Data integration in microbial genomics ... - Jacobs University

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52 3. CDinFusion and upload it with the Tomcat manager. Further installation details can be found in the README.txt file that is included in the source bundle and that is also available in the documentation section of the CDinFusion web page. On some platforms the CATALINA HOME environment variable needs to be set, in order for CDinFusion to write and read files. Relative to the path specified, CDinFusion will create a “data” folder, where temporary files will be saved. The application has been tested on Debian GNU Linux installations, but should be platform-independent and run on all platforms that support Java and Apache Tomcat installation such as Windows TM or MAC OS TM . Availability and Future Directions The public installation of CDinFusion is hosted and maintained at the Microbial Genomics and Bioinformatics Group (MGG) of the Max Planck Institute of Marine Microbiology Bremen and accessible under: http://www.megx.net/cdinfusion. The source code is available under GNU LGPL 3 and deposited in a public repository: http: //code.google.com/p/cdinfusion. As open source software it is the intention of the MGG to support this software well into the future. Currently CDinFusion supports submission of CD enriched sequence data to the INSDC using Sequin and tbl2asn for large data sets. Support for installations outside the MPI cannot be granted. The direct submission to EMBL/ENA and DDBJ is planned. Furthermore the integration of GCDML [Kottmann et al., 2008] as an exchange format would be advantageous. The GSC and life science community is encouraged to download the source code and to modify and extend the software to make it even more useful. Acknowledgments Thanks to S. Emil Ruff and the Geotechnologien project COMET/MUMM II (03G0608A, BMBF) for providing unpublished data and for the beta-testing. Thanks to Michael Richter for genome data and beta-testing. Thanks to Rudolf Amann, Bernhard Fuchs and Hanno Teeling for the MIMAS data. Thanks to Jens Harder, Richard Hahnke and the M.Sc. Marine Microbiology (MarMic) class of 2014 for data and beta-testing.
3.4. Design and Implementation 53 Figure 3.5: Data model. The central Java class is the CDElement class, which is a composition of of the classes “report type” and “environmental package”. These classes implement the MIGS, MIMS and MIMARKS (MIxS) checklists specified by the GSC. The two strings “firstSequenceID” and “lastSequenceID” define if the CDElement contains CD for a single or a range of sequences. Instances of the CDFastaHeader class contain the data that is generated into the FASTA headers in the FASTA file.
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Max Planck Institute for Marine Mic
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Thesis abstract Deoxyribonucleic ac
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4.2 Introduction . . . . . . . . .
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CHAPTER 9 ACKNOWLEDGEMENTS First, I
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Data integration in microbial genomics ... - Jacobs University

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