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Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S. The bio.tools registry of software tools and data resources for the life sciences. Genome Biol 2019; 20:164. [PMID: 31405382 PMCID: PMC6691543 DOI: 10.1186/s13059-019-1772-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/22/2019] [Indexed: 11/28/2022] Open
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.
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Affiliation(s)
- Jon Ison
- National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark.
| | - Hans Ienasescu
- National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark
| | - Piotr Chmura
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Emil Rydza
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Hervé Ménager
- Hub de Bioinformatique et de Biostatistiques, Institut Pasteur, C3BI USR, 3756 IP CNRS, Paris, France
| | - Matúš Kalaš
- Computational Biology Unit, Department of Informatics, University of Bergen, N-5020, Bergen, Norway
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Björn Grüning
- Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, 79110, Freiburg, Germany
| | - Niall Beard
- School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Rodrigo Lopez
- The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Severine Duvaud
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, CH-1015, Lausanne, Switzerland
| | - Heinz Stockinger
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, CH-1015, Lausanne, Switzerland
| | - Bengt Persson
- Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, S-75124, Uppsala, Sweden
| | - Radka Svobodová Vařeková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Tomáš Raček
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 160 00, Prague, Czech Republic
| | - Hedi Peterson
- ELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia
| | - Ahto Salumets
- ELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, N-5020, Bergen, Norway
| | - Rob Hooft
- Dutch Techcentre for Life Sciences, Jaarbeursplein 6, 3521, AL, Utrecht, The Netherlands
| | - Tommi Nyrönen
- CSC - IT Center for Science, PO BOX 405, FI-02101, Espoo, Finland
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), 08034, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluıs Companys 23, 08010, Barcelona, Spain
| | | | - Josep Gelpí
- Barcelona Supercomputing Centre (BSC), 08034, Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, University of Barcelona, INB / BSC-CNS, Barcelona, Spain
| | - Federico Zambelli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), via Amendola 165/A, Bari, Italy
- Department of Biosciences, University of Milano, Via Celoria 26, Milan, Italy
| | - Babis Savakis
- Biomedical Sciences Research Centre, Alexander Fleming 34 Al. Fleming Str, 16672, Vari, Greece
| | - Brane Leskošek
- Faculty of Medicine / ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000, Ljubljana, Slovenia
| | - Kristoffer Rapacki
- National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark
| | - Christophe Blanchet
- CNRS, UMS 3601, Institut Français de Bioinformatique, IFB-core, 2 rue Gaston Crémieux, F-91000, Evry, France
| | - Rafael Jimenez
- ELIXIR-Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Arlindo Oliveira
- INESC-ID / Instituto Superior Técnico, R. Alves Redol 9, Lisbon, Portugal
| | - Gert Vriend
- Radboud University Medical Centre, CMBI, Postbus 9101, 6500 HB, Nijmegen, Netherlands
| | - Olivier Collin
- Plateforme GenOuest Univ Rennes, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Jacques van Helden
- Aix-Marseille Univ, INSERM, lab. Theory and Approaches of Genome Complexity (TAGC), Marseille, France
| | - Peter Løngreen
- National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
- Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark
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Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SCE, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res 2015; 44:D38-47. [PMID: 26538599 PMCID: PMC4702812 DOI: 10.1093/nar/gkv1116] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/13/2015] [Indexed: 01/24/2023] Open
Abstract
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.
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Affiliation(s)
- Jon Ison
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Kristoffer Rapacki
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Hervé Ménager
- Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, France
| | - Matúš Kalaš
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Emil Rydza
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Piotr Chmura
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Christian Anthon
- Department of Veterinary Clinical and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niall Beard
- School of Computer Science, University of Manchester, UK
| | - Karel Berka
- Department of Physical Chemistry, RCPTM, Faculty of Science, Palacky University, Czech Republic
| | - Dan Bolser
- The European Bioinformatics Institute (EMBL-EBI), UK
| | - Tim Booth
- NEBC Wallingford, Centre for Ecology and Hydrology, UK
| | - Anthony Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), France INRIA, IRISA, GenOuest Core Facility, France
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Czech Republic
| | - Rita Casadio
- Bologna Biocomputing Group, University of Bologna, Italy
| | | | - Frederik Coppens
- Department of Plant Systems Biology, VIB, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium
| | | | | | - Kristian Davidsen
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | | | - Tunca Dogan
- UniProt, European Bioinformatics Institute (EMBL-EBI), UK
| | | | - Laura Emery
- The European Bioinformatics Institute (EMBL-EBI), UK
| | | | - Thomas Gatter
- Faculty of Technology and Center for Biotechnology, Universität Bielefeld, Germany
| | | | - Marie Grosjean
- Institut Français de Bioinformatique (French Institute of Bioinformatics), CNRS, UMS3601, France
| | - Björn Grüning
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085 Freiburg
| | | | - Hans Ienasescu
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
| | | | - Martin Closter Jespersen
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | | | - Nick Juty
- The European Bioinformatics Institute (EMBL-EBI), UK
| | - Peter Juvan
- Centre for Functional Genomics and Biochips, Faculty of Medicine, University of Ljubljana, Slovenia
| | | | - Camille Laibe
- The European Bioinformatics Institute (EMBL-EBI), UK
| | - Jing-Woei Li
- Faculty of Medicine, The Chinese University of Hong Kong, China Hong Kong Bioinformatics Centre, School of Life Sciences,The Chinese University of Hong Kong, China
| | - Luana Licata
- Dept. of Biology, University of Rome Tor Vergata, Italy
| | - Fabien Mareuil
- Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, France
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padua, Italy
| | | | - Sebastien Moretti
- SIB Swiss Institute of Bioinformatics, Switzerland Department of Ecology and Evolution, Biophore, Evolutionary Bioinformatics group, University of Lausanne, Switzerland
| | | | - Steffen Möller
- Department of Dermatology, University of Lübeck, Germany Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Germany
| | | | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Estonia
| | | | - Peter Rice
- Department of Computing, William Penney Laboratory, Imperial College London, UK
| | | | | | - Rabie Saidi
- UniProt, European Bioinformatics Institute (EMBL-EBI), UK
| | | | - Veit Schwämmle
- Protein Research Group, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
| | | | - Maria Maddalena Sperotto
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | | | | | | | - Victor de la Torre
- National Bioinformatics Institute Unit (INB), Fundacion Centro Nacional de Investigaciones Oncologicas, Spain
| | | | - Allegra Via
- Dept. of Physics, Sapienza University, Italy
| | - Guy Yachdav
- Department of Informatics, Bioinformatics-I12, TUM, Germany
| | - Federico Zambelli
- Institute of Biomembranes and Bioenergetics, National Research Council (CNR), and Dept. of Biosciences, University of Milano, Italy
| | - Gert Vriend
- Radboud University Medical Centre, CMBI, Netherlands
| | - Burkhard Rost
- Department of Informatics, Bioinformatics-I12, TUM, Germany
| | | | - Peter Løngreen
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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