Data integration in microbial genomics ... - Jacobs University

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66 4. MIMARKS Note: Supplementary information is available on the Nature Biotechnology website. Funding sources are listed in the Supplementary Note. Competing financial interests The authors declare no competing financial interests. Published online at http://www.nature.com/nbt/index.html. Reprints and permissions information is available online at http:// www.nature.com/reprints/index.html.
CHAPTER 5 MEGX.NET Integrated database resource for marine ecological genomics Authors: Renzo Kottmann, Ivaylo Kostadinov, Melissa Beth Duhaime, Pier Luigi Buttigieg, Pelin Yilmaz, Wolfgang Hankeln, Frank Oliver Glöckner Published in: Nucleic Acids Research, October 2010 Personal Contribution: Involvement in the web portal design and programming, bug fixing and improvement of the environmental data layers in the Genes Mapserver (with Renzo Kottmann, Ivaylo Kostadinov, Pier Luigi Buttigieg, Pelin Yilmaz). Relevance: To enhance the core megx.net concept to the research platform of the Microbial Genomics Group at Max Planck Institute for Marine Microbiology. 5.1 Abstract Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. The extended system provides access to several hundreds of genomes and metagenomes from prokaryotes and phages, as well as over a million small and large subunit ribosomal RNA sequences. With the refined Genes Mapserver, all data can be interactively visualized on a world map and statistics describing envi-
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Max Planck Institute for Marine Mic
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List of abbreviations BLAST Basic L
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Thesis abstract Deoxyribonucleic ac
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4.2 Introduction . . . . . . . . .
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2 1. Introduction syntax: data leve
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4 1. Introduction used to derive ne
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6 1. Introduction croorganisms thri
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8 1. Introduction the middle at the
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10 1. Introduction marker genes hel
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12 1. Introduction what kind and wh
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14 1. Introduction possibilities li
Page 24 and 25: 16 1. Introduction tual data acquis
Page 26 and 27: 18 1. Introduction Doug Wendel, Owe
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Page 31 and 32: 2.2. Background 23 molecular sequen
Page 33 and 34: 2.2. Background 25 printing of data
Page 35 and 36: 2.4. Results 27 KML export function
Page 37 and 38: 2.4. Results 29 Figure 2.3: Screens
Page 39 and 40: 2.5. Discussion 31 taking samples i
Page 41 and 42: 2.5. Discussion 33 Handlebar MetaBa
Page 43 and 44: 2.6. Conclusion 35 rine Microbiolog
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Page 54 and 55: 46 3. CDinFusion offered the option
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Page 65 and 66: 4.2. Introduction 57 edge generatio
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Page 71 and 72: 4.5. The MIMARKS checklist 63 Resul
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Page 81 and 82: 5.4. User Access 73 5.4 User Access
Page 83 and 84: 5.4. User Access 75 tal context, co
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Page 97 and 98: 7.2. GSC standards development 89 T
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Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
Page 112 and 113: 104 BIBLIOGRAPHY oceanic regions by
Page 114 and 115: 106 BIBLIOGRAPHY [Giovannoni et al.
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Page 118 and 119: 110 BIBLIOGRAPHY pathways in marine
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Page 122 and 123: 114 BIBLIOGRAPHY (2006). Microbial
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116 BIBLIOGRAPHY [Williamson et al.
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CHAPTER 9 ACKNOWLEDGEMENTS First, I
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