A satellite event of Petri Nets 2011 - Newcastle upon Tyne, UK, June 20, 2011
The workshop enjoyed an open-minded and productive atmosphere having 20-25 participants in each session.
See you all next year at BioPPN 2012 in Hamburg.
CEUR Workshop Proceedings Vol. 724
Human Genome Center, Institute of Medical Science, The University of Tokyo 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
We developed a software platform XiP (eXtensible integrative Pipeline) that is a flexible, editable and modular environment with a user-friendly interface for systems biology. With XiP, we can build various analysis workflows including simulation, visualization, pathway modeling, etc. Construction of a workflow under XiP follows the intuitive notion of dragging and dropping. XiP already equips with several “ready to use” pipeline flows for the most common analysis and more than 300 statistical/computational analysis components, and XiP also recognizes components written in R (http://www.r-project.org). It runs under multiprocessors environments. The source code is available as open source under the Lesser General Public License (LGPL) (download: http://xip.hgc.jp/wiki/en/).
On the other hand, we have been developing a modeling and simulation tool Cell Illustrator Online 5.0 (CIO, https://cionline.hgc.jp/) that enables us to draw, model, elucidate and simulate complex biological processes and systems such as metabolic pathways, signal transduction cascades, gene regulatory pathways and dynamic interactions of various biological entities. Cell System Ontology (CSO) (http://www.csml.org/) and Cell System Markup Language (CSML) constitute the basis of CIO. CIO uses Hybrid Functional Petri Net with extension (HFPNe) which is defined by enhancing some functions to hybrid Petri net so that various aspects in biological pathways can be intuitively modeled. CIO has been used to build, for example, a simulatable macrophage pathway knowledge base (MACPAK) (http://macpak.csml.org/). A key technology for driving systems biology is a method for automatic parameter estimation for models. For this purpose, we developed a method for HFPNe, namely CIO, by using a technology called data assimilation which "blends" simulation models and observational data "rationally". This data assimilation method requires supercomputer systems.
We are currently creating the next generation supercomputing environment for systems biology on XiP by enrolling CIO, data assimilation, model checking, and various systems biology tools such as SiGN (large-scale gene network estimation software package (http://sign.hgc.jp/) on XiP.
Integrative biology, made possible by the spectacular growth of biological information, intends to decipher 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.
Since about 15 years Petri nets have proved their usefulness for the modelling, analysis, and simulation 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. Indeed, because of their complexity, size and heterogeneity, biological networks raise distinctive challenges to the modeller.
The goal of this workshop is to provide a platform for researchers aiming at such fundamental research and real life applications.
This workshop intends to gather students and researchers, especially from Asian countries, 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 activities of Asian countries in Petri net applications on biological processes.
All papers should be in LNCS format, and will have to be submitted via EasyChair. Submitted papers should describe original work that has not been previously published and is not under review for publication elsewhere. There are three categories of papers:
Proceedings will be electronically published with CEUR Workshop Proceedings (http://ceur-ws.org) with five consecutive volume numbers for each workshop allocated with PETRI NET 2011, 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
Graduate School of Science and Engineering, Yamaguchi University, Japan
matsuno (at) sci.yamaguchi-u.ac.jp