Science Data Center BioDATEN as part of the NFDI process

Published on Tuesday, 20 August 2019

Together with colleagues from Tübingen, Konstanz, Freiburg, Heidelberg, ... parts of the BioDATEN community joined forces with the DaPLUS+ consortium from Kaiserlautern, Jülich and Düsseldorf to paticipate in the process to create a National Research Data Infrastructure. The newly formed consortium centers around plant data in bioinformatics and handed in a binding "Letter of Interest".

In modern hypothesis-driven science, researchers increasingly rely on effective research data management services and infrastructures that facilitate the acquisition, processing, exchange and archival of research data sets, to enable the linking of interdisciplinary expertise and the combination of different analytical results. The immense additional insight obtained through comparative and integrative analyses provides additional value in the examination of research questions that goes far beyond individual experiments. Specifically, in the research area of fundamental plant research that this consortium focuses on, modern approaches need to integrate analyses across different system levels (such as genomics, transcriptomics, proteomics, metabolomics, phenomics). This is necessary to understand system-wide molecular physiological responses as a complex dynamic adjustment of the interplay between genes, proteins and metabolites. As a consequence, a wide range of different technologies as well as experimental and computational methods are employed to pursue state-of-the-art research questions, rendering the research objective a team effort across disciplines. The overall goal of DataPLANT is to provide the research data management practices, tools, and infrastructure to enable such collaborative research in plant biology. In this context, common standards, software, and infrastructure can ensure availability, quality, and interoperability of data, metadata, and data-centric workflows and are thus a key success factor and crucial precondition in barrier-free, high-impact collaborative plant biology research. Toward this, the key objectives pursued by this consortium are:

1. A specific community standard for fundamental plant research (meta)data and workflow annotation, based on generic, existing and emerging standards (e.g., ISA model, MIAPPE) and ontologies in plant science.
2. Assistive mechanisms and services to build, link and maintain the complete research context during data acquisition, curation, analysis, and publication.
3. Mechanisms for collaborative research based on enrichment and automatized crosslinking of plant-research specific (meta)data to facilitate research context management.
4. A cloud-based open reference implementation of these mechanisms and services, and a central hosted instance thereof.
5. A robust, federated infrastructure both for data computation and management covering the complete data lifecycle.
6. Comprehensive training of community members through workshops and summer schools and providing open training material.

The final grant application is due to the 15th October.

Science Data Center "BioDATEN" at GCC 2019 conference in Freiburg

Published on Thursday, 04 July 2019

The just started Science Data Center "BioDATEN" was present at this year's Galaxy conference in Freiburg, the GCC 2019. The Science Data Center BioDATEN - Bioinformatics DATa ENvironment is a community effort in standardization, services and sustainable research data management. It plans to combine the tools and services provided in frameworks like Galaxy with efforts towards standardization and research data management.

The digitalization changes the working habits in almost all scientific disciplines with vast impact on teaching, research and interdisciplinary collaboration. The challenges faced in bioinformatics arising from vastly growing amounts of data are exemplary for a discipline establishing new ways of scientific work and insight. Galaxy as a platform already provides a wide range of tools used by a significant proportion of the community presented in BioDATEN. Through the formed consortium, comprising of bioinformaticians, core facilities, compute centers and libraries, a science data center for life sciences for Baden-Württemberg just got established. The four-year project will report about the anticipated goals and the work plan intended to achieve them in the relevant communities.

BioDATEN will heavily depend on the technical infrastructure available through Galaxy and the project partners such as bwSFS, BinAC and bwCloud or the repositories provided by the university libraries in Konstanz and Tübingen. State-wide activities will be orchestrated through the work group on research data management. The SDC creates a multi institutional network among the strongest bioinformatics research sites. The consortium brings together the compute centers of the universities of Freiburg and Tübingen; the DKFZ, the EMBL and the university (BioQuant) in Heidelberg; the university libraries of Konstanz and Tübingen; the Quantitative Biology Center Tübingen; Bioinformatics and Plant Biotechnology Freiburg; CLARIN-D Center Tübingen; Livestock Microbial Ecology Hohenheim; Disease Ecology and Evolutionary Genetics Konstanz; Clinic of Neurology Ulm.

The project within the third line of the eScience initiative of the state - the BioDATEN SCD is funded by the Ministry of Science, Research and the Arts Baden-Württemberg - got acquired and is handled by the eScience group of the computer center. It is part of the RDMG activities. The conference poster at GCC 2019 is one of it's first activities.

Positive appraisal for Science Data Center "BioDATEN"

Published on Wednesday, 27 March 2019

The request for SDC BioDATEN, which was handed in together with various partners from Tubingen, Konstanz, Heidelberg and many others, has received a funding recommendation. The project is planned to start by the middle of the year and will run as part of the third eScience funding line by the department for science, research and culture in Baden-Wurttemberg. The project complements the efforts for virtualized research environments (ViCE), bwSFS and the bwHPC-S5 activites, with the objective of establishing long-term infrastructures for a qualified research data management in the field of bioinformatics.

The consortium that applied for the funding includes data-using researchers from all life sciences as well as bioinformatic method developers and infrastructure providers. The members of the consortium are leaders in digital data-driven research in life sciences as well as in information scientific questions. Between some of the members, long-lasting bilateral cooperations already exist. These should now be transfered to a consortium. Discipline-specific and information scientific aspects of research data management have already been tackled in shared projects or are part of current cooperation taking place as part of the de.NBI and bwHPC on a national and ELIXIR and Galaxy on an international level.

The coordination in Freiburg is done by the eScience department at the University IT Services. The project will receive financing for four years as part of the third eScience funding line of the department of science, research and culture in Baden-Wurttemberg.