[CEUR Workshop Proceedings] Vol-724

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.

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

    Invited Talk

  1. Systems Biology in Supercomputing Environment 6
    Satoru Miyano
  2. Session A: Modelling

  3. Optimal Control of Asynchronous Boolean Networks Modeled by Petri Nets 7-20
    Koichi Kobayashi, Kunihiko Hiraishi
  4. 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
  5. Modelling Reaction Systems with Petri Nets 36-52
    Jetty Kleijn, Maciej Koutny, Grzegorz Rozenberg
  6. Session B: Analysis

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

  11. MPath2PN - Translating Metabolic Pathways into Petri Nets 102-116
    Paolo Baldan, Nicoletta Cocco, Francesco De Nes, Merce Llabres Segura, Andrea Marin, Marta Simeoni
  12. 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
  13. 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