Filters








5,679 Hits in 4.2 sec

Petri net applications in molecular biology. Preface

Edgar Wingender
2010 In Silico Biology  
As a result, Petri net technology appears to be a very promising approach to modeling biological systems.  ...  Several years ago, Petri nets have been suggested to be well suited for modeling metabolic networks by overcoming some of the limitations outlined above [Reddy et al., 1993] .  ...  This recent overview has been published as Special Issue on Petri Net Applications in Molecular Biology of ISB volume 10, whereas the whole collection now constitutes this First ISB Book on Biological  ... 
doi:10.3233/isb-2010-0420 pmid:22430218 fatcat:zu2bx2iairgdplamyz2niblmh4

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 experimental findings in the current literature, we constructed a PN model in terms of detailed molecular reactions for the molecular players, protein complexes, post-translational modifications  ...  mentioned application to chemical networks already in 1976  First paper on biochemical application by Venkatramana Reddy et al. in 1993 Koch, Reisig, Schreiber (2011) Modeling in Systems Biology -The  ... 
doi:10.5281/zenodo.4462577 fatcat:mbwnhrzu5jfx3cmsbxaki4xga4

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  
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  ...  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  ...  There is currently a considerable amount of literature on the application of petri nets to Systems Biology [22, 4, 13] .  ... 
doi:10.1007/978-3-642-02481-8_161 fatcat:a4jah5qo5vekpcol3c6fqyn2ua

MODELING AND SIMULATION OF MOLECULAR BIOLOGY SYSTEMS USING PETRI NETS: MODELING GOALS OF VARIOUS APPROACHES

SIMON HARDY, PIERRE N. ROBILLARD
2004 Journal of Bioinformatics and Computational Biology  
Various extensions to the original theory of Petri nets have been used for modeling molecular biology systems and metabolic networks. These extensions are stochastic, colored, hybrid and functional.  ...  Petri nets are a discrete event simulation approach developed for system representation, in particular for their concurrency and synchronization properties.  ...  This work was supported in part by NSERC grant A-0141 and a Canada Graduate Scholarship.  ... 
doi:10.1142/s0219720004000764 pmid:15617157 fatcat:62xyu5m2fvd7bcwrrp5zonh4ny

Advantages of Petri-Net Modeling and Simulation for Biological Networks

Ralf Hofestädt
2017 International Journal of Bioscience Biochemistry and Bioinformatics  
This paper will present the advantages of Petri-Nets for modeling and simulation of biological networks.  ...  Furthermore, different higher Petri-Nets are available to realize the adequate modeling of cellular processes.  ...  An object-oriented Petri-Net simulation tool for hybrid biological processes for MODELICA applications is presented in [14] .  ... 
doi:10.17706/ijbbb.2017.7.4.221-229 fatcat:ustmo4vfpfdn7dn54a6attvc2a

A module-based approach to biomodel engineering with Petri Nets

Wolfgang Marwan, Mary Ann Blatke
2012 Proceedings Title: Proceedings of the 2012 Winter Simulation Conference (WSC)  
The composable, metadata-containing Petri net modules are organized in a database with version control and accessible through a web interface.  ...  Prospects for automatic model generation including its application to systems biology, synthetic biology, and to functional genomics are discussed. 1 978-1-4673-4780-8/12/$31.00 ©2012 IEEE 3383 978-1-4673  ...  We also thank David Gilbert for stimulating discussions regarding possible applications of modular modelling to synthetic biology.  ... 
doi:10.1109/wsc.2012.6465259 dblp:conf/wsc/MarwanB12 fatcat:xge44fon35gu5emvgxi34wtqgq

What Can Formal Methods Bring to Systems Biology? [chapter]

Nicola Bonzanni, K. Anton Feenstra, Wan Fokkink, Elzbieta Krepska
2009 Lecture Notes in Computer Science  
We discuss one example: a recent Petri net analysis of C. elegans vulval development.  ...  The results can be complementary to the traditional mathematical descriptive modelling approaches used in systems biology.  ...  In [13] we explained a method to represent biological knowledge as a Petri net.  ... 
doi:10.1007/978-3-642-05089-3_2 fatcat:guyiwjok3vemdlv7nxkr5txbwm

PetriScape - A plugin for discrete Petri net simulations in Cytoscape

Diogo Almeida, Vasco Azevedo, Artur Silva, Jan Baumbach
2016 Journal of Integrative Bioinformatics  
SummarySystems biology plays a central role for biological network analysis in the post-genomic era.  ...  PetriScape comes with the following main functionalities: (1) import of biological networks in SBML format, (2) conversion into a Petri net, (3) visualization as Petri net, and (4) simulation and visualization  ...  This is important for our understanding of biology but may also result in potential medical and biotechnological applications [4, 5] .  ... 
doi:10.1515/jib-2016-284 fatcat:7ejacz5yozh63dhhsymw2axeey

PetriScape - A plugin for discrete Petri net simulations in Cytoscape

Diogo Almeida, Vasco Azevedo, Artur Silva, Jan Baumbach
2016 Journal of Integrative Bioinformatics  
Systems biology plays a central role for biological network analysis in the post-genomic era.  ...  PetriScape comes with the following main functionalities: (1) import of biological networks in SBML format, (2) conversion into a Petri net, (3) visualization as Petri net, and (4) simulation and visualization  ...  This is important for our understanding of biology but may also result in potential medical and biotechnological applications [4, 5] .  ... 
doi:10.2390/biecoll-jib-2016-284 pmid:27402693 fatcat:rbpw4gnifffvxaxxmadqalfsq4

Biomodel Engineering – From Structure to Behavior [chapter]

Rainer Breitling, Robin A. Donaldson, David R. Gilbert, Monika Heiner
2010 Lecture Notes in Computer Science  
It forms a systematic and powerful extension of earlier mathematical modeling approaches and has recently gained popularity in systems biology and synthetic biology.  ...  We also present a more detailed outline of one of the major techniques of biomodel engineering -Petri net models -which provides a flexible and powerful tool for building, validating and exploring computational  ...  The two major application areas of biomodel engineering are systems biology and synthetic biology.  ... 
doi:10.1007/978-3-642-11712-1_1 fatcat:i4o5zmhigneh5mz5oaqcqnw474

Agent Petri Nets Framework for Modeling Staphylococcus epidermidis Biofilm Formation

Borhan Marzougui, Kamel Barkaoui, Mohamed Amine Makni
2016 E-Health Telecommunication Systems and Networks  
This paper describes the thriving application of Petri net theory for modeling of interaction between different regulations actors leading S. epidermidis to switch from Planctonik to Biofilm.  ...  We propose Agent Petri Nets model to describe and analyze the process of formation of Biofilm molecule. This model presents a formal framework based on Multi Agents system characteristics.  ...  Various extensions to the original theory of Petri nets have been used for modeling molecular biology systems and metabolic [2] . Such systems permit to coordinate various molecules.  ... 
doi:10.4236/etsn.2016.51003 fatcat:mpgxvtd2zffjhodzkugztxikqq

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  
Petri nets composed from modules can be executed as ODE system, stochastic, hybrid, or merely qualitative models and exported in SMBL format.  ...  These Petri net modules are graphically displayed, can be executed individually, and allow the automatic composition into coherent models containing an arbitrary number of molecular species chosen ad hoc  ...  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

VANESA - a software application for the visualization and analysis of networks in system biology applications

Christoph Brinkrolf, Sebastian Jan Janowski, Benjamin Kormeier, Martin Lewinski, Klaus Hippe, Daniela Borck, Ralf Hofestädt
2014 Journal of Integrative Bioinformatics  
These structures can then be further investigated in the Petri net environment of VANESA. It is platform-independent, free-of-charge, and available at http://vanesa.sf.net.  ...  It is now possible for scientists to automatically reconstruct important molecular systems with information from the databases KEGG, MINT, IntAct, HPRD, and BRENDA.  ...  Christian Kaltschmidt (Cell Biology, Faculty of Biology, Bielefeld University, Germany) and Prof. Dr. Barbara Kaltschmidt (Molecular Neurobiology, Faculty of Biology, Bielefeld University, Germany).  ... 
doi:10.2390/biecoll-jib-2014-239 pmid:24953454 fatcat:j472dwnhkzhpjk2ljpe2fszxji

VANESA - A Software Application for the Visualization and Analysis of Networks in Systems Biology Applications

Christoph Brinkrolf, Sebastian Jan Janowski, Benjamin Kormeier, Martin Lewinski, Klaus Hippe, Daniela Borck, Ralf Hofestädt
2014 Journal of Integrative Bioinformatics  
These structures can then be further investigated in the Petri net environment of VANESA. It is platform-independent, free-of-charge, and available at http://vanesa.sf.net.  ...  It is now possible for scientists to automatically reconstruct important molecular systems with information from the databases KEGG, MINT, IntAct, HPRD, and BRENDA.  ...  Christian Kaltschmidt (Cell Biology, Faculty of Biology, Bielefeld University, Germany) and Prof. Dr. Barbara Kaltschmidt (Molecular Neurobiology, Faculty of Biology, Bielefeld University, Germany).  ... 
doi:10.1515/jib-2014-239 fatcat:mdgwzzigbrfolb7eqt6yvepbfa

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

Junhui Gao, Li Li, Xiaolin Wu, Dong-Qing Wei
2012 Protein & Cell  
Similar to other Petri net-based softwares, BioNetSim does well in graphic application and mathematic construction.  ...  BioNetSim, a Petri net-based software for modeling and simulating biochemistry processes, is developed, whose design and implement are presented in this paper, including logic construction, real-time access  ...  Petri net is widely used in bioinformatics for its advantage on graphic application and mathematic theory.  ... 
doi:10.1007/s13238-012-2019-4 pmid:22410784 pmcid:PMC4875423 fatcat:rbyzlcc3lbafnig3pmqsqhdnqu
« Previous Showing results 1 — 15 out of 5,679 results