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An integrated in silico simulation and biomatter compilation approach to cellular computation

Lookup NU author(s): Dr Harold Fellermann, Daven Sanassy, Professor Natalio KrasnogorORCiD


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Recent advances in 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 I BW platform. Our results show that membrane computing provides a suitable formalism for building synthetic biology models. Thesoftware 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.

Publication metadata

Author(s): Konur S, Fellermann H, Mierla LM, Sanassy D, Ladroue C, Kalvala S, Gheorghe M, Krasnogor N

Editor(s): Adamatzky A

Publication type: Book Chapter

Publication status: Published

Book Title: Advances in Unconventional Computing

Year: 2017

Volume: 2

Pages: 655-676

Print publication date: 08/08/2016

Acceptance date: 01/08/2016

Publisher: Springer

Place Published: Cham


Notes: 9783319339214 ebook ISBN

Library holdings: Search Newcastle University Library for this item

ISBN: 9783319339207