Monika Heiner   Hiroshi Matsuno (Eds.)




BioPPN 2011
International Workshop on
Biological Processes & Petri Nets
Workshop co-located with PETRI NETS 2011
Newcastle upon Tyne, United Kingdom, June 20, 2010
Proceedings




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(C) 2011 for the individual papers by the papers’ authors. Copying permitted for private
and academic purposes. Re-publication of material from this volume requires permission
by the copyright owners.



Editors’ addresses:
Monika Heiner
Brandenburg University of Technology at Cottbus
Faculty of Mathematics, Natural Sciences and Computer Science
Postbox 10 13 44
D-03013 Cottbus, Germany
monika.heiner@informatik.tu-cottbus.de

Hiroshi Matsuno
Yamaguchi University
Graduate School of Science and Engineering
1677-1 Yoshida, Yamaguchi
753-8512 Japan
matsuno@sci.yamaguchi-u.ac.jp




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Preface

These proceedings contain the nine peer-reviewed contributions accepted for the Second
International Workshop on Biological Processes & Petri Nets (BioPPN 2011), held as a
satellite event of PETRI NETS 2011, in Newcastle, UK, on June 20, 2011. This work-
shop has been organised as a communication platform for researchers interested in the
application of Petri nets in the broad field of integrative biology.
Integrative biology aims at deciphering essential biological processes that are driven by
complex mechanisms, involving miscellaneous interacting molecular compounds. In this
context, the need for appropriate mathematical and computational modelling tools is widely
advocated. Petri nets have proved their usefulness for the modelling, analysis, and simula-
tion of a diversity of biological networks, covering qualitative, stochastic, continuous and
hybrid models. The deployment of Petri nets to study biological applications has not only
generated original models, but has also motivated fundamental research.
We received two types of contributions: research papers and work-in-progress papers. All
papers have been reviewed by four to six reviewers coming from or being recommended
by the workshop’s Program Committee. The list of reviewers comprises 30 professionals
of the field. The nine accepted papers (with an acceptance rate of 82%) involve 41 authors
coming from 9 different countries. In summary, the workshop proceedings enclose theo-
retical contributions as well as biological applications, demonstrating the interdisciplinary
nature of the topic.
The workshop was complemented by an invited talk Systems Biology in Supercomputing
Environment given by Satoru Miyano from Human Genome Center, Institute of Medical
Science at the University of Tokyo in Japan.
As the hosting conference was originally planned to take place in Japan, it was an explicit
goal of our workshop to promote the communication between Europe and Asia. We are es-
pecially glad that three papers from Japanese authors made it into the workshop. We would
like to express our sympathy with the Japanese people and do hope that the precautions by
the Steering committee will turn out to be overprotecting ones.
For more details see the workshop’s website
http://www-dssz.informatik.tu-cottbus.de/BME/BioPPN2011.



June 2011                                             Monika Heiner and Hiroshi Matsuno




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Program Committee

David Angeli, I
Gianfranco Balbo, I
Rainer Breitling, NL, UK
Jorge Carneiro, PT
Claudine Chaouiya, F, PT
Austin H. Chen, TW
Ming Chen, CN
David Gilbert, UK
Simon Hardy, CA
Ralf Hofestädt, D
Hsueh-Fen Juan, TW
Peter Kemper, US
Hanna Klaudel, F
Dong-Yup Lee, KR, SG
Chen Li, CN, JP
Wolfgang Marwan, D
Eduardo Mendoza, Philippines, D
Hirotada Mori, JP
Morikazu Nakamura, JP
P.S. Thiagarajan, SG
Toshimitsu Ushio, JP




Subreviewers

Liu Bing
Francesca Cordero
Lukasz Fronc
Blaise Genest
Andras Horvath
Sylvain Sen
Jeremy Sproston




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Contents

Invited Talk: Systems Biology in Supercomputing Environment
   Satoru Miyano                                                                   6

Optimal Control of Asynchronous Boolean Networks Modeled by Petri Nets
  Koichi Kobayashi and Kunihiko Hiraishi                                           7

GReg : a Domain Specific Language for the Modeling of Genetic Regulatory
  Mechanisms
  Nicolas Sedlmajer, Didier Buchs, Steve Hostettler, Alban Linard, Edmundo Lopez
  and Alexis Marechal                                                            21

Modelling Reaction Systems with Petri Nets
  Jetty Kleijn, Maciej Koutny and Grzegorz Rozenberg                              36

Parameter Estimation of Biological Pathways Using Data Assimilation and Model
   Checking
   Chen Li, Keisuke Kuroyanagi, Masao Nagasaki and Satoru Miyano              53

Studying Steady States in Biochemical Reaction Systems by Time Petri Nets
   Louchka Popova-Zeugmann and Elisabeth Pelz                                     71

Two Modeling Methods for Signaling Pathways with Multiple Signals using UP-
  PAAL
  Shota Nakano and Shingo Yamaguchi                                         87

MPath2PN - Translating Metabolic Pathways into Petri Nets
  Paolo Baldan, Nicoletta Cocco, Francesco De Nes, Mercè Llabrés Segura, Andrea
  Marin and Marta Simeoni                                                         102

Pain Signaling - A Case Study of the Modular Petri Net Modeling Concept with
   Prospect to a Protein-Oriented Modeling Platform
   Mary Ann Blätke, Sonja Meyer and Wolfgang Marwan                         117

Multi-cell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity
  Qian Gao, Fei Liu, David Tree and David Gilbert                              135




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