| Vol-724 urn:nbn:de:0074-724-4 Copyright © 2011 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.

# BioPPN-2011
International Workshop on Biological Processes & Petri Nets

### Proceedings of the International Workshop on Biological Processes & Petri Nets

### Newcastle upon Tyne, United Kingdom, June 20, 2011.

Edited by

### Monika Heiner *
Hiroshi Matsuno **

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

## Table of Contents

- Preface

### Invited Talk

1. Systems Biology in Supercomputing Environment 6
   Satoru Miyano

### Session A: Modelling

2. Optimal Control of Asynchronous Boolean Networks Modeled by Petri Nets 7-20
   Koichi Kobayashi, Kunihiko Hiraishi
3. GReg : a Domain Specific Language for the Modeling of Genetic Regulatory Mechanisms 21-35
   Nicolas Sedlmajer, Didier Buchs, Steve Hostettler, Alban Linard, Edmundo Lopez, Alexis Marechal
4. Modelling Reaction Systems with Petri Nets 36-52
   Jetty Kleijn, Maciej Koutny, Grzegorz Rozenberg

### Session B: Analysis

5. Parameter Estimation of Biological Pathways Using Data Assimilation and Model Checking 53-70
   Chen Li, Keisuke Kuroyanagi, Masao Nagasaki, Satoru Miyano
6. Studying Steady States in Biochemical Reaction Systems by Time Petri Nets 71-86
   Louchka Popova-Zeugmann, Elisabeth Pelz
7. Two Modeling Methods for Signaling Pathways with Multiple Signals using UPPAAL 87-101
   Shota Nakano, Shingo Yamaguchi

### Session C: Applications

8. MPath2PN - Translating Metabolic Pathways into Petri Nets 102-116
   Paolo Baldan, Nicoletta Cocco, Francesco De Nes, Merce Llabres Segura, Andrea Marin, Marta Simeoni
9. Pain Signaling - A Case Study of the Modular Petri Net Modeling Concept with Prospect to a Protein-Oriented Modeling Platform 117-134
   Mary Ann Blaetke, Sonja Meyer, Wolfgang Marwan
10. Multi-cell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity 135-150
    Qian Gao, Fei Liu, David Tree, David Gilbert

The whole proceedings can also be downloaded as a single file (PDF, including title pages, preface, and table of contents).

09-Jun-2011: submitted by Hiroshi Matsuno
11-Jun-2011: published on CEUR-WS.org