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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan

4 Issues per year


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 10, Issue 2

Issues

BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology

Goksel Misirli
  • School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1, 7RU, United Kingdom of Great Britain and Northern Ireland
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/ Anil Wipat
  • School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
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/ Joseph Mullen
  • School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
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/ Katherine James
  • School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
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/ Matthew Pocock
  • School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1, 7RU, United Kingdom of Great Britain and Northern Ireland
  • TAMH Ltd., Newcastle upon Tyne United Kingdom of Great Britain and Northern Ireland
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/ Wendy Smith
  • School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
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/ Nick Allenby
  • Demuris Ltd., Newcastle upon Tyne, NE2 4HH, United Kingdom of Great Britain and Northern Ireland
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/ Jennifer S. Hallinan
  • Corresponding author
  • School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2013-224

Summary

BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 SNPs with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that BacillOndex is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism.

About the article

Published Online: 2016-10-18

Published in Print: 2013-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 10, Issue 2, Pages 103–116, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2013-224.

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© 2013 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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[2]
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ACS Synthetic Biology, 2018
[3]
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