Literature DB >> 22144165

Petri nets in Snoopy: a unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks.

Wolfgang Marwan1, Christian Rohr, Monika Heiner.   

Abstract

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 features of the software tool Snoopy.

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Year:  2012        PMID： 22144165     DOI： 10.1007/978-1-61779-361-5_21

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  7 in total

1.  A graphical and computational modeling platform for biological pathways.

Authors:  Alessandra Livigni; Laura O'Hara; Marta E Polak; Tim Angus; Derek W Wright; Lee B Smith; Tom C Freeman
Journal:  Nat Protoc       Date:  2018-03-15       Impact factor: 13.491

2.  Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks.

Authors:  Markus Durzinsky; Annegret Wagler; Wolfgang Marwan
Journal:  BMC Syst Biol       Date:  2011-07-15

3.  Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters.

Authors:  Fei Liu; Monika Heiner; Ming Yang
Journal:  PLoS One       Date:  2016-02-24       Impact factor: 3.240

4.  Analyzing the Behavior of Neuronal Pathways in Alzheimer's Disease Using Petri Net Modeling Approach.

Authors:  Javaria Ashraf; Jamil Ahmad; Amjad Ali; Zaheer Ul-Haq
Journal:  Front Neuroinform       Date:  2018-05-23       Impact factor: 4.081

5.  In Silico Gene Regulatory Network of the Maurer's Cleft Pathway in Plasmodium falciparum.

Authors:  Itunuoluwa Isewon; Jelili Oyelade; Benedikt Brors; Ezekiel Adebiyi
Journal:  Evol Bioinform Online       Date:  2015-10-22       Impact factor: 1.625

6.  Modeling biological systems with uncertain kinetic data using fuzzy continuous Petri nets.

Authors:  Fei Liu; Siyuan Chen; Monika Heiner; Hengjie Song
Journal:  BMC Syst Biol       Date:  2018-04-24

7.  Dynamic Modeling of Streptococcus pneumoniae Competence Provides Regulatory Mechanistic Insights Into Its Tight Temporal Regulation.

Authors:  Mathias Weyder; Marc Prudhomme; Mathieu Bergé; Patrice Polard; Gwennaele Fichant
Journal:  Front Microbiol       Date:  2018-07-24       Impact factor: 5.640
  7 in total

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