Articles and Poster contributions of ELIXIR-DE:

Articles:

  • Systems Biology in ELIXIR: modelling in the spotlight; among others by M. Golebiewski, W. Müller, U. Wittig. F1000Research 05/2024.
  • A research data management (RDM) community for ELIXIR; among others by N.C. Lübke, H. Schnitzer, D. Wibberg & U. Wittig. F1000Research 03/2024.
  • Implementation of FAIR Practices in Computational Metabolomics Workflows-A Case Study; M. Zulfiqar, M.R. Crusoe, B. König-Ries, C. Steinbeck, K. Peters, L. Gadelha. Metabolites 02/2024.
  • Establishing the ELIXIR Microbiome Community; among others by N. Ishaque & B. Batut. F1000Research 01/2024.
  • An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond; among others by B. Batut, L. Paladin. PLoS One. 11/2023.
  • ELIXIR and Toxicology: a community in development; among others by S. Neumann. F1000Research 10/23.
  • The next challenge: data management, submission and FAIRness in multi-omics experiments; among others by S. Neumann. F1000Research 10/2023.
  • ELIXIR’s Impact Toolkit; among others by N. Hoffmann, I. Maus, H. Schnitzer F1000Research 09/2023.
  • The Plant Phenomics and Genomics Research Data Repository: An On-Premise Approach for FAIR-Compliant Data Acquisition; D. Arend, U. Scholz, M. Lange. Methods Mol Biol. 08/2023.
  • The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond; among others by B. Batut, H. Rasche, B. Grüning. Genome Research 02/23.
  • Galaxy Training: A powerful framework for teaching! among others by B. Serrano-Solano, W. Meier, B. Grüning & B. Batut. Plos Computational Biology 01/23.
  • Transformer-based tool recommendation system in Galaxy; A. Kumar, B. Grüning & R. Backofen. BioHackrXiv 12/22,
  • Systems Biology in ELIXIR: modelling in the spotlight; among others by M. Golebiewski, W. Müller & U. Wittig. F1000Research 11/22,
  • A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfor Community); among others by M. Rarey. F1000Research 09/2022.
  • Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR; among others by C. Quast, A. Nunes-Jorge & F.O. Glöckner. F1000Research 08/22.
  • Community-driven ELIXIR activities in single-cell omics; among others by B. Grüning & N. Ishaque. F1000Research 07/22,
  • Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR; S. Beier, A. Fiebig, C. Pommier, I. Liyanage, M. Lange, ..., & U. Scholz. F1000 Research 05/22,
  • Ten simple rules for making a software tool workflow-ready; among others by B. Grüning. PLOS Comput Biol 04/22,
  • The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update; The Galaxy Community. Nucleic Acids Research 04/22,
  • Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR; among others by C. Quast, F. O. Glöckner & A. Nunes-Jorge. F1000 Research 03/22,
  • Packaging research artefacts with RO-Crate; among others by B. Grüning. Data Science 01/22.
  • The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences; among others by A. Frericks-Zipper, M. Eisenacher. Nucleic Acids Res. 01/2022.
  • Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR; among others by C. Quast, F. O. Glöckner. F1000Research 12/2021.
  • ELIXIR Software Management Plan for Life Sciences; among others by R. Alves. BioHackrXiv 10/21.
  • Data management of sensitive human proteomics data: current practices, recommendations and perspectives for the future; N. Bandeira, E. W. Deutsch, O. Kohlbacher, L. Martens, J. A. Vizcaíno. MCP 03/21,
  • ELIXIR Plant sciences 2020-2023 Roadmap; C. Pommier, K. Gruden, A. Junker, F. Coppens, R. Finkers, K. Hassani-Pak, D. Faria, J. M. Hancock, S. Beier, B. Costa, C. Miguel, I. Chaves, R. Davey, B. Contreras-Moreira. F1000 Research 02/21,
  • BRENDA, the ELIXIR core data resource in 2021: new developments and updates; among others by D. Jahn, D. Schomburg. Nucleic Acids Res. 01/2021.
  • isa4j: a scalable Java library for creating ISA-Tab metadata; D. Psaroudakis, F. Liu, P. König, U. Scholz, A. Junker, M. Lange, D. Ahrend. F1000 Research 12/20,
  • The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research; among others by J. Korbel. F1000 Research 10/20,
  • The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition; D. Arend, P. König, A. Junker, U. Scholz, M. Lange. Gigascience 10/2020.
  • A framework to assess the quality and impact of bioinformatics training across ELIXIR; among others by D. Wibberg. PloSComputBiol 07/20,
  • Ten simple rules for making training materials FAIR; among others by B. Batut. PLoSComputBiol 05/20,
  • A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community); among others by M. Rarey. F1000Research 04/2020.
  • Towards a European health research and innovation cloud (HRIC); among others by J. O. Korbel. Genome Med. 02/2020.
  • Leveraging European infrastructures to access 1 million human genomes by 2022; among others by J. O. Korbel. Nat Rev Genet. 11/2019.
  • The de.NBI / ELIXIR-DE training platform—Bioinformatics training in Germany and across Europe within ELIXIR; by D. Wibberg, B. Batut, P. Belmann, J. Blom, F. O. Glöckner, B. Grüning, N. Hoffmann, N. Kleinbölting, R. Rahn, M. Rey, U. Scholz, M. Sharan, A. Tauch, U. Trojahn, B. Usadel, O. Kohlbacher. F1000 Research 11/19,
  • An intrinsically disordered proteins community for ELIXIR; among others by M. Sharan & M. Turewicz. F1000 Research 10/19,
  • de.NBI Cloud federation through ELIXIR AAI; by P. Belmann, B. Fischer, J. Krüger, H. Rasche, M. Prinz, M. Hanussek, M. Lang, F. Bartusch, B. Gläßle, J. Krüger, A. Pühler & A. Sczyrba. F1000 Research 06/19,
  • The bio.tools registry of software tools and data resources for the life sciences; among others by B. Grüning. Genome Biol. 08/2019.
  • Recommendations for the packaging and containerizing of bioinformatics software; among others by B. Grüning & T. Sachsenberg. F1000 Research 03/19, 
  • BRENDA in 2019: a European ELIXIR core data resource; among others by S. Placzek, I. Schomburg, D. Schomburg. Nucleic Acids Res. 01/2019.
  • Common ELIXIR Service for Researcher Authentication and Authorisation; among others by P. Belmann & A. Sczyrba. F1000 Research 08/18,
  • Authoring Bioconductor workflows with BiocWorkflowTool; by M. L. Smith, A. K. Oleś & W. Huber. F1000 Research 04/18,
  • Using bio.tools to generate and annotate workbench tool descriptions; among others by H. Rasche. F1000 Research 02/18,
  • The future of metabolomics in ELIXIR; among others by O. Kohlbacher, S. Neumann, C. Steinbeck. F1000 Research 09/17,
  • A community proposal to integrate proteomics activities in ELIXIR; among others by A. Pühler, M. Eisenacher & O. Kohlbacher. F1000 Research 06/17,
  • Four simple recommendations to encourage best practices in research software; among others by B. Batut & B. Grüning. F1000 Research 06/17,

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    Posters:

    Poster contributions in 2024

    • Simplifying virtual research environments with SimpleVM: A comprehensive platform to boost research and training productivity. N. Hoffmann, P. Belmann, D. Weinholz, V. Rudko, Q. Mok, A. Sczyrba. F1000Research (poster) 06/2024.
    • Scorpion enables uniform KPI monitoring of heterogeneous Services within the Biodiversity Community. M. Feser & U. Scholz. F1000Research (poster) 06/2024.

    Poster contributions in 2023

    • Enabling an operational, open and FAIR EOSC ecosystem. S. Schaaf, A. Erxleben-Eggenhofer, B. Grüning & The EuroScienceGateway Project. F1000Research (poster) 09/2023.
    • WESkit: Workflow execution for HTC and cloud. P. R. Kensche, V. Schneider-Lunitz, C. S. Baby et al. (among others with S. Twardziok, I. Buchhalter). F1000Research (poster) 08/2023.
    • ELIXIR RDM trainer network building a stronger community of trainers. P. S. Xènia, … N. C. Lübke, … H. Schnitzer, D. Wibberg, ELIXIR-Converge WP2 leads. F1000Research (poster) 08/2023.
    • Automatic metadata driven reanalysis in cloud infrastructures. D. Winkelhardt, K. Marcus-Alic & M. Eisenacher. F1000Research (poster) 08/2023.
    • The German contribution to the European bioinformatics research infrastructure for life sciences ELIXIR: Services, training & cloud computing. R. Schwacke, M. Bolger, J. P. Buchmann, D. Arend, H. Gundlach, M. Lange, K. F. X. Mayer, U. Scholz, B. Usadel, S. Beier. F1000Research (poster) 07/2023.
    • B4W-ELIXIR leadership and diversity mentoring programme – ELEAD. A. Jene-Sanz, I. Maus & N. C. Lübke. F1000Research (poster) 06/2023.
    • Galaxy Training: A powerful framework for teaching! H. Rasche, S. Hiltemann & B. Batut. F1000Research (poster) 06/2023.
    • Establishing the ELIXIR microbiome community. B. Batut, E. Pelletier, R. Finn & K. Heil. F1000Research (poster) 06/2023.
    • Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and tracking. E. Nasr, A. Henger, T. Schindler, P. Zierep, B. Grüning & B. Batut. F1000Research (poster) 06/2023.

    Poster contributions in 2022

    • More findability, more interoperability for SABIO-RK, the curated database for biochemical reaction kinetics. A. Weidemann, D. Dudas, M. Rey, U. Wittig, W. Müller. F1000Research (poster) 08/2022.
    • The new de.NBI / ELIXIR-DE training platform in 2022. D. Wibberg. F1000Research (poster) 07/2022.
    • The new Community of Practice for DM/DS Training. H. Schnitzer, N. C. Lübke, I. Maus, T. Dammann-Kalinowski, …, A. Tauch, … D. Wibberg. F1000Research (poster) 06/2022.
    • SimpleVM – a simple to use cloud computing environment for the life sciences. N. Hoffmann, P. Belmann, D. Weinholz, E. Katchko, V. Rudko, Q. Mok, A. Walender, J. Krüger, A. Sczyrba. F1000Research (poster) 06/2022.
    • GPU-powered AI in docker-based Jupyterlab on Galaxy Europe. A. Kumar, G. Cuccuru & B. Grüning. F1000Research (poster) 06/2022.
    • BioData: an ELIXIR-DE hub of databases for the study of Biodiversity. A. Nunes-Jorge, J. Felden, J. Gerken et al. F1000Research (poster) 06/2022.
    • Contributions from IPK Gatersleben to support the ELIXIR plant science community. M. Lange, D. Arend, J. A. Memon, ... S. Beier, U. Scholz. F1000Research (poster) 06/2022. 

    Poster contributions in 2020

    f1000research 311433     f1000research 301226     f1000research 299637 2     f1000research 301156 2     f1000research 301145     f1000research 301038     f1000research 301342     f1000research 301380     f1000research 301019     f1000research 300432    

    Poster contributions in 2019

    f1000research 254669     f1000research 256905     f1000research 250759     f1000research 256019     f1000research 254779     f1000research 254658   f1000research 255611    

    Poster contributions in 2018

    f1000research 208627    

    Poster contributions in 2017

    f1000research 170111     f1000research 178034    f1000research 169624    f1000research 177245

    Poster contributions in 2016

    Videos:

    • Talks ELIXIR All Hands Meeting 2020, including Daniel Arend "For FAIRification of plant genetic resources at IPK Gatersleben" and Sebastian Beier "How to FAIRify and link plant genotyping data using ELIXIR Platforms"