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Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets

Li Chen, Ge Qi-Wei, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano
2007 Journal of Biosciences  
This paper first presents basic Petri net components representing molecular interactions and mechanisms of signaling pathways, and introduces a method to construct a Petri net model of a signaling pathway  ...  Then a simulation method of determining the delay time of transitions of Petri net model, i.e. the time taken in firing of each transition, is proposed based on some simple principles that the number of  ...  Acknowledgments The authors are grateful to Dr. Atsushi Doi at University of Tokyo for valuable discussions.  ... 
doi:10.1007/s12038-007-0011-6 pmid:17426385 fatcat:5ybobi7tzbgffgliods7ctxzj4

Petri nets for the analysis of disease maps: applied to the TNFR1 signaling pathway

Ina Koch
2021 Zenodo  
The talk introduces Petri net (PN) basics and discusses their application to modeling signaling pathways.  ...  Based on the PN model, we investigated the detailed knockout behavior and identified important checkpoints of the TNFR1 signaling pathway in terms of ubiquitination within complex I and the gene expression  ...  Systems Biology 11:72 linear combinations of TI to represent a complete signal flow from the receptor to the cell response  In silico knockout Petri nets  Mathematical theory that describes systems  ... 
doi:10.5281/zenodo.4462577 fatcat:mbwnhrzu5jfx3cmsbxaki4xga4

Application of Petri net based analysis techniques to signal transduction pathways

Andrea Sackmann, Monika Heiner, Ina Koch
2006 BMC Bioinformatics  
We propose an approach for model validation of signal transduction pathways based on the network structure only.  ...  The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways.  ...  Acknowledgements This work has been partly supported by the Federal German Ministry of Education and Research (BMBF), BCB project 0312705D.  ... 
doi:10.1186/1471-2105-7-482 pmid:17081284 pmcid:PMC1686943 fatcat:ekpf4p3rmfaoljbdbvn4d5okjq

Model Structure Validation of Cell Signaling Pathways Using Colored Petri nets*

Dvid Csercsik, Katalin M. Hangos
2012 IFAC Proceedings Volumes  
In this paper we propose a novel colored timed Petri net modelling approach for model structure validation of cell signaling pathways.  ...  The aim is to distinguish between models of different structures based on typically qualitative, roughly detailed measurement data.  ...  In this approach, on which vast majority of literature corresponding to Petri net modelling of biochemical pathways is based, the Petri net representation of an interaction is based on its molecular mechanism  ... 
doi:10.3182/20120710-4-sg-2026.00005 fatcat:rpth5wx6dfcbtdiiw6moops5au

Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis [chapter]

Monika Heiner, Ina Koch, Jürgen Will
2003 Lecture Notes in Computer Science  
This paper demonstrates the first steps of a new integrating methodology to develop and analyse models of biological pathways in a systematic manner using well established Petri net technologies.  ...  This paper explains how to model and validate this pathway using qualitative Petri nets.  ...  Acknowledgements One of the authors has been supported by BMBF (Federal Ministry of Education and Research of Ger-  ... 
doi:10.1007/3-540-36481-1_22 fatcat:ovybskojajbhlplxkmmngb2qxm

Model validation of biological pathways using Petri nets—demonstrated for apoptosis

Monika Heiner, Ina Koch, Jürgen Will
2004 Biosystems (Amsterdam. Print)  
This paper demonstrates the first steps of a new integrating methodology to develop and analyse models of biological pathways in a systematic manner using well established Petri net technologies.  ...  This paper explains how to model and validate this pathway using qualitative Petri nets.  ...  Acknowledgements One of the authors has been supported by BMBF (Federal Ministry of Education and Research of Ger-  ... 
doi:10.1016/j.biosystems.2004.03.003 pmid:15245801 fatcat:mqwc3mionzctdigr3wlygno3ui

STRUCTURAL MODELING AND ANALYSIS OF SIGNALING PATHWAYS BASED ON PETRI NETS

CHEN LI, SHUNICHI SUZUKI, QI-WEI GE, MITSURU NAKATA, HIROSHI MATSUNO, SATORU MIYANO
2006 Journal of Bioinformatics and Computational Biology  
The purpose of this paper is to discuss how to model and analyze signaling pathways by using Petri net.  ...  T-invariant in the Petri net models.  ...  This research was partially supported by Grant-in-Aid for Scientific Research Modeling and Analysis of Signaling Pathways Based on Petri Net 1137 on Priority Areas "Systems Genomics" from the Ministry  ... 
doi:10.1142/s021972000600234x pmid:17099944 fatcat:qo7d6mz6ejge7aakdl77ubpfcu

A Combined In Vitro/In Silico Approach to Identifying Off-Target Receptor Toxicity

Joseph Leedale, Kieran J. Sharkey, Helen E. Colley, Áine M. Norton, David Peeney, Chantelle L. Mason, Jean G. Sathish, Craig Murdoch, Parveen Sharma, Steven D. Webb
2018 iScience  
Petri Nets The stochastic Petri net model of the histamine H1 receptor signalling pathway was formulated using Snoopy software (Heiner et al., 2012) .  ...  A stochastic Petri net model of the histamine H1 receptor signaling pathway was formulated based on existing knowledge of the pathway and network interactions with the five critical transcription factors  ...  The systems of ODEs representing the histamine H1 receptor signaling pathway are provided below. á[â]/ám represents the rate of change of variable â over time, m.  ... 
doi:10.1016/j.isci.2018.05.012 pmid:30240756 pmcid:PMC6147237 fatcat:uykh74dmmvb3pky4xdjjl4xd2u

A Stochastic Petri Net-Based Model of the Involvement of Interleukin 18 in Atherosclerosis

Dorota Formanowicz, Agnieszka Rybarczyk, Marcin Radom, Krzysztof Tanaś, Piotr Formanowicz
2020 International Journal of Molecular Sciences  
To investigate the influence of IL-18 cytokine on atherosclerosis development, a stochastic Petri net model was built and then analyzed.  ...  Our results gave us better insight into the studied phenomenon and allow revealing that activation of macrophages by the classical pathway and IL-18-MyD88 signaling axis is crucial for the modeled process  ...  (black boxes in Results and Discussion Building a Stochastic Petri Net Based Model Here, a stochastic Petri net-based model of the involvement of the IL-18 cytokine in the formation of the atherosclerotic  ... 
doi:10.3390/ijms21228574 pmid:33202974 pmcid:PMC7696504 fatcat:ss4a2cwpcnfbda4btjzuocxjpa

Modularization of biochemical networks based on classification of Petri net t-invariants

Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Bjorn H Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch
2008 BMC Bioinformatics  
One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants.  ...  Conclusion: We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis.  ...  Authors acknowledge the support from an operating grant from the German Society of Muscle Diseased Persons and a Studentship from the Hypatia Program, Technical University of Applied Sciences Berlin, Germany  ... 
doi:10.1186/1471-2105-9-90 pmid:18257938 pmcid:PMC2277402 fatcat:brssi43cevekvneq5ydqw4bahu

Formal Executable Models of Cell Signaling Primitives

Carolyn Talcott
2006 Second International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (isola 2006)  
The following we give informal descriptions of some of the signaling reactions in this pathway along with the Maude and/or Petri net representation.  ...  Currently Pathway Logic has a knowledge base of over 1000 rules and 600 basic components and is used to analyze signaling in different cell types.  ... 
doi:10.1109/isola.2006.66 dblp:conf/isola/Talcott06 fatcat:app6qyvmpzd2beqiqku67nw4y4

JAK/STAT signalling – an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology

Mary Ann Blätke, Anna Dittrich, Christian Rohr, Monika Heiner, Fred Schaper, Wolfgang Marwan
2013 Molecular Biosystems  
We describe a molecule-oriented modelling approach based on a collection of Petri net models organized in the form of modules into a prototype database accessible through a web interface.  ...  The JAK/STAT signalling pathway with the extensive crosstalk of its components is selected as case study.  ...  Acknowledgemnts We thank Professor David Gilbert for critical reading of the manuscript and for suggesting module based automatic biomodel engineering and its application to  ... 
doi:10.1039/c3mb25593j pmid:23443149 fatcat:6c2ttcuimffd3d5aezzpapg4ce

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  ...  The mechanisms of the complex signaling network are explored by applying the established framework to the signal transduction induced by potent proinflammatory cytokines, IL-1beta and TNF-alpha The corresponding  ...  This work was supported by the Korean Systems Biology Research Program (M10309020000-03B5002-00000) of the Ministry of Science and Technology and by the BK21 project.  ... 
pmid:15706509 fatcat:zk4xssfcxjgmllu2mcyz7f7z7m

BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes

Junhui Gao, Li Li, Xiaolin Wu, Dong-Qing Wei
2012 Protein & Cell  
Gene regulatory networks, metabolic pathways, signaling pathways, and kinetics of cell interaction are all available in BioNetSim, which makes modeling more efficient and effective.  ...  Similar to other Petri net-based softwares, BioNetSim does well in graphic application and mathematic construction.  ...  Specifically, Petri net is a triple N = (P, T, F) where: P is a set of states, called places; T is a set of transitions; F where F ⊂ (P × T) ∪ (T × P) is a set of flow relations called "arcs" between places  ... 
doi:10.1007/s13238-012-2019-4 pmid:22410784 pmcid:PMC4875423 fatcat:rbyzlcc3lbafnig3pmqsqhdnqu

Theoretical Studies on the Engagement of Interleukin 18 in the Immuno-Inflammatory Processes Underlying Atherosclerosis

Dorota Formanowicz, Kaja Gutowska, Piotr Formanowicz
2018 International Journal of Molecular Sciences  
For this purpose, a model of the studied phenomenon, including selected pathways, based on the Petri-net theory, has been created and then analyzed.  ...  natural killers (NKs) and T cells to interferon gamma (IFN- γ ) synthesis.  ...  Classical Petri nets have some limitation, e.g., analysis of Petri net-based model which includes inhibition reactions.  ... 
doi:10.3390/ijms19113476 pmid:30400655 fatcat:u3v23d4zdjc3vkm2jkyqshtnsa
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