ArticleGenome biology2019
The bio.tools registry of software tools and data resources for the life sciences.
Abstract readLetter
In one paragraph
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
35citing papers in PubMed, 1 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.Metabolomics : Official journal of the Metabolomic Society · 2023Pooled it
- PROBEAT: PRObiotic Bacterial gEnome Analysis Toolkit.Current issues in molecular biology · 2026Article
- bio.tools: an expanded web service for research software in the life sciences.Nucleic acids research · 2026Article
- Ten quick tips to SNIFF out sustainable and secure scientific software.PLoS computational biology · 2026Article
- FAIR in practice: minimum metadata schema for bioinformatics analytics by machines.Journal of biomedical semantics · 2026Article
- Federated learning frameworks: quality and interoperability for biomedical research.NAR genomics and bioinformatics · 2026Review
- Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.bioRxiv : the preprint server for biology · 2025Article
- RDMkit: A research data management toolkit for life sciences.Patterns (New York, N.Y.) · 2025Article
- WorkflowHub: a registry for computational workflows.Scientific data · 2025Article
- An outlook on structural biology after AlphaFold: tools, limits and perspectives.FEBS open bio · 2025Review
- Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction.GigaByte (Hong Kong, China) · 2025Article
- DataDesc: A framework for creating and sharing technical metadata for research software interfaces.Patterns (New York, N.Y.) · 2024Article
- Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection.Acta crystallographica. Section D, Structural biology · 2024Article
- BioTreasury: a community-based repository enabling indexing and rating of bioinformatics tools.Science China. Life sciences · 2024Article
- ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era.Nucleic acids research · 2024Article
- Generalized open-source workflows for atomistic molecular dynamics simulations of viral helicases.GigaScience · 2024Article
- A qualitative assessment of using ChatGPT as large language model for scientific workflow development.GigaScience · 2024Article
- Using text-mining to measure the scientific impact and legacy of ELIXIR, a distributed research infrastructure for life science data.F1000Research · 2024Article
- BioConvert: a comprehensive format converter for life sciences.NAR genomics and bioinformatics · 2023Article
- Ten quick tips for building FAIR workflows.PLoS computational biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
36 authors.
Jon IsonNational Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark. jison@bioinformatics.dtu.dk.ORCID 0000-0001-6666-1520
Hans IenasescuNational Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark.
Piotr ChmuraNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark.
Emil RydzaNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark.
Hervé MénagerHub de Bioinformatique et de Biostatistiques, Institut Pasteur, C3BI USR, 3756 IP CNRS, Paris, France.
Matúš KalašComputational Biology Unit, Department of Informatics, University of Bergen, N-5020, Bergen, Norway.
Veit SchwämmleDepartment of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark.
Björn GrüningDepartment of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, 79110, Freiburg, Germany.
Niall BeardSchool of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
Rodrigo LopezThe EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Severine DuvaudSIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, CH-1015, Lausanne, Switzerland.
Heinz StockingerSIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, CH-1015, Lausanne, Switzerland.
Bengt PerssonBioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, S-75124, Uppsala, Sweden.
Radka Svobodová VařekováCEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic.
Tomáš RačekCEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic.
Jiří VondrášekInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 160 00, Prague, Czech Republic.
Hedi PetersonELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia.
Ahto SalumetsELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia.
Inge JonassenComputational Biology Unit, Department of Informatics, University of Bergen, N-5020, Bergen, Norway.
Rob HooftDutch Techcentre for Life Sciences, Jaarbeursplein 6, 3521, AL, Utrecht, The Netherlands.
Tommi NyrönenCSC - IT Center for Science, PO BOX 405, FI-02101, Espoo, Finland.
Alfonso ValenciaBarcelona Supercomputing Centre (BSC), 08034, Barcelona, Spain.
Salvador CapellaBarcelona Supercomputing Centre (BSC), 08034, Barcelona, Spain.
Josep GelpíBarcelona Supercomputing Centre (BSC), 08034, Barcelona, Spain.
Federico ZambelliInstitute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), via Amendola 165/A, Bari, Italy.
Babis SavakisBiomedical Sciences Research Centre, Alexander Fleming 34 Al. Fleming Str, 16672, Vari, Greece.
Brane LeskošekFaculty of Medicine / ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000, Ljubljana, Slovenia.
Kristoffer RapackiNational Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark.
Christophe BlanchetCNRS, UMS 3601, Institut Français de Bioinformatique, IFB-core, 2 rue Gaston Crémieux, F-91000, Evry, France.
Rafael JimenezELIXIR-Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Arlindo OliveiraINESC-ID / Instituto Superior Técnico, R. Alves Redol 9, Lisbon, Portugal.
Gert VriendRadboud University Medical Centre, CMBI, Postbus 9101, 6500 HB, Nijmegen, Netherlands.
Olivier CollinPlateforme GenOuest Univ Rennes, Inria, CNRS, IRISA, F-35000, Rennes, France.
Jacques van HeldenAix-Marseille Univ, INSERM, lab. Theory and Approaches of Genome Complexity (TAGC), Marseille, France.
Peter LøngreenNational Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark.
Søren BrunakNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.
Indexed as
Biological Science DisciplinesDatabases, FactualSoftwareInternet
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
Read underepoch 390
Registered trials
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.