An Integrated In Silico Simulation and Biomatter Compilation Approach to Cellular Computation
| Autor: | Marian Gheorghe, Daven Sanassy, Larentiu Marian Mierla, Natalio Krasnogor, Sara Kalvala, Harold Fellermann, Christophe Ladroue, Savas Konur |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Theoretical computer science Computer science business.industry Distributed computing Computation Information processing 0102 computer and information sciences computer.software_genre 01 natural sciences 03 medical and health sciences Synthetic biology 030104 developmental biology Software 010201 computation theory & mathematics Logic gate Workbench Compiler business Membrane computing computer |
| Zdroj: | Emergence, Complexity and Computation ISBN: 9783319339207 |
| DOI: | 10.1007/978-3-319-33921-4_25 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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