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From Artificial Chemistries to Systems Biology

Software for Chemical Organization Theory

  • Chapter
Artificial Life Models in Software

Artificial Chemistries abstract from real-world chemistries by reducing them to systems of interacting and reacting molecules. They have been used to study phenomena in a wide array of fields like social and ecological modelling, evolution or chemical computing. Artificial Chemistries are inherently difficult to study and, thus, methods have been proposed to analyze their complexity. This chapter outlines how the concept of chemical organization and software dedicated at their analysis can help to ease this task. The chemical organizations of a reaction network correspond to sets of molecules that can coexist over long periods of (simulation-) time. Thus, they can be used to study the full dynamic behavior a system can exhibit without the need to simulate it in every detail. Due to this appealing property, Chemical Organization Theory has been used in the study of a wide array of systems ranging from Artificial Chemistries to real-world chemistries and biological systems. Especially the analysis of biological systems motivated an integration of the tools dedicated to the study of chemical organizations into an application framework from Systems Biology. The benefit of this integration is that tools from Systems Biology can be used without much effort along with the tools for the computation of chemical organizations and vice versa. Thus, software for the analysis of chemical organizations seamlessly integrates into a framework covering almost any aspect of network design and analysis.

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Author information

Authors and Affiliations

  1. Bio Systems Analysis Group, Jena Centre for Bioinformatics (JCB), and School of Mathematics and Computer Science, Friedrich-Schiller-University, Jena, D-07743, Germany

    Christoph Kaleta

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  1. Christoph Kaleta
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Editors and Affiliations

  1. Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland

    Maciej Komosinski

  2. Faculty of Computing, Engineering and Mathematical Sciences, University of the West of England, Bristol, BS16 1QY, UK

    Andrew Adamatzky

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© 2009 Springer-Verlag London Limited

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Kaleta, C. (2009). From Artificial Chemistries to Systems Biology. In: Komosinski, M., Adamatzky, A. (eds) Artificial Life Models in Software. Springer, London. https://doi.org/10.1007/978-1-84882-285-6_10

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  • DOI: https://doi.org/10.1007/978-1-84882-285-6_10

  • Publisher Name: Springer, London

  • Print ISBN: 978-1-84882-284-9

  • Online ISBN: 978-1-84882-285-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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