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A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets [chapter]

David Gilbert, Monika Heiner, Sebastian Lehrack
Lecture Notes in Computer Science  
We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms.  ...  In a previous paper [GH06] we developed an approach for modelling and analysing biochemical networks using discrete and continuous Petri nets.  ...  We would like to thank Richard Orton and Xu Gu for the constructive discussions as well as Vladislav Vyshermirsky for his support in the computational experiments.  ... 
doi:10.1007/978-3-540-75140-3_14 fatcat:lcuoeu3y2fgsdaaw2wvc6qxkyu

A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems [chapter]

Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira
2009 Lecture Notes in Computer Science  
Aware that no formalism can fit all purposes we realize Petri Nets as a suitable model for Metabolic Engineering and take a deeper perspective on the role of this formalism as an integrating framework  ...  We briefly review modelling formalisms that have been used in Systems Biology and identify the criteria that must be addressed by an integrating framework capable of modelling, analysing and simulating  ...  Our future developments will use petri nets as the basis of a framework for modelling and analysis of integrated regulatory and metabolic networks.  ... 
doi:10.1007/978-3-642-02481-8_161 fatcat:a4jah5qo5vekpcol3c6fqyn2ua

Integrative Analysis of Metabolic Models – from Structure to Dynamics

Anja Hartmann, Falk Schreiber
2015 Frontiers in Bioengineering and Biotechnology  
Here, we describe a method for an integrative analysis of the structure and dynamics represented by qualitative and quantitative metabolic models.  ...  The System Biology Metabolic Model Framework (SBM 2 -Framework) implements the developed method and, as an example, is applied for the integrative analysis of the crop plant potato.  ...  Heiner et al. (2012) and Nagasaki et al. (2010) propose a unifying Petri net framework comprised of a family of related Petri net types.  ... 
doi:10.3389/fbioe.2014.00091 pmid:25674560 pmcid:PMC4306315 fatcat:begf6j3fazhqpfkua6pmgovhmq

An overview of data models for the analysis of biochemical pathways

Y. Deville
2003 Briefings in Bioinformatics  
His current research interests include modelling and analysis of biochemical networks, and constraint programming.  ...  The authors wish also to thank Christian Lemer, Jean Richelle and Aik Choon Tan for useful discussions. We are grateful to anonymous reviewers for their constructive comments.  ...  Acknowledgments The two first authors acknowledge the support received from the UK Engineering and Physical Sciences Research Council (EPSRC, project GR/ S07490/01).  ... 
doi:10.1093/bib/4.3.246 pmid:14582519 fatcat:fpepdsmexveipi6dxf3vlbeytq

The biology Petri net markup language

Ming Chen, Andreas Freier, Jacob Köhler, Alexander Rüegg
2002 Entwicklungsmethoden für Informationssysteme und deren Anwendung: Fachtagung  
BioPNML is designed to provide a starting point for the development of a standard interchange format for Bioinformatics and Petri nets.  ...  In this paper a proposal for the Biology Petri Net Markup Language (BioPNML) is presented.  ...  Philippi for useful suggestions. We would like to thank the anonymous referee for his/her valuable comments and suggestions.  ... 
dblp:conf/emisa/ChenFKR02 fatcat:hdwx24cokbbw5p7zwyebyqyfym

An Overview of Data Models for the Analysis of Biochemical Pathways [chapter]

Yves Deville, David Gilbert, Jacques van Helden, Shoshana Wodak
2003 Lecture Notes in Computer Science  
In particular, we classify the different types of data models found in the literature using a unified framework.  ...  Pathway analysis is hence a challenging problem in systems biology and in bioinformatics. Various forms of data models have been devised for the analysis of biochemical pathways.  ...  The authors wish also to thank Christian Lemer, Jean Richelle and Aik Choon Tan for useful discussions. We are grateful to the anonymous reviewers for their constructive comments.  ... 
doi:10.1007/3-540-36481-1_23 fatcat:2gjxyxaklfdtjgf2akdsmrzjlu

Pathway analysis in metabolic databases via differential metabolic display (DMD)

R. Kuffner, R. Zimmer, T. Lengauer
2000 Bioinformatics  
We present a unifying, systematic approach based on PETRI nets for storing, displaying, comparing, searching and simulating such nets from a number of different sources.  ...  Results: Information from each data source is extracted and compiled into a PETRI net.  ...  We thank our colleagues Klaus Voss for providing Figure 11 and Alexander Zien for helpful discussions.  ... 
doi:10.1093/bioinformatics/16.9.825 pmid:11108705 fatcat:sxwejam6s5dffj53wl657pelpa

Computational methodologies for modelling, analysis and simulation of signalling networks

D. Gilbert, H. Fuss, X. Gu, R. Orton, S. Robinson, V. Vyshemirsky, M. J. Kurth, C. S. Downes, W. Dubitzky
2006 Briefings in Bioinformatics  
This article is a critical review of computational techniques used to model, analyse and simulate signalling networks.  ...  We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal transduction, cellular rhythms and cell-to-cell communication.  ...  O. and V. V. have been supported by a DTI 'Post-genomics Beacons' grant.  ... 
doi:10.1093/bib/bbl043 pmid:17116646 fatcat:cf42u6jo6fgq5lp63c22gh4xqe

Knowledge Representation Model for Systems-Level Analysis of Signal Transduction Networks

Dong-Yup Lee, Ralf Zimmer, Sang-Yup Lee, Daniel Hanisch, Sunwon Park
2004 Genome Informatics Series  
A Petri-net based model for knowledge representation has been developed to describe as explicitly and formally as possible the molecular mechanisms of cell signaling and their pathological implications  ...  A conceptual framework has been established for reconstructing and analyzing signal transduction networks on the basis of the formal representation.  ...  indicate TNF-a as unclear Petri-net mechanisms representation A major future and/or pathways. using the ToPNet challenge is to explore program. drug (b) Resultant effects on the screen pharmacological  ... 
doi:10.11234/gi1990.15.2_234 fatcat:fpauzojv5rg2hfyaygrkem4f4y

Knowledge representation model for systems-level analysis of signal transduction networks

Dong-Yup Lee, Ralf Zimmer, Sang-Yup Lee, Daniel Hanisch, Sunwon Park
2004 Genome Informatics Series  
A Petri-net based model for knowledge representation has been developed to describe as explicitly and formally as possible the molecular mechanisms of cell signaling and their pathological implications  ...  A conceptual framework has been established for reconstructing and analyzing signal transduction networks on the basis of the formal representation.  ...  Further supports by the LG Chemicals Chair Professorship, IBM-SUR program, and the Center for Ultramicrochemical Process Systems are appreciated.  ... 
pmid:15706509 fatcat:zk4xssfcxjgmllu2mcyz7f7z7m

Petri Nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks [chapter]

Wolfgang Marwan, Christian Rohr, Monika Heiner
2011 Msphere  
Using the example of phosphate regulation in enteric bacteria, we demonstrate the particular suitability of stochastic Petri nets to model biochemical phenomena and their simulative exploration by various  ...  Petri nets provide a unifying framework for modelling and simulation in systems biology. Petri nets can be used to perform all major modelling and simulation approaches central to systems biology.  ...  With Snoopy, we provide a tool that supports the use of Petri nets as • a common communication platform (modelling language) for experimentalists and theoreticians, together with • a unifying framework  ... 
doi:10.1007/978-1-61779-361-5_21 pmid:22144165 fatcat:ltlv3x6iijhsfo3xrevqof75mu

BioModel engineering for multiscale Systems Biology

Monika Heiner, David Gilbert
2013 Progress in Biophysics and Molecular Biology  
Our methodology is based on a structured family of Petri net classes which enables the investigation of a given system using various modelling abstractions: qualitative, stochastic, continuous and hybrid  ...  We discuss some motivational challenges arising from the need to model and analyse complex biological systems at multiple scales (spatial and temporal), and present a biomodel engineering framework to  ...  In the following we present a framework, see Fig. 3 , to give a formal structure over qualitative and quantitative descriptions of biochemical networks using Petri nets incorporating individual and population-based  ... 
doi:10.1016/j.pbiomolbio.2012.10.001 pmid:23067820 fatcat:mf4cq3jawbbfrgqb6kut5b4equ

Petri nets for modelling metabolic pathways: a survey

Paolo Baldan, Nicoletta Cocco, Andrea Marin, Marta Simeoni
2010 Natural Computing  
We point out the main problems that arise in the construction of a Petri net model of a metabolic pathway and we outline some solutions proposed in the literature.  ...  Second, we present a comprehensive review of recent research on this topic, in order to assess the maturity of the field and the availability of a methodology for modelling a metabolic pathway by a corresponding  ...  Acknowledgements The authors are grateful to Marcantonio Bragadin of the Dipartimento di Scienze Ambientali-Università Ca' Foscari di Venezia, for enlightening discussions on metabolic pathways and biochemical  ... 
doi:10.1007/s11047-010-9180-6 fatcat:acu6ojeywrhllphpo7cpmdgtwu

Understanding Network Behavior by Structured Representations of Transition Invariants [chapter]

Monika Heiner
2009 Natural Computing Series  
Petri nets offer a bipartite and concurrent paradigm, and consequently represent a natural choice for modeling and analyzing biochemical networks.  ...  This structuring technique is especially helpful for analyzing biochemically interpreted Petri nets, where it supports model validation of biochemical reaction systems reflecting current comprehension  ...  This paper is an outcome of his faith in the potential of biochemically interpreted Petri nets.  ... 
doi:10.1007/978-3-540-88869-7_19 fatcat:vtl2sn4yprgmnhxxb7cv4klu3m

Rewriting Logic and Symbolic Systems Biology applied to EGF Signaling Pathway

Gustavo Santos-García, Javier De Las Rivas, Carolyn L. Talcott
2014 International Work-Conference on Bioinformatics and Biomedical Engineering  
In this paper we describe the Pathway Logic approach to the modeling and analysis of signal transduction, and the use of the Pathway Logic Assistant (PLA) tool to browse and query these models.  ...  In particular, formal executable models of processes such as signal transduction, metabolic pathways, and immune system cell-cell signaling are developed using the rewriting logic language Maude and a  ...  We have described the use of Pathway Logic to model signal transduction processes, and the use of the Pathway Logic Assistant to browse and analyse these models.  ... 
dblp:conf/iwbbio/Santos-GarciaRT14 fatcat:gygmxquubna4vpkl3la43vuha4
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