Data integration in microbial genomics ... - Jacobs University

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50 3. CDinFusion able separately and is also released under the GNU LGPL 3 license. It may also be used for other projects. If only one sequence is detected in the FASTA upload, the control flow will be directed towards the 2a GSC SELECTED 1to1 JSP (use case 1 in the Results section), shown in Figure 3. If the user opts to annotate all sequences of a MultiFASTA file (Figure 3.4) with either one CD set or many CD sets, the control flow will be directed either to the 3b CD INPUT 1tom JSP (use case 2 in the Results section) or to the 3b1 CD INPUT ntom JSP (use case 3 in the Results section), respectively. After the CD have been entered into the web forms, these data may be downloaded as comma separated value (CSV) files. The CSV files may serve as local backups and can be edited off-line and uploaded to CDinFusion to re-populate the web forms. Each session concludes with a confirmation step, where users can revisit any previous step and correct CD input if necessary. This holds true for all three branches of the workflow (Figure 3.3 and 3.4). If the user chooses to proceed to the file download, a CD FASTA file and a structured comment file are generated and can, depending on their size, either be imported to Sequin or merged on the command line using tbl2asn (http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2.html, accessed: 30.03.2011) before submission. Implementation of the GSC checklists in CDinFusion Once the user has uploaded a MultiFASTA file and its contents have been validated, the data is processed along the data model shown in Figure 3.5. For each CD set a CDElement is created that contains an object for a “type of report” and an object for an “environmental package”. These Java classes were auto-generated from the relations in the PostgreSQL GSC database using the Ibator tool from the iBatis project (http://ibatis.apache.org). The GSC database is hosted and maintained at the Max Planck Institute for Marine Microbiology, Bremen, Germany. The Java classes cover the MIGS, MIMS and MIMARKS (MIxS) specifications. The GSC plans to refine these standards annually. With every new version of the standards the Java classes can easily be updated using the Ibator tool. The short names of the parameters are resolved using a web service
3.4. Design and Implementation 51 that was developed within the frame of this project. The web service offers details about all GSC parameters stored in the GSC database. Web forms (see Figure 3.2) are dynamically rendered during runtime and therefore always contain the latest information including all definitions and descriptions of the GSC checklists parameters. If a user wants to know how a certain GSC parameter is specified, the “more info” link opens a window with information about the full name of the parameter, its definition, the expected value, the syntax and an example. This information is directly retrieved from the GSC database. For CDinFusion to be fully functional, there needs to be Internet access to the web service. If a certain type of report and environmental package has been selected, these parameters are cached. The next time these packages are selected the web forms are rebuild from cache without re-using the web service. Two Strings “first SequenceID” and “lastSequenceID” in the CDElement object store the range of the associated sequence identifiers for each CD set. The CDFastaHeader object contains those parameters that are covered by the web forms in addition to the GSC parameters that are later used to extend the FASTA header lines. Installation details There are two ways to install CDinFusion: 1) CDinFusion can be installed by downloading and deploying the pre-compiled web archive file (war) on an Apache Tomcat (version > 5.5.25). In this case the war file only has to be uploaded in the Tomcat manager. Afterwards the application can be accessed under http:///CDinFusion. This method is preferable if users do not want to compile the program from its source code. 2) CDinFusion can also be installed by downloading and compiling the source code and subsequently deploying the software on an Apache Tomcat web server (version > 5.5.25). To compile the code, the generic build.xml and build.properties files can be adjusted to local settings. If the standard settings in these files are not changed, the war file will be compiled into the CDinFusion root folder. The project can be compiled by executing the Apache ant build tasks, “deploy” or “deploywar”, respectively. The build.xml can additionally be configured to directly deploy the tool on an Apache Tomcat web server or to create the war file
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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
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 56 and 57: 48 3. CDinFusion AMD Opteron TM pro
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
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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
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Page 106 and 107: 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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