trackswitch.js: A Versatile Web-Based Audio Player for Presenting Scientific Results

trackswitch.js is a versatile web-based audio player that enables researchers to conveniently present examples and results from scientific audio processing applications. Based on a multitrack architecture, trackswitch.js allows a listener to seamlessly switch between multiple audio tracks, while synchronously indicating the playback position within images associated to the audio tracks. These images may correspond to feature representations such as spectrograms or to visualizations of annotations such as structural boundaries or musical note information. The provided switching and playback functionalities are simple yet useful tools for analyzing, navigating, understanding, and evaluating results obtained from audio processing algorithms. Furthermore, trackswitch.js is an easily extendible and manageable software tool, designed for non-expert developers and unexperienced users. Offering a small but useful selection of options and buttons, trackswitch.js requires only basic knowledge to implement a versatile range of components for web-based audio demonstrators and user interfaces. Besides introducing the underlying techniques and the main functionalities of trackswitch.js we provide several use cases that indicate the flexibility and usability of our software for different audio- related research areas

Barcoding Fauna Bavarica – Capturing Central European Animal Diversity

The Barcoding Fauna Bavarica (BFB) is an All Species Barcoding campaign ran by the Zoologische Staatssammlung in Munich and the Canadian Centre for DNA Barcoding (www. faunabavarica.de). Core funding comes from the Bavarian Ministry for Science, Research and the Arts and from Genome Canada through the Ontario Genomics Institute. The initial funding period is from 2009–2013. Bavaria has the highest biodiversity of all German states, with at least 35000 animal species reported, representing a significant portion of the central European species diversity. Ecoregions include high altitude biomes, foothill areas and forested lowlands. The Zoologische Staatssammlung (ZSM) is one of the largest German natural history research institutions. It holds the world’s largest collection of Lepidoptera and Germany’s largest Hymenoptera collection. Since mid-2009, the BFB project has contributed DNA barcode records from 7208 specimens representing 3000 species and is therefore, after less than one year, one of the most comprehensive sources for local DNA barcode data. The focus groups for the initial phase were Lepidoptera (1820 species barcoded), bees (316 species), ants (39 species) and aquatic insects (322 species). Work on these focal groups will continue during 2010, with the goal to complete 80% of the Bavarian focal group species by the end of the year. New focal groups are Diptera, Mollusca, all Vertebrata and terrestrial Coleoptera, targeting 2000 species in 2010. Most tissue samples come from specimens in the ZSM collection, and where this was not feasible from freshly collected and identified specimens. This rapid progress reflects the strong involvement of taxonomists throughout the process, which is one of our key missions. We have implemented a system which co-ordinates vouchers stored in our main collection, with tissues as well as DNA samples in our DNA bank

DiversityScanner: Robotic handling of small invertebrates with machine learning methods

Invertebrate biodiversity remains poorly understood although it comprises much of the terrestrial animal biomass, most species and supplies many ecosystem services. The main obstacle is specimen-rich samples obtained with quantitative sampling techniques (e.g., Malaise trapping). Traditional sorting requires manual handling, while molecular techniques based on metabarcoding lose the association between individual specimens and sequences and thus struggle with obtaining precise abundance information. Here we present a sorting robot that prepares specimens from bulk samples for barcoding. It detects, images and measures individual specimens from a sample and then moves them into the wells of a 96-well microplate. We show that the images can be used to train convolutional neural networks (CNNs) that are capable of assigning the specimens to 14 insect taxa (usually families) that are particularly common in Malaise trap samples. The average assignment precision for all taxa is 91.4% (75%–100%). This ability of the robot to identify common taxa then allows for taxon-specific subsampling, because the robot can be instructed to only pick a prespecified number of specimens for abundant taxa. To obtain biomass information, the images are also used to measure specimen length and estimate body volume. We outline how the DiversityScanner can be a key component for tackling and monitoring invertebrate diversity by combining molecular and morphological tools: the images generated by the robot become training images for machine learning once they are labelled with taxonomic information from DNA barcodes. We suggest that a combination of automation, machine learning and DNA barcoding has the potential to tackle invertebrate diversity at an unprecedented scale

INDOBIOSYS – DNA BARCODING AS A TOOL FOR THE RAPID ASSESSMENT OF HYPERDIVERSE INSECT TAXA IN INDONESIA: A STATUS REPORT

A status report with preliminary results for the IndoBioSys project is presented and the impact of the project results for our knowledge of the Indonesian fauna is discussed. Using the REST API available on the Barcode of Life Data System we recover 21,153 public records (3,390 BINs) from Indonesia and compare against the 21,813 records (3,580 BINs) generated by the IndoBioSys project. From all IndoBioSys BINs, 3,366 (94%) are new to Indonesia. IndoBioSys is responsible for a BIN increase of 36.5% in Lepidoptera, 62.6% in Trichoptera, 986% in Coleoptera, and 1,086% in Hymenoptera. After two years of the IndoBioSys project, the Museum Zoologicum Bogoriense became the depository institution of 51.9% of Lepidoptera records, 95.8% of Coleoptera records, 97.6% of Hymenoptera records and 59.4% of Trichoptera records for Indonesia available on Barcode of Life Data System (BOLD). Now, with 55% of all Indonesian records available on BOLD, it is the most important depository for records of Indonesian genetic biodiversity, housing more than 23,000 new voucher specimens in their collections. Before IndoBioSys, the Museum Zoologicum Bogoriense was responsible for only 9% of all records available in the Barcode of Life Data System for Indonesia, showing the importance of those pipelines in empowering the local institutions in becoming the reference depository of the local fauna

Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix

The German Barcoding initiatives BFB and GBOL have generated a reference library of more than 16,000 metazoan species, which is now ready for applications concerning next generation molecular biodiversity assessments. To streamline the barcoding process, we have developed a meta-barcoding pipeline: We pre-sorted a single malaise trap sample (obtained during one week in August 2014, southern Germany) into 12 arthropod orders and extracted DNA from pooled individuals of each order separately, in order to facilitate DNA extraction and avoid time consuming single specimen selection. Aliquots of each ordinal-level DNA extract were combined to roughly simulate a DNA extract from a non-sorted malaise sample. Each DNA extract was amplified using four primer sets targeting the CO1-5' fragment. The resulting PCR products (150-400bp) were sequenced separately on an Illumina Mi-SEQ platform, resulting in 1.5 million sequences and 5,500 clusters (coverage >10;CD-HIT-EST, 98%). Using a total of 120,000 DNA barcodes of identified, Central European Hymenoptera, Coleoptera, Diptera, and Lepidoptera downloaded from BOLD we established a reference sequence database for a local CUSTOM BLAST. This allowed us to identify 529 Barcode Index Numbers (BINs) from our sequence clusters derived from pooled Malaise trap samples. We introduce a scoring matrix based on the sequence match percentages of each amplicon in order to gain plausibility for each detected BIN, leading to 390 high score BINs in the sorted samples;whereas 268 of these high score BINs (69%) could be identified in the combined sample. The results indicate that a time consuming pre-sorting process will yield approximately 30% more high score BINs compared to the nonsorted sample in our case. These promising results indicate that a fast, efficient and reliable analysis of next generation data from malaise trap samples can be achieved using this pipeline

PubPharm - Der Fachinformationsdienst Pharmazie

Der Fachinformationsdienst (FID) Pharmazie verfolgt das Ziel, die Informationsinfrastruktur und die Literaturversorgung für die pharmazeutische Hochschulforschung nachhaltig zu verbessern. Das Projekt wird seit dem 1. Januar 2015 von der Deutschen Forschungsgemeinschaft gefördert. Eine Besonderheit stellt die Kooperation zwischen der Universitätsbibliothek Braunschweig und dem Institut für Informationssysteme (IfIS) der TU Braunschweig dar, wodurch aktuelle Forschung auf dem Gebiet der Informatik in die Implementierung innovativer FID-Dienste mündet. Im Zentrum des Projektes steht der nutzerzentrierte Aufbau einer erweiterbaren und personalisierbaren Informationsinfrastruktur. Das vom FID entwickelte Discovery System „PubPharm“ zur pharmaziespezifischen Recherche basiert, als Weiterentwicklung des beluga-Systems der SUB Hamburg, auf der Open Source Software VuFind. Als Datengrundlage enthält es u.a. die Medline Daten, erweitert durch Normdaten, die unter anderem die Suche nach chemischen Strukturen erlauben. Gleichzeitig werden vom Institut für Informationssysteme innovative Suchmöglichkeiten basierend auf Narrativer Intelligenz untersucht und perspektivisch in das Retrieval des Discovery Systems eingebunden. Im Rahmen von sog. FID-Lizenzen bietet der FID Pharmazie Wissenschaftlern/innen Volltextzugriff auf pharmazeutische Fachzeitschriften. Bestandteil der Lizenzen ist das Recht zur Langzeitarchivierung. Bei deren technischer Umsetzung kooperiert der FID mit der TIB Hannover. Der FID Pharmazie koppelt seine Aktivitäten eng an die pharmazeutische Fachcommunity: unter anderem begleitet ein Fachbeirat die Entwicklungen. Im Rahmen der Öffentlichkeitsarbeit werden Nutzer/innen umfassend über die Angebote informiert, u.a. in Webcasts und im PubPharm Blog.The Specialised Information Service (SIS) Pharmacy aims at sustainably improving the information infrastructure and the supply of literature for academic pharmaceutical research in Germany. The project is being funded by the German Research Foundation since January 1st 2015. A special feature of the project is the collaboration between Braunschweig University Library and the Institute for Information Systems (IfIS) at Braunschweig University, through which cutting edge informatics research is being incorporated into SIS services. A core aspect is the user-centric implementation of an extensible and customizable information infrastructure. The “PubPharm” discovery system, developed by SIS Pharmacy for pharmacy-specific literature search, is an extension of the beluga-System (SUB Hamburg) which is based on the open source software VuFind. Its database comprises, amongst other sources, Medline data, and also authority data which enables specialised searches, e.g. for chemical structures. At the same time the IfIS is evaluating innovative search functions which, if proving to be beneficial, will be incorporated into the retrieval mechanisms of the discovery system. Within the scope of the SIS licenses, full text access to pharmaceutical journals is being provided to scientists. Part of the licenses is the right to long-term preservation. For technical implementation SIS Pharmacy is cooperating with the TIB Hanover. SIS Pharmacy liaises closely with the pharmaceutical research community, e.g. an advisory board is involved in steering the development of services. As part of public relations, users are being comprehensively informed, e.g. by web casts and the PubPharm blog

DNA barcoding data release for Coleoptera from the Gunung Halimun canopy fogging workpackage of the Indonesian Biodiversity Information System (IndoBioSys) project

We present the results of a DNA barcoding pipeline that was established as part of the German-Indonesian IndobioSys project - Indonesian Biodiversity Information System. Our data release provides the first large-scale diversity assessment of Indonesian coleoptera obtained by canopy fogging. The project combined extensive fieldwork with databasing, DNA barcode based species delineation and the release of results in collaboration with Indonesian counterparts, aimed at supporting further analyses of the data. Canopy fogging on 28 trees was undertaken at two different sites, Cikaniki and Gunung Botol, in the south-eastern area of the Gunung Halimun-Salak National Park in West Java, Indonesia. In total, 7,447 specimens of Coleoptera were processed, of which 3,836 specimens produced DNA barcode sequences that were longer than 300 bp. A total of 3,750 specimens were assigned a Barcode Index Number (BIN), including 2,013 specimens from Cikaniki and 1,737 specimens from Gunung Botol. The 747 BINs, that were obtained, represented 39 families of Coleoptera. The distribution of specimens with BINs per tree was quite heterogeneous in both sites even in terms of the abundance of specimens or diversity of BINs. The specimen distribution per taxon was heterogeneous as well. Some 416 specimens could not be identified to family level, corresponding to 72 BINs that lack a family level identification. The data have shown a large heterogeneity in terms of abundance and distribution of BINs between sites, trees and families of Coleoptera. From the total of 747 BINs that were recovered, 421 (56%) are exclusive from a single tree. Although the two study sites were in close proximity and separated by a distance of only about five kilometres, the number of shared BINs between sites is low, with 81 of the 747 BINs. With this data release, we expect to shed some light on the largely hidden diversity in the canopy of tropical forests in Indonesia and elsewhere

Site‐selective substitution and resulting magnetism in arc‐melted perovskite ATiO₃₋δ (A = Ca, Sr, Ba)

Magnetic properties in perovskite titanates ATiO₃₋δ (A = Ca, Sr, Ba) were investigated before and after arc melting. Crystal structure analysis was conducted by powder synchrotron X‐ray diffraction with Rietveld refinements. Quantitative chemical element analysis was carried out by X‐ray photoelectron spectroscopy. Magnetic measurements were conducted by vibrating sample magnetometer and X‐ray magnetic circular dichroism (XMCD). The magnetic properties are found to be affected by impurities of 3d elements such as Fe, Co, and Ni. Depending on the composition and crystal structure, the occupation of the magnetic ions in perovskite titanates is selectively varied, which is interpreted to be the origin of the different magnetic behaviors in arc‐melted perovskite titanates ATiO₃₋δ (A = Ca, Sr, Ba). In addition, both formation of oxygen vacancies and the reduction of Ti⁴⁺ to Ti³⁺ during arc‐melting also play a role as proven by XMCD. Nevertheless, preferential site occupation of magnetic impurities is dominant in the magnetic properties of arc‐melted perovskite ATiO₃₋δ (A = Ca, Sr, Ba)