A satellite event of Petri Nets 2012 & ACSD 2012 - Hamburg, Germany, June 25, 2012
The workshop attracted 18 participants, who enjoyed an open-minded and productive atmosphere. Excellent idea of the local organisers to join the invited talks of the workshops running in parallel.
See you all next year at BioPPN 2013 in Milano.
CEUR Workshop Proceedings Vol. 852
session chair: Gianfranco Balbo
session chair: Hiroshi Matsuno
session chair: Wolfgang Marwan
session chair: Monika Heiner
Petri Nets - an Integrative Framework for Advanced Biomodel Engineering
Petri nets are employed as a multifunctional integrative framework for biomodel engineering. We describe the general concept of a modular modelling approach that consideres the functional coupling of components of genome, transcriptome, and proteome with complex cellular phenotypes. For this purpose, the effects of genes and their mutated alleles on downstream components are modeled by composable, metadata-containing Petri net models organized in a database with version control, accessible through a web interface. Gene modules are coupled to protein modules through mRNA modules by specific interfaces designed for the automatic, database-assisted composition. Automatically assembled executable models may then consider cell type-specific gene expression patterns and take the resulting protein concentrations into account. With a sufficient number of protein modules in the database, the composed Petri nets can predict complex effects of gene mutations or uncover complex genotype/phenotype relationships. In this context, forward and reverse engineered modules are fully compatible.
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.
Case studies in systems and synthetic biology demonstrating the specific power by the combined use of different Petri net classes are especially encouraged.
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.
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.
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 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.
Best papers will be proposed to be invited for the follow-up publication in Transactions on Petri Nets and other models of Concurrency (ToPNoC).
Brandenburg University of Technology at Cottbus, Computer Science Institute, Germany
monika.heiner (at) informatik.tu-cottbus.de
Bielefeld University, Faculty of Technology, Bioinformatics Department, Germany
ralf.hofestaedt (at) uni-bielefeld.de
Registration is handled by the hosting conference website. Early registration fees (workshop only): 100 € for students, 130 € else; early registration ends May 23, 2012.