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Erschienen in:
Implementing Molecular Logic Gates, Circuits, and Cascades Using DNAzymes Kapitel lesen Erstes Kapitel lesen

2017 | OriginalPaper | Buchkapitel

25. An Integrated In Silico Simulation and Biomatter Compilation Approach to Cellular Computation

verfasst von : Savas Konur, Harold Fellermann, Larentiu Marian Mierla, Daven Sanassy, Christophe Ladroue, Sara Kalvala, Marian Gheorghe, Natalio Krasnogor

Erschienen in: Advances in Unconventional Computing

Verlag: Springer International Publishing

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Abstract

Recent advances Synthetic Biology are ushering a new practical computational substrate based on programmable information processing via biological cells. Due to the difficulties in orchestrating complex programmes using myriads of relatively simple, limited and highly stochastic processors such as living cells, robust computational technology to specify, simulate, analyse and compile cellular programs are in demand. We provide the Infobiotics Workbench (Ibw) tool, a software platform developed to model and analyse stochastic compartmentalized systems, which permits using various computational techniques, such as modelling, simulation, verification and biocompilation. We report here the details of our work for modelling, simulation and, for the first time, biocompilation, while verification is reported elsewhere in this book. We consider some basic genetic logic gates to illustrate the main features of the Ibw platform. Our results show that membrane computing provides a suitable formalism for building synthetic biology models. The software platform we developed permits analysing biological systems through the computational methods integrated into the workbench, providing significant advantages in terms of time, and enhanced understanding of biological functionality.

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Vorheriges Kapitel Computing a Worm: Reverse-Engineering Planarian Regeneration
Nächstes Kapitel Plant Roots as Excellent Pathfinders: Root Navigation Based on Plant Specific Sensory Systems and Sensorimotor Circuits
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Metadaten
Titel
An Integrated In Silico Simulation and Biomatter Compilation Approach to Cellular Computation
verfasst von
Savas Konur
Harold Fellermann
Larentiu Marian Mierla
Daven Sanassy
Christophe Ladroue
Sara Kalvala
Marian Gheorghe
Natalio Krasnogor
Copyright-Jahr
2017
Buch
Advances in Unconventional Computing

Print ISBN: 978-3-319-33920-7

Electronic ISBN: 978-3-319-33921-4

Copyright-Jahr: 2017

DOI
https://doi.org/10.1007/978-3-319-33921-4_25