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Multi-agent-based bio-network for systems biology: protein–protein interaction network as an example

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Abstract

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. This research requires the ability to simulate particular biological systems as cells, organs, organisms, and communities. In this paper, a novel bio-network simulation platform is proposed for system biology studies by combining agent approaches. We consider a biological system as a set of active computational components interacting with each other and with an external environment. Then, we propose a bio-network platform for simulating the behaviors of biological systems and modelling them in terms of bio-entities and society-entities. As a demonstration, we discuss how a protein–protein interaction (PPI) network can be seen as a society of autonomous interactive components. From interactions among small PPI networks, a large PPI network can emerge that has a remarkable ability to accomplish a complex function or task. We also simulate the evolution of the PPI networks by using the bio-operators of the bio-entities. Based on the proposed approach, various simulators with different functions can be embedded in the simulation platform, and further research can be done from design to development, including complexity validation of the biological system.

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Acknowledgements

This work was supported in part by the Key Project of the National Nature Science Foundation of China (No. 60534020), the National Nature Science Foundation of China (No. 60775052), the Cultivation Fund of the Key Scientific and Technical Innovation Project from the Ministry of Education of China (No. 706024), International Science Cooperation Foundation of Shanghai (No. 061307041), and Specialized Research Fund for the Doctoral Program of Higher Education from Ministry of Education of China (No. 20060255006).

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Authors and Affiliations

  1. College of Information Sciences and Technology, Donghua University, Shanghai, 201620, People’s Republic of China

    Li-Hong Ren, Yong-Sheng Ding, Yi-Zhen Shen & Xiang-Feng Zhang

  2. Engineering Research Center of Digitized Textile and Fashion Technology, Donghua University, Shanghai, 201620, People’s Republic of China

    Yong-Sheng Ding

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  1. Li-Hong Ren
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  2. Yong-Sheng Ding
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  4. Xiang-Feng Zhang
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Correspondence to Li-Hong Ren or Yong-Sheng Ding.

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Ren, LH., Ding, YS., Shen, YZ. et al. Multi-agent-based bio-network for systems biology: protein–protein interaction network as an example. Amino Acids 35, 565–572 (2008). https://doi.org/10.1007/s00726-008-0081-2

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  • DOI: https://doi.org/10.1007/s00726-008-0081-2

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