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<a href="http://ceur-ws.org/"><img src="http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/CEUR-WS-logo.png" alt="[CEUR Workshop Proceedings]" border="0"></a>
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<span class="CEURVOLNR">Vol-724</span> <br>
<span class="CEURURN">urn:nbn:de:0074-724-C</span>
<p align="justify"><font color="#777777" size="-2">Copyright &copy; 
<span class="CEURPUBYEAR">2011</span> for the individual papers
by the papers' authors. Copying permitted only for private and academic purposes.
This volume is published and copyrighted by its editors.</font></p>

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<h1><a href="http://www-dssz.informatik.tu-cottbus.de/DSSZ/BME/BioPPN2011">BioPPN-2011</a><br>
<span class="CEURVOLTITLE">International Workshop on Biological Processes & Petri Nets </span></h1>
<br>

<h3>
<span class="CEURFULLTITLE">Proceedings of the International Workshop on Biological Processes & Petri Nets </span><br>
</h3>
<h3><span class="CEURLOCTIME">Newcastle upon Tyne, United Kingdom, June 20, 2011</span>.</h3> 
<br>
<b> Edited by </b>
<p>

</p><h3>
   <a href="http://www-dssz.informatik.tu-cottbus.de/DSSZ/"><span class="CEURVOLEDITOR">Monika Heiner</span></a> *<br>
   <a href="http://genome.ib.sci.yamaguchi-u.ac.jp/matsunohp/"><span class="CEURVOLEDITOR">Hiroshi Matsuno</span></a> **<br>

</h3>

* Brandenburg University of Technology at Cottbus,
  Faculty of Mathematics, Natural Sciences and Computer Science, D-03013 Cottbus, Germany<br>
** Yamaguchi University,
   Graduate School of Science and Engineering, 753-8512 Yamaguchi, Japan <br>
  <br>

<hr>

<br><br><br>


<div class="CEURTOC">
<h2> Table of Contents </h2>

<ul>
<li>
<A href="preface.pdf">Preface</A><BR><BR>
</li>
</ul>
<ol>


<h3><span class="CEURSESSION">Invited Talk</span></h3>


<li><a href="paper1.pdf">
<span class="CEURTITLE">Systems Biology in Supercomputing Environment</span></a>
<span class="CEURPAGES">6</span> <br>
<span class="CEURAUTHORS">Satoru Miyano</span>
</li>

<h3><span class="CEURSESSION">Session A: Modelling</span></h3>

<li><a href="paper2.pdf">
<span class="CEURTITLE">Optimal Control of Asynchronous Boolean Networks Modeled by Petri Nets</span></a>
<span class="CEURPAGES">7-20</span> <br>
<span class="CEURAUTHORS">Koichi Kobayashi and Kunihiko Hiraishi</span>  
</li>

<li><a href="paper3.pdf">
<span class="CEURTITLE">GReg : a Domain Specific Language for the Modeling of Genetic Regulatory Mechanisms</span></a>
<span class="CEURPAGES">21-35</span> <br>
<span class="CEURAUTHORS">Nicolas Sedlmajer, Didier Buchs, Steve Hostettler, Alban Linard, Edmundo Lopez and Alexis Marechal</span>
</li>

<li><a href="paper4.pdf">
<span class="CEURTITLE">Modelling Reaction Systems with Petri Nets</span></a>
<span class="CEURPAGES">36-52</span> <br>
<span class="CEURAUTHORS">Jetty Kleijn, Maciej Koutny and Grzegorz Rozenberg</span>
</li>

<h3><span class="CEURSESSION">Session B: Analysis </span></h3>

<li><a href="paper5.pdf">
<span class="CEURTITLE">Parameter Estimation of Biological Pathways Using Data Assimilation and Model Checking</span></a>
<span class="CEURPAGES">53-70</span> <br>
<span class="CEURAUTHORS">Chen Li, Keisuke Kuroyanagi, Masao Nagasaki and Satoru Miyano</span>
</li>

<li><a href="paper6.pdf">
<span class="CEURTITLE">Studying Steady States in Biochemical Reaction Systems by Time Petri Nets</span></a>
<span class="CEURPAGES">71-86</span> <br>
<span class="CEURAUTHORS">Louchka Popova-Zeugmann and Elisabeth Pelz</span>
</li>

<li><a href="paper7.pdf">
<span class="CEURTITLE">Two Modeling Methods for Signaling Pathways with Multiple Signals using UPPAAL</span></a>
<span class="CEURPAGES">87-101</span> <br>
<span class="CEURAUTHORS">Shota Nakano and Shingo Yamaguchi</span>
</li>

<h3><span class="CEURSESSION">Session C: Applications </span></h3>

<li><a href="paper8.pdf">
<span class="CEURTITLE">MPath2PN - Translating Metabolic Pathways into Petri Nets</span></a>
<span class="CEURPAGES">102-116</span> <br>
<span class="CEURAUTHORS">Paolo Baldan, Nicoletta Cocco, Francesco De Nes, Merce Llabres Segura, Andrea Marin and Marta Simeoni</span>
</li>

<li><a href="paper9.pdf">
<span class="CEURTITLE">Pain Signaling - A Case Study of the Modular Petri Net Modeling Concept with Prospect to a Protein-Oriented Modeling Platform</span></a>
<span class="CEURPAGES">117-134</span> <br>
<span class="CEURAUTHORS">Mary Ann Blaetke, Sonja Meyer and Wolfgang Marwan</span>
</li>

<li><a href="paper10.pdf">
<span class="CEURTITLE">Multi-cell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity</span></a>
<span class="CEURPAGES">135-150</span> <br>
<span class="CEURAUTHORS">Qian Gao, Fei Liu, David Tree and David Gilbert</span>
</li>

</ol>

</div>

<p>
The whole proceedings can also be downloaded as a single file (<a href="BioPPN2011_proceedings.pdf">PDF</a>, including title pages, preface, and table of contents).


<hr>
<font color="#777777" size="-1">
09-06-2011: submitted by Hiroshi Matsuno<br>
: published on CEUR-WS.org
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