BioFNet: biological functional network database for analysis and synthesis of biological systems

In synthetic biology and systems biology, a bottom-up approach can be used to construct a complex, modular, hierarchical structure of biological networks. To analyze or design such networks, it is critical to understand the relationship between network structure and function, the mechanism through w...

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Bibliographic Details
Published in:Briefings in bioinformatics 2014-09, Vol.15 (5), p.699-709
Main Authors: Kurata, Hiroyuki, Maeda, Kazuhiro, Onaka, Toshikazu, Takata, Takenori
Format: Article
Language:English
Subjects:
Biological
Biomolecules
Biosynthesis
Construction
Database Management Systems
Design engineering
Mathematical analysis
Mathematical models
Models, Theoretical
Molecular biology
Networks
Simulation
Synthetic biology
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Summary:In synthetic biology and systems biology, a bottom-up approach can be used to construct a complex, modular, hierarchical structure of biological networks. To analyze or design such networks, it is critical to understand the relationship between network structure and function, the mechanism through which biological parts or biomolecules are assembled into building blocks or functional networks. A functional network is defined as a subnetwork of biomolecules that performs a particular function. Understanding the mechanism of building functional networks would help develop a methodology for analyzing the structure of large-scale networks and design a robust biological circuit to perform a target function. We propose a biological functional network database, named BioFNet, which can cover the whole cell at the level of molecular interactions. The BioFNet takes an advantage in implementing the simulation program for the mathematical models of the functional networks, visualizing the simulated results. It presents a sound basis for rational design of biochemical networks and for understanding how functional networks are assembled to create complex high-level functions, which would reveal design principles underlying molecular architectures.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbt048