The bio.tools registry of software tools and data resources for the life sciences

Jon Ison¹, Hans Ienasescu², Piotr Chmura³, Emil Rydza³, Hervé Ménager⁴, Matúš Kalaš⁵, Veit Schwämmle⁶, Björn Grüning⁷, Niall Beard⁸, Rodrigo Lopez⁹, Severine Duvaud¹⁰, Heinz Stockinger¹⁰, Bengt Persson¹¹, Radka Svobodová Vařeková¹², Tomáš Raček¹², Jiří Vondrášek¹³, Hedi Peterson¹⁴, Ahto Salumets¹⁴, Inge Jonassen⁵, Rob Hooft¹⁵, Tommi Nyrönen¹⁶, Alfonso Valencia^{17

18}, Salvador Capella¹⁷, Josep Gelpí^{17

19}, Federico Zambelli^{20

21}, Babis Savakis²², Brane Leskošek²³, Kristoffer Rapacki², Christophe Blanchet²⁴, Rafael Jimenez²⁵, Arlindo Oliveira²⁶, Gert Vriend²⁷, Olivier Collin²⁸, Jacques van Helden²⁹, Peter Løngreen², Søren Brunak^{3

30}

Affiliations

¹ National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark. jison@bioinformatics.dtu.dk.
² National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark.
³ Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark.
⁴ Hub de Bioinformatique et de Biostatistiques, Institut Pasteur, C3BI USR, 3756 IP CNRS, Paris, France.
⁵ Computational Biology Unit, Department of Informatics, University of Bergen, N-5020, Bergen, Norway.
⁶ Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark.
⁷ Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, 79110, Freiburg, Germany.
⁸ School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
⁹ The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
¹⁰ SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, CH-1015, Lausanne, Switzerland.
¹¹ Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, S-75124, Uppsala, Sweden.
¹² CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic.
¹³ Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 160 00, Prague, Czech Republic.
¹⁴ ELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia.
¹⁵ Dutch Techcentre for Life Sciences, Jaarbeursplein 6, 3521, AL, Utrecht, The Netherlands.
¹⁶ CSC - IT Center for Science, PO BOX 405, FI-02101, Espoo, Finland.
¹⁷ Barcelona Supercomputing Centre (BSC), 08034, Barcelona, Spain.
¹⁸ Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluıs Companys 23, 08010, Barcelona, Spain.
¹⁹ Department of Biochemistry and Molecular Biomedicine, University of Barcelona, INB / BSC-CNS, Barcelona, Spain.
²⁰ Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), via Amendola 165/A, Bari, Italy.
²¹ Department of Biosciences, University of Milano, Via Celoria 26, Milan, Italy.
²² Biomedical Sciences Research Centre, Alexander Fleming 34 Al. Fleming Str, 16672, Vari, Greece.
²³ Faculty of Medicine / ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000, Ljubljana, Slovenia.
²⁴ CNRS, UMS 3601, Institut Français de Bioinformatique, IFB-core, 2 rue Gaston Crémieux, F-91000, Evry, France.
²⁵ ELIXIR-Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
²⁶ INESC-ID / Instituto Superior Técnico, R. Alves Redol 9, Lisbon, Portugal.
²⁷ Radboud University Medical Centre, CMBI, Postbus 9101, 6500 HB, Nijmegen, Netherlands.
²⁸ Plateforme GenOuest Univ Rennes, Inria, CNRS, IRISA, F-35000, Rennes, France.
²⁹ Aix-Marseille Univ, INSERM, lab. Theory and Approaches of Genome Complexity (TAGC), Marseille, France.
³⁰ Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark.

PMID: 31405382
PMCID: PMC6691543
DOI: 10.1186/s13059-019-1772-6

The bio.tools registry of software tools and data resources for the life sciences

Jon Ison et al. Genome Biol. 2019.

. 2019 Aug 12;20(1):164.

doi: 10.1186/s13059-019-1772-6.

Authors

Affiliations

¹ National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark. jison@bioinformatics.dtu.dk.
² National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark.
³ Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark.
⁴ Hub de Bioinformatique et de Biostatistiques, Institut Pasteur, C3BI USR, 3756 IP CNRS, Paris, France.
⁵ Computational Biology Unit, Department of Informatics, University of Bergen, N-5020, Bergen, Norway.
⁶ Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark.
⁷ Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, 79110, Freiburg, Germany.
⁸ School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
⁹ The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
¹⁰ SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, CH-1015, Lausanne, Switzerland.
¹¹ Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, S-75124, Uppsala, Sweden.
¹² CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic.
¹³ Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 160 00, Prague, Czech Republic.
¹⁴ ELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia.
¹⁵ Dutch Techcentre for Life Sciences, Jaarbeursplein 6, 3521, AL, Utrecht, The Netherlands.
¹⁶ CSC - IT Center for Science, PO BOX 405, FI-02101, Espoo, Finland.
¹⁷ Barcelona Supercomputing Centre (BSC), 08034, Barcelona, Spain.
¹⁸ Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluıs Companys 23, 08010, Barcelona, Spain.
¹⁹ Department of Biochemistry and Molecular Biomedicine, University of Barcelona, INB / BSC-CNS, Barcelona, Spain.
²⁰ Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), via Amendola 165/A, Bari, Italy.
²¹ Department of Biosciences, University of Milano, Via Celoria 26, Milan, Italy.
²² Biomedical Sciences Research Centre, Alexander Fleming 34 Al. Fleming Str, 16672, Vari, Greece.
²³ Faculty of Medicine / ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000, Ljubljana, Slovenia.
²⁴ CNRS, UMS 3601, Institut Français de Bioinformatique, IFB-core, 2 rue Gaston Crémieux, F-91000, Evry, France.
²⁵ ELIXIR-Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
²⁶ INESC-ID / Instituto Superior Técnico, R. Alves Redol 9, Lisbon, Portugal.
²⁷ Radboud University Medical Centre, CMBI, Postbus 9101, 6500 HB, Nijmegen, Netherlands.
²⁸ Plateforme GenOuest Univ Rennes, Inria, CNRS, IRISA, F-35000, Rennes, France.
²⁹ Aix-Marseille Univ, INSERM, lab. Theory and Approaches of Genome Complexity (TAGC), Marseille, France.
³⁰ Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800, Kongens Lyngby, Denmark.

PMID: 31405382
PMCID: PMC6691543
DOI: 10.1186/s13059-019-1772-6

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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Conflict of interest statement

The authors declare that they have no competing interests.

References

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The bio.tools registry of software tools and data resources for the life sciences

Affiliations

The bio.tools registry of software tools and data resources for the life sciences

Authors

Affiliations

Abstract

Conflict of interest statement

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Other Literature Sources