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Petri net models for the semi-automatic construction of large scale biological networks

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Abstract

For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. During the last 15 years, Petri nets have attracted more and more attention to help to solve this key problem. Regarding the published papers, it seems clear that hybrid functional Petri nets are the adequate method to model complex biological networks. Today, a Petri net model of biological networks is built manually by drawing places, transitions and arcs with mouse events. Therefore, based on relevant molecular database and information systems biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the application of Petri nets for modeling and simulation of biological networks. Furthermore, we will present a type of access to relevant metabolic databases such as KEGG, BRENDA, etc. Based on this integration process, the system supports semi-automatic generation of the correlated hybrid Petri net model. A case study of the cardio-disease related gene-regulated biological network is also presented. MoVisPP is available at http://agbi.techfak.uni-bielefeld.de/movispp/.

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Acknowledgements

The work is supported in part by the EU project “CardioWorkBench” (http://www.cardioworkbench.eu/) and the BMBF Project (CHN 08/001). Ming Chen would like to thank DAAD fellowship and NSFC, MOST of China for related project financial support. Sridhar Hariharaputran would like to thank the DFG Graduate College Bioinformatics and Bioinformatics Department, Faculty of Technology at Bielefeld University for their financial support.

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Authors and Affiliations

  1. Bioinformatics Department, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China

    Ming Chen

  2. Bioinformatics Department, Faculty of Technology, Bielefeld University, 33615, Bielefeld, Germany

    Sridhar Hariharaputran, Ralf Hofestädt, Benjamin Kormeier & Sarah Spangardt

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  1. Ming Chen
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  2. Sridhar Hariharaputran
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  3. Ralf Hofestädt
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Correspondence to Ralf Hofestädt.

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Chen, M., Hariharaputran, S., Hofestädt, R. et al. Petri net models for the semi-automatic construction of large scale biological networks. Nat Comput 10, 1077–1097 (2011). https://doi.org/10.1007/s11047-009-9151-y

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