Design and Implementation of the first Generic Archive Storage Service for Research Data in Germany

Research data as the true valuable good in science must be saved and subsequently kept findable, accessible and reusable for reasons of proper scientific conduct for a time span of several years. However, managing long-term storage of research data is a burden for institutes and researchers. Because of the sheer size and the required retention time apt storage providers are hard to find. Aiming to solve this puzzle, the bwDataArchive project started development of a long-term research data archive that is reliable, cost effective and able store multiple petabytes of data. The hardware consists of data storage on magnetic tape, interfaced with disk caches and nodes for data movement and access. On the software side, the High Performance Storage System (HPSS) was chosen for its proven ability to reliably store huge amounts of data. However, the implementation of bwDataArchive is not dependant on HPSS. For authentication the bwDataArchive is integrated into the federated identity management for educational institutions in the State of Baden-Württemberg in Germany. The archive features data protection by means of a dual copy at two distinct locations on different tape technologies, data accessibility by common storage protocols, data retention assurance for more than ten years, data preservation with checksums, and data management capabilities supported by a flexible directory structure allowing sharing and publication. As of September 2019, the bwDataArchive holds over 9 PB and 90 million files and sees a constant increase in usage and users from many communities

Design and Implementation of the first Generic Archive Storage Service for Research Data in Germany

Research data as the true valuable good in science must be saved and subsequently kept findable, accessible and reusable for reasons of proper scientific conduct for a time span of several years. However, managing long-term storage of research data is a burden for institutes and researchers. Because of the sheer size and the required retention time apt storage providers are hard to find. Aiming to solve this puzzle, the bwDataArchive project started development of a long-term research data archive that is reliable, cost effective and able store multiple petabytes of data. The hardware consists of data storage on magnetic tape, interfaced with disk caches and nodes for data movement and access. On the software side, the High Performance Storage System (HPSS) was chosen for its proven ability to reliably store huge amounts of data. However, the implementation of bwDataArchive is not dependant on HPSS. For authentication the bwDataArchive is integrated into the federated identity management for educational institutions in the State of Baden-Württemberg in Germany. The archive features data protection by means of a dual copy at two distinct locations on different tape technologies, data accessibility by common storage protocols, data retention assurance for more than ten years, data preservation with checksums, and data management capabilities supported by a flexible directory structure allowing sharing and publication. As of September 2019, the bwDataArchive holds over 9 PB and 90 million files and sees a constant increase in usage and users from many communities

D7.3: Report on the validation statistics, operational infrastructure services and recommendations for future integration work

This document describes the methodology adopted to assess the maturity level of services from the service delivery perspective and the outcome of our analysis of 17 services provided by EOSC-Pillar. Our approach to assess the maturity of the services delivered in EOSC-Pillar is to require each service provider to fill a checklist template with all the defined requirements to be considered in order to deliver a good service and meet the customer’s satisfaction.The maturity model assessment tool of the EOSC-Nordic regional project was used as a starting point. We added data repository requirements specific to data repository owners or managers who are offering data repository as a service. We also introduced a specific score taking only into account the positive answers to requirements considered as mandatory. As a result, our evaluation framework consists of 44 requirements regarding service management, data repository, accessibility and legal requirements, sustainability and EOSC architecture compatibility. Our assessment tool was tested on 17 services currently provided by EOSC-Pillar partners, classified as 8 thematic services, 5 research data management services and 4 generic (common) services. Our analysis indicates that the services achieve an overall average (64,67%) level compliance to the service delivery requirements. Hence, they already comply with most of the EOSC on-boarding validation criteria and are ready to serve a broader range of users

Deutschland in der European Open Science Cloud

Schlagwörter wie Open Access, Open Data und Open Science beschäftigen bereits seit einigen Jahren die Wissenschaftswelt im Zeitalter der Digitalisierung. Forschungsdatenmanagement (FDM) und die European Open Science Cloud (EOSC) sind dabei zuletzt die Hauptstoßrichtungen. In der folgenden Abhandlung wird auf den aktuellen Stand von „Deutschland in der EOSC“ zum Zeitpunkt Ende 2019/Anfang 2020 eingegangen; ohne jedoch einen Anspruch auf Vollständigkeit zu stellen. Nach einer Einführung in die Entstehungsgeschichte der EOSC werden die relevanten Initiativen und Projekte beschrieben, in denen Institutionen aus Deutschland beteiligt sind. Alsdann folgen Beschreibungen ausgewählter nationaler Initiativen, die einen Bezug zur EOSC aufweisen, sowie Ausführungen zu technischen Aspekten wie auch zu Beiträgen aus den verschiedenen Wissenschaftsdisziplinen

Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining α-l-Arabinofuranosidases

Identifying and characterizing the enzymes responsible for an observed activity within a complex eukaryotic catabolic system remains one of the most significant challenges in the study of biomass-degrading systems. The debranching of both complex hemicellulosic and pectinaceous polysaccharides requires the production of α-l-arabinofuranosidases among a wide variety of coexpressed carbohydrate-active enzymes. To selectively detect and identify α-l-arabinofuranosidases produced by fungi grown on complex biomass, potential covalent inhibitors and probes which mimic α-l-arabinofuranosides were sought. The conformational free energy landscapes of free α-l-arabinofuranose and several rationally designed covalent α-l-arabinofuranosidase inhibitors were analyzed. A synthetic route to these inhibitors was subsequently developed based on a key Wittig-Still rearrangement. Through a combination of kinetic measurements, intact mass spectrometry, and structural experiments, the designed inhibitors were shown to efficiently label the catalytic nucleophiles of retaining GH51 and GH54 α-l-arabinofuranosidases. Activity-based probes elaborated from an inhibitor with an aziridine warhead were applied to the identification and characterization of α-l-arabinofuranosidases within the secretome of A. niger grown on arabinan. This method was extended to the detection and identification of α-l-arabinofuranosidases produced by eight biomass-degrading basidiomycete fungi grown on complex biomass. The broad applicability of the cyclophellitol-derived activity-based probes and inhibitors presented here make them a valuable new tool in the characterization of complex eukaryotic carbohydrate-degrading systems and in the high-throughput discovery of α-l-arabinofuranosidases

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.</p

Status Report of the DPHEP Study Group: Towards a Global Effort for Sustainable Data Preservation in High Energy Physics

Data from high-energy physics (HEP) experiments are collected with significant financial and human effort and are mostly unique. An inter-experimental study group on HEP data preservation and long-term analysis was convened as a panel of the International Committee for Future Accelerators (ICFA). The group was formed by large collider-based experiments and investigated the technical and organisational aspects of HEP data preservation. An intermediate report was released in November 2009 addressing the general issues of data preservation in HEP. This paper includes and extends the intermediate report. It provides an analysis of the research case for data preservation and a detailed description of the various projects at experiment, laboratory and international levels. In addition, the paper provides a concrete proposal for an international organisation in charge of the data management and policies in high-energy physics

Correction:How the COVID-19 pandemic highlights the necessity of animal research (vol 30, pg R1014, 2020)

(Current Biology 30, R1014–R1018; September 21, 2020) As a result of an author oversight in the originally published version of this article, a number of errors were introduced in the author list and affiliations. First, the middle initials were omitted from the names of several authors. Second, the surname of Dr. van Dam was mistakenly written as “Dam.” Third, the first name of author Bernhard Englitz was misspelled as “Bernard” and the surname of author B.J.A. Pollux was misspelled as “Pullox.” Finally, Dr. Keijer's first name was abbreviated rather than written in full. These errors, as well as various errors in the author affiliations, have now been corrected online

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog