Data integration in microbial genomics ... - Jacobs University

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48 3. CDinFusion AMD Opteron TM processor 246, with 4 GB main memory and Debian GNU/Linux 5.0.3 (lenny). Figure 3.3: CDinFusion implementation details along the workflow 1, when a single sequence is submitted to the INSDC. CDinFusion implements the Model-View-Controller design pattern. Classes implementing the data model and its manipulation methods are shown in blue, components belonging to the web user interface (view) are shown in white and components directing the workflow (control) are shown in green. Figures 3.3 and 3.4 show the implementation details of the software’s workflow. FASTA files are parsed and validated, when uploaded by the FastaReader class. It implements the FastaValidatorCallback interface
3.4. Design and Implementation 49 Figure 3.4: CDinFusion implementation details along the workflows 2 and 3 covering the primary scenarios of sequence data submission to the INSDC are shown. CDinFusion implements the Model-View-Controller design pattern. Classes implementing the data model and its manipulation methods are shown in blue, components belonging to the web user interface (view) are shown in white and components directing the workflow (control) are shown in green. of the FastaValidator package (http://www.megx.net/FastaValidator), which has been developed within the frame of this project. This eventdriven parser is designed to quickly parse and validate arbitrarily large FASTA files with minimal time and memory requirements. It facilitates the processing of gigabases of FASTA files containing millions of sequences on common desktop PC architectures. The parser is avail-
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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
Page 12 and 13: 4 1. Introduction used to derive ne
Page 14 and 15: 6 1. Introduction croorganisms thri
Page 16 and 17: 8 1. Introduction the middle at the
Page 18 and 19: 10 1. Introduction marker genes hel
Page 20 and 21: 12 1. Introduction what kind and wh
Page 22 and 23: 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
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
Page 43 and 44: 2.6. Conclusion 35 rine Microbiolog
Page 45: 2.6. Conclusion 37 RK advised progr
Page 48 and 49: 40 3. CDinFusion Genomic Standards
Page 50 and 51: 42 3. CDinFusion sortium (GSC), an
Page 52 and 53: 44 3. CDinFusion tiFASTA file with
Page 54 and 55: 46 3. CDinFusion offered the option
Page 58 and 59: 50 3. CDinFusion able separately an
Page 60 and 61: 52 3. CDinFusion and upload it with
Page 63 and 64: CHAPTER 4 MIMARKS The Minimum infor
Page 65 and 66: 4.2. Introduction 57 edge generatio
Page 67 and 68: 4.3. Development of MIMARKS 59 in t
Page 69 and 70: 4.4. Survey of published parameters
Page 71 and 72: 4.5. The MIMARKS checklist 63 Resul
Page 73 and 74: 4.6. Conclusions and call for actio
Page 75 and 76: CHAPTER 5 MEGX.NET Integrated datab
Page 77 and 78: 5.3. New database structure and con
Page 79 and 80: 5.3. New database structure and con
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
Page 85: 5.5. Summary 77 access charge: Max
Page 88 and 89: 80 6. Domains of unknown function 6
Page 90 and 91: 82 6. Domains of unknown function F
Page 92 and 93: 84 6. Domains of unknown function p
Page 95 and 96: CHAPTER 7 SUMMARY AND DISCUSSION Th
Page 97 and 98: 7.2. GSC standards development 89 T
Page 99 and 100: 7.2. GSC standards development 91 o
Page 101 and 102: 7.4. In silico Hypothesis Generatio
Page 103: 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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Data integration in microbial genomics ... - Jacobs University

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