><em>Lecture Notes in Computer Science, Computational Methods in Systems Biology 2008</em></div>
</dd>
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<dd>
<a href="https://link.springer.com/chapter/10.1007%2F978-3-540-88562-7_15">https://link.springer.com/chapter/10.1007%2F978-3-540-88562-7_15</a>
</dd>
-->
<dd>
DOI: <a href="https://doi.org/10.1007/978-3-540-88562-7_15">10.1007/978-3-540-88562-7_15</a>
</dd>
</dl>
</li>
</ul>
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