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data structures and software dependability

computer science department

brandenburg university of technology cottbus

3rd International Workshop on Biological Processes & Petri Nets (BioPPN 2012)

A satellite event of Petri Nets 2012 & ACSD 2012

where

Hamburg, Germany

when

June 25, 2012

Index

Technical Description

The goal of this workshop is to provide a platform for researchers aiming at fundamental research and real life applications of Petri nets in Systems and Synthetic Biology.

Systems and Synthetic Biology are full of challenges and open issues, with adequate modelling and analysis techniques being one of them.

Petri nets offer a family of related models, which can be used as a kind of umbrella formalism — models may share the network structure, but vary in their kinetic details (quantitative information). This clearly contributes to bridging the gap between different formalisms, and helps to unify diversity.

Topics of interest include, but are not limited to:

  • standard Petri nets for qualitative modelling and analysis, if kinetics are unknown or deliberately abstracted away;
  • discrete quantitative modelling by time(d) Petri nets;
  • stochastic Petri nets to account for intrinsic noise of molecular fluctuation, and/or sources of extrinsic noise;
  • continuous Petri nets (and thus Ordinary Differential Equations), back and forth;
  • hybrid Petri nets, or how to handle different abstraction and time scales in biological processes;
  • dedicated support of multi-scale issues;
  • case studies of metabolic, signalling, regulatory, and combined networks, or other biological applications;
  • dedicated analysis and simulation techniques;
  • related tool debvelopment, including exchange formats, dedicated to biological processes;

Case studies in systems and synthetic biology demonstrating the specific power by the combined use of different Petri net classes are especially encouraged.

Objectives

This workshop intends to gather students and researchers, who have interests in the application of Petri nets for biological processes. Its main goal will be to demonstrate that Petri net can be an effective technique to tackle the issues which reside in many biological problems. The workshop also promotes discussions between advanced researchers and beginners, which may enhance the world-wide activities in Petri net applications on biological processes.

Paper Submission

Submitted papers should describe original work that has not been previously published and is not under review for publication elsewhere. All papers should be in LNCS format, and have to be submitted via EasyChair. The page limit given below includes figures, tables and references.

There are the following categories of submissions.

  • Regular papers should not exceed 15 p. in LNCS format.
  • "Work in progress" papers should not exceed 15 p. in LNCS format.
  • Short papers should not exceed 6 p. in LNCS format.
  • Posters up to A0 format.

A submission should be clearly assigned to one category.

Based on the review process, a submission may be accepted as is, accepted with minor changes, rejected or selected for oral presentation only. In the latter case, a 1-page abstract will be published.

Proceedings

Workshop Proceedings

Proceedings will be electronically published with CEUR Workshop Proceedings (http://ceur-ws.org) with consecutive volume numbers for each workshop allocated with PETRI NET 2012, as well as local proceedings distributed via USB Memory Sticks.

Special Issue

Best papers will be proposed to be invited for the follow-up publication in Transactions on Petri Nets and other models of Concurrency (ToPNoC).

Programme

Invited speaker

Wolfgang Marwan, D

Petri Nets - an Integrative Framework for Advanced Biomodel Engineering

Building realistic models of complex biosystems at the molecular and the cellular level is greatly facilitated by employing Petri nets as a multifunctional formal language providing an integrative framework for forward and reverse biomodel engineering. Modeling the behaviour or response of biological systems as it is observed in the wet lab with one and the same framework requires the application of continuous, stochastic, or hybrid paradigms. In order to create realistic scenarios in terms of functional mechanisms and the simulation of experimental data, one may need to consider populations of models representing populations of biomolecular complexes or populations of entire cells. Colored Petri nets are an extremely powerful extension in providing these options as they combine the strengths of standard Petri nets with the expressive power of a programming language. Taking canonic signaling pathways in bacterial cells as case studies, we demonstrate the power of (coloured) Petri nets for forward and reverse biomodel engineering.

Schedule

tba

Organizers -- Programme Committee

Monika Heiner

Brandenburg University of Technology at Cottbus, Computer Science Institute, Germany
monika.heiner (at) informatik.tu-cottbus.de

Ralf Hofestädt

Bielefeld University, Faculty of Technology, Bioinformatics Department, Germany
ralf.hofestaedt (at) uni-bielefeld.de

Program Committee

Deadlines

  • April, 15th: Submission of papers.
  • May, 13th: Notification of acceptance/rejection.
  • June, 1st: Final version of papers.

Registration

Registration is handled by the hosting conference website. Early registration fees (workshop only): 100 € for students, 130 € else; early registration ends May 15th, 2012.

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