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NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI)

Frank Oliver Glöckner, Michael Diepenbroek, Janine Felden, Anton Güntsch, Jens Stoye, Jörg Overmann, Klaus Wimmers, Ivaylo Kostadinov, Ramin Yahyapour, Wolfgang Müller, Uwe Scholz, Dagmar Triebel (+6 others)
2020 Zenodo  
23 use cases with community-driven topics and cross-domain user groups.  ...  The FAIR data principles provide a framework towards such integration.  ...  The German Network for Bioinformatics Infrastructure (de.NBI) community The German Network for Bioinformatics Infrastructure (de.NBI) [34] is a dynamic and distributed bioinformatics infrastructure, which  ... 
doi:10.5281/zenodo.3943644 fatcat:lltfs5w6y5hn3ixe5bw2sitoa4

DataPLANT - NFDI Consortium for Fundamental Plant Research

Dirk Von Suchodoletz, Björn Usadel, Jens Krüger, Timo Mühlhaus
2021 Zenodo  
The FAIR Data and Linked Open Data Principles provide critical guidelines for RDM.  ...  Therefore, comprehensive information on the required quality for use by third parties is rarely available.  ...  He is also operating the de.NBI Cloud Tübingen, a compute and storage environment for bioinformatics research as part of the German Network for Bioinformatics Infrastructure.  ... 
doi:10.5281/zenodo.4836394 fatcat:ru7a4tmlxbcetibyryofsdx52i

Digital services for science – where is the journey heading? [article]

Uwe Konrad, Konrad Förstner, Johannes Reetz, Klaus Wannemacher, Jürgen Kett, Florian Mannseicher
2021 Zenodo  
them fully available for use.  ...  used by stakeholders in research and science.  ...  One successful example is de.NBI (German Network for Bioinformatics Infrastructure) platform, which has been funded by the BMBF since 2013.  ... 
doi:10.5281/zenodo.4301946 fatcat:waha7fedmnbzfktd4jbftv7hse

NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany

Christoph Steinbeck, Oliver Koepler, Felix Bach, Sonja Herres-Pawlis, Nicole Jung, Johannes Liermann, Steffen Neumann, Matthias Razum, Carsten Baldauf, Frank Biedermann, Thomas Bocklitz, Franziska Boehm (+18 others)
2020 Research Ideas and Outcomes  
Key Objective 4: Engage with the chemistry community in Germany through a wide range of measures to create awareness for and foster the adoption of FAIR data management.  ...  Key Objective 3: Foster cultural and digital change towards Smart Laboratory Environments by promoting the use of digital tools in all stages of research and promote subsequent Research Data Management  ...  PhenoMeNal on computational metabolomics, is PI in the BMBF funded MASH which is part of the german Network of Bioinformatics infrastructures (de.NBI).  ... 
doi:10.3897/rio.6.e55852 fatcat:fvde2vhzyfc27ieavgkzjhxlaa

In silico design of ligand triggered RNA switches [article]

Sven Findeiß, Stefan Hammer, Michael T. T. Wolfinger, Felix Kuehnl, Christoph Flamm, Ivo L. Hofacker
2018 bioRxiv   pre-print
We exemplify the principles using the well known theophylline aptamer throughout this work.  ...  We elucidate a commonly used design process by explicitly dissecting and explaining the necessary steps in detail.  ...  Bioinformatics Infrastructure (de.NBI) by the German Federal Ministry of Education and Research (BMBF; support code 031A538B), and by the German Research Foundation (DFG; grant STA 850/15-2) The frequency  ... 
doi:10.1101/245464 fatcat:kq7e4xgswnfpdlaypyxmo5zcdu

Proceedings of the 5th bwHPC Symposium [article]

Michael Janczyk, Dirk Von Suchodoletz, Bernd Wiebelt, University, My, University, My
Additionally, the symposium served as a platform for discussing and exchanging ideas concerning the use of these large scientific infrastructures as well as its further development.  ...  In modern science, the demand for more powerful and integrated research infrastructures is growing constantly to address computational challenges in data analysis, modeling and simulation.  ...  Lode for their help regarding the implementation of the SGF algorithm and Mctdhx method, respectively. We also thank T. Roscilde for his contribution in the development of the GMC method.  ... 
doi:10.15496/publikation-29062 fatcat:rtffnd5u6zeoxaezoijeyv4ldy

Proceedings of the 4th bwHPC Symposium

Jens Krüger, Thomas Walter, Anna Górska, Silke Peter, Matthias Willmann, Robert Schlaberg, Bodo R. Martin, Peter Comba, Daniel Huson, Christoph M. Schäfer, Thomas I. Maindl, Christoph Burger (+25 others)
It focused on the presentation of scientific computing projects as well as on the progress and the success stories of the bwHPC realization concept.  ...  The event offered a unique opportunity to engage in an active dialogue between scientific users, operators of bwHPC sites, and the bwHPC support team.  ...  The plots in this publication have been made by the use of the matplotlib package by [3].  ... 
doi:10.15496/publikation-25195 fatcat:ravolyw3bbatzfl4uy44aa5dp4

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences

Vitor C. Piro, Temesgen H. Dadi, Enrico Seiler, Knut Reinert, Bernhard Y. Renard, Universitätsbibliothek Der FU Berlin
With the same dataset against the complete RefSeq, ganon improved the F1-score by 65% at the genus level.  ...  However, currently available methods struggle to manage the increasing amount of sequences and their frequent updates.  ...  NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) [031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A and 031A532B].  ... 
doi:10.17169/refubium-28766 fatcat:i7sqkynwhva7vkv5sbsmpvl6gq