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Abstract Machines of Systems Biology

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Transactions on Computational Systems Biology III

Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 3737))

Abstract

Living cells are extremely well-organized autonomous systems, consisting of discrete interacting components. Key to understanding and modeling their behavior is modeling their system organization. Four distinct chemical toolkits (classes of macromolecules) have been characterized, each combinatorial in nature. Each toolkit consists of a small number of simple components that are assembled (polymerized) into complex structures that interact in rich ways. Each toolkit abstracts away from chemistry; it embodies an abstract machine with its own instruction set and its own peculiar interaction model. These interaction models are highly effective, but are not ones commonly used in computing: proteins stick together, genes have fixed output, membranes carry activity on their surfaces. Biologists have invented a number of notations attempting to describe these abstract machines and the processes they implement. Moving up from molecular biology, systems biology aims to understand how these interaction models work, separately and together.

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Author information

Authors and Affiliations

  1. Microsoft Research,  

    Luca Cardelli

Authors
  1. Luca Cardelli
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Editor information

Editors and Affiliations

  1. Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Piazza Manci, 17, 38050, Povo (TN), Italy

    Corrado Priami

  2. Dipartimento di Matematica e Informatica, Università di Camerino, I-62032, Camerino, Italy

    Emanuela Merelli

  3. DEIS, Università di Bologna, Via Venezia 52, 47023, Cesena, Italy

    Pablo Gonzalez

  4. Alma Mater Studiorum Università di Bologna a Cesena,, via Venezia 52, 47023, Cesena, Italy

    Andrea Omicini

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Cardelli, L. (2005). Abstract Machines of Systems Biology. In: Priami, C., Merelli, E., Gonzalez, P., Omicini, A. (eds) Transactions on Computational Systems Biology III. Lecture Notes in Computer Science(), vol 3737. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11599128_10

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  • DOI: https://doi.org/10.1007/11599128_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-30883-6

  • Online ISBN: 978-3-540-31446-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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