Featured projects (7)
GBOL is a national network of various natural history museums and other biodiversity research institutions in Germany. The GBOL partners provide their professional taxonomic expertise and existing infrastructure (collections / biobanks, databases, bioinformatics platforms and laboratories) to comprehensively collect, catalog, describe, and sequence the animal, plant and fungi species in Germany. While the focus in GBOL during the first phase (2012-2015) was laid on the creation of a reference database, we will now also develop different applications of DNA barcoding in the second project phase (2016-2018). Sequence and metadata generated in GBOL will be integrated in the global barcode reference database " BOLD ". www.bolgermany.de
Featured research (1)
Background: Today a variety of phylogenetic file formats exists, some of which are well-established but limited in their data model, while other more recently introduced ones offer advanced features for metadata representation. Although most currently available software only supports the classical formats with a limited metadata model, it would be desirable to have support for the more advanced formats. This is necessary for users to produce richly annotated data that can be efficiently reused and make underlying workflows easily reproducible. A programming library that abstracts over the data and metadata models of the different formats and allows supporting all of them in one step would significantly simplify the development of new and the extension of existing software to address the need for better metadata annotation. Results: We developed the Java library JPhyloIO, which allows event-based reading and writing of the most common alignment and tree/network formats. It allows full access to all features of the nine currently supported formats. By implementing a single JPhyloIO-based reader and writer, application developers can support all of these formats. Due to the event-based architecture, JPhyloIO can be combined with any application data structure, and is memory efficient for large datasets. JPhyloIO is distributed under LGPL. Detailed documentation and example applications (available on http://bioinfweb.info/JPhyloIO/) significantly lower the entry barrier for bioinformaticians who wish to benefit from JPhyloIO's features in their own software. Conclusion: JPhyloIO enables simplified development of new and extension of existing applications that support various standard formats simultaneously. This has the potential to improve interoperability between phylogenetic software tools and at the same time motivate usage of more recent metadata-rich formats such as NeXML or phyloXML.