Data integration in microbial genomics ... - Jacobs University

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36 2. MetaBar Statistical analysis of phylogenetic and functional biodiversity in their environmental context will reveal new insights into the biogeography and habitat adaptation of organisms. In the medical field, for example, it will be possible to create detailed disease maps which reveal mutation patterns of a certain pathogenic organism over time [Janies et al., 2007,Schriml et al., 2010]. Such maps might help to predict the dispersal of epidemics and pandemics around the globe. For marine microbiology, Ed DeLong and coworkers have successfully shown that there is a stratification of genomic variability along the depth continuum in the water column at a specific sampling location [DeLong et al., 2006]. It has also been demonstrated that specific diversity patterns are annually recurring [Fuhrman et al., 2006]. A dense network of data points, enriched with contextual data, will lead to new insights into the complex interplay of organisms by comparing different sampling sites around the globe and over time. The denser this network of data points, the more will be revealed about the influence of the biotic factor in the elementary nutrient cycles that profoundly affect Earth’s climate. Availability and Requirements Software Project name: MetaBar Project homepage: http://www.megx.net/metabar Operating systems: Linux and Windows Programming language: Java JRE 1.5 or higher Other requirements: Microsoft R○ Excel R○ 2003 or higher, Google Earth R○ (optional) License: GNU General Public License version 3 (GNU GPL3) Hardware At least 1024 Mb of RAM EPL barcode printer (e.g. a Zebra TLP 2824) (optional) Barcode handscanner (optional) The software can be tested anonymously using the login: ”anonymous” with the password: ”testmetabar”. Authors’ contribution WH developed and implemented MetaBar and wrote the manuscript.
2.6. Conclusion 37 RK advised programming design and helped with the integration of MetaBar with MegDB and megx.net. DF tested the software on cruises and provided feedback for design improvements. PY assured the MIGS/MIMS/MIENS standard compliance in MetaBar. PLB critically revised the manuscript and took care of EnvO integration. PY, PLB and RK tested the tool in the field. FOG supervised the work and helped with writing the manuscript. All authors read and approved the final manuscript. Acknowledgments Thanks to Jens Harder, Christine Klockow, Mirja Meiners and all the testers. Thanks to Dawn Field and Tim Booth at NERC, UK for feedback and useful input during the design phase of MetaBar. Thanks to Norma Wendel for her help in finalizing the MetaBar source code. The study was supported by the Max Planck Society.
Page 1: Max Planck Institute for Marine Mic
Page 4 and 5: List of abbreviations BLAST Basic L
Page 6 and 7: Thesis abstract Deoxyribonucleic ac
Page 8 and 9: 4.2 Introduction . . . . . . . . .
Page 10 and 11: 2 1. Introduction syntax: data leve
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Page 24 and 25: 16 1. Introduction tual data acquis
Page 26 and 27: 18 1. Introduction Doug Wendel, Owe
Page 29 and 30: CHAPTER 2 METABAR A tool for consis
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
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Page 63 and 64: CHAPTER 4 MIMARKS The Minimum infor
Page 65 and 66: 4.2. Introduction 57 edge generatio
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Page 83 and 84: 5.4. User Access 75 tal context, co
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CHAPTER 7 SUMMARY AND DISCUSSION Th
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7.2. GSC standards development 89 T
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7.2. GSC standards development 91 o
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7.4. In silico Hypothesis Generatio
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7.5. Getting the most out of the da
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98 8. Conclusion and outlook nities
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100 8. Conclusion and outlook plina
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102 BIBLIOGRAPHY [Beynon-Davies, 20
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104 BIBLIOGRAPHY oceanic regions by
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106 BIBLIOGRAPHY [Giovannoni et al.
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108 BIBLIOGRAPHY [Kitano, 2002] Kit
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110 BIBLIOGRAPHY pathways in marine
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112 BIBLIOGRAPHY [Ramette, 2007] Ra
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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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