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

. 2019 Aug 12 ; 20 (1) : 164. [epub] 20190812

Jazyk angličtina Země Anglie, Velká Británie Médium electronic

Typ dokumentu dopisy, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid31405382
Odkazy

PubMed 31405382
PubMed Central PMC6691543
DOI 10.1186/s13059-019-1772-6
PII: 10.1186/s13059-019-1772-6
Knihovny.cz E-zdroje

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.

Aix Marseille Univ INSERM lab Theory and Approaches of Genome Complexity Marseille France

Barcelona Supercomputing Centre 08034 Barcelona Spain

Bioinformatics Infrastructure for Life Sciences Science for Life Laboratory Dept of Cell and Molecular Biology Uppsala University S 75124 Uppsala Sweden

Biomedical Sciences Research Centre Alexander Fleming 34 Al Fleming Str 16672 Vari Greece

CEITEC Central European Institute of Technology Masaryk University Brno Kamenice 5 625 00 Brno Bohunice Czech Republic

CNRS UMS 3601 Institut Français de Bioinformatique IFB core 2 rue Gaston Crémieux F 91000 Evry France

Computational Biology Unit Department of Informatics University of Bergen N 5020 Bergen Norway

CSC IT Center for Science PO BOX 405 FI 02101 Espoo Finland

Department of Bio and Health Informatics Technical University of Denmark Building 208 DK 2800 Kongens Lyngby Denmark

Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences University of Southern Denmark Campusvej 55 5230 Odense Denmark

Department of Biochemistry and Molecular Biomedicine University of Barcelona INB BSC CNS Barcelona Spain

Department of Biosciences University of Milano Via Celoria 26 Milan Italy

Department of Computer Science Albert Ludwigs University Freiburg Georges Köhler Allee 106 79110 Freiburg Germany

Dutch Techcentre for Life Sciences Jaarbeursplein 6 3521 AL Utrecht The Netherlands

ELIXIR EE Institute of Computer Science University of Tartu J Liivi 2 Tartu Estonia

ELIXIR Hub Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK

Faculty of Medicine ELIXIR SI University of Ljubljana Vrazov trg 2 SI 1000 Ljubljana Slovenia

Hub de Bioinformatique et de Biostatistiques Institut Pasteur C3BI USR 3756 IP CNRS Paris France

INESC ID Instituto Superior Técnico R Alves Redol 9 Lisbon Portugal

Institució Catalana de Recerca i Estudis Avançats Pg Lluıs Companys 23 08010 Barcelona Spain

Institute of Biomembranes Bioenergetics and Molecular Biotechnologies National Research Council via Amendola 165 A Bari Italy

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo namesti 2 160 00 Prague Czech Republic

National Life Science Supercomputing Center Technical University of Denmark Building 208 DK 2800 Kongens Lyngby Denmark

Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen DK 2200 Copenhagen Denmark

Plateforme GenOuest Univ Rennes Inria CNRS IRISA F 35000 Rennes France

Radboud University Medical Centre CMBI Postbus 9101 6500 HB Nijmegen Netherlands

School of Computer Science The University of Manchester Oxford Road Manchester M13 9PL UK

SIB Swiss Institute of Bioinformatics Quartier Sorge Batiment Amphipole CH 1015 Lausanne Switzerland

The EMBL European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK

Zobrazit více v PubMed

Lesk AM. Sequence analysis in molecular biology; treasure trove or trivial pursuit. Trends Biochem Sci. 1988;13(10):410. doi: 10.1016/0968-0004(88)90198-3.. DOI

Park Young M., Squizzato Silvano, Buso Nicola, Gur Tamer, Lopez Rodrigo. The EBI search engine: EBI search as a service—making biological data accessible for all. Nucleic Acids Research. 2017;45(W1):W545–W549. doi: 10.1093/nar/gkx359. PubMed DOI PMC

Möller S, et al. Community-driven computational biology with Debian Linux. BMC Bioinformatics. 2010;11(S12). 10.1186/1471-2105-11-s12-s5. PubMed PMC

O'connor BD, et al. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000Research. 2017;6:52. doi: 10.12688/f1000research.10137.1. PubMed DOI PMC

Editorial: the 16th annual nucleic acids research web server issue 2018. Nucleic Acids Res. 2018;46(W1). 10.1093/nar/gky518. PubMed PMC

Artimo P., Jonnalagedda M., Arnold K., Baratin D., Csardi G., de Castro E., Duvaud S., Flegel V., Fortier A., Gasteiger E., Grosdidier A., Hernandez C., Ioannidis V., Kuznetsov D., Liechti R., Moretti S., Mostaguir K., Redaschi N., Rossier G., Xenarios I., Stockinger H. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research. 2012;40(W1):W597–W603. doi: 10.1093/nar/gks400. PubMed DOI PMC

Ison Jon, Rapacki Kristoffer, Ménager Hervé, Kalaš Matúš, Rydza Emil, Chmura Piotr, Anthon Christian, Beard Niall, Berka Karel, Bolser Dan, Booth Tim, Bretaudeau Anthony, Brezovsky Jan, Casadio Rita, Cesareni Gianni, Coppens Frederik, Cornell Michael, Cuccuru Gianmauro, Davidsen Kristian, Vedova Gianluca Della, Dogan Tunca, Doppelt-Azeroual Olivia, Emery Laura, Gasteiger Elisabeth, Gatter Thomas, Goldberg Tatyana, Grosjean Marie, Grüning Björn, Helmer-Citterich Manuela, Ienasescu Hans, Ioannidis Vassilios, Jespersen Martin Closter, Jimenez Rafael, Juty Nick, Juvan Peter, Koch Maximilian, Laibe Camille, Li Jing-Woei, Licata Luana, Mareuil Fabien, Mičetić Ivan, Friborg Rune Møllegaard, Moretti Sebastien, Morris Chris, Möller Steffen, Nenadic Aleksandra, Peterson Hedi, Profiti Giuseppe, Rice Peter, Romano Paolo, Roncaglia Paola, Saidi Rabie, Schafferhans Andrea, Schwämmle Veit, Smith Callum, Sperotto Maria Maddalena, Stockinger Heinz, Vařeková Radka Svobodová, Tosatto Silvio C.E., de la Torre Victor, Uva Paolo, Via Allegra, Yachdav Guy, Zambelli Federico, Vriend Gert, Rost Burkhard, Parkinson Helen, Løngreen Peter, Brunak Søren. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. 2015;44(D1):D38–D47. doi: 10.1093/nar/gkv1116. PubMed DOI PMC

Ison J., Kalas M., Jonassen I., Bolser D., Uludag M., McWilliam H., Malone J., Lopez R., Pettifer S., Rice P. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics. 2013;29(10):1325–1332. doi: 10.1093/bioinformatics/btt113. PubMed DOI PMC

Farnham A, et al. Early career researchers want Open Science. Genome Biol. 2017;18(1). 10.1186/s13059-017-1351-7. PubMed PMC

Ison J, et al. Community curation of bioinformatics software and data resources. Briefings Bioinformatics(accepted). 10.1093/bribio/bbz075. PubMed PMC

bio.tools documentation, https://biotools.readthedocs.io/en/latest. Accessed Aug 2019.

Wise John, de Barron Alexandra Grebe, Splendiani Andrea, Balali-Mood Beeta, Vasant Drashtti, Little Eric, Mellino Gaspare, Harrow Ian, Smith Ian, Taubert Jan, van Bochove Kees, Romacker Martin, Walgemoed Peter, Jimenez Rafael C., Winnenburg Rainer, Plasterer Tom, Gupta Vibhor, Hedley Victoria. Implementation and relevance of FAIR data principles in biopharmaceutical R&D. Drug Discovery Today. 2019;24(4):933–938. doi: 10.1016/j.drudis.2019.01.008. PubMed DOI

Palmblad M, et al. Automated workflow composition in mass spectrometry-based proteomics. Bioinformatics. 2018;35(4):656–664. doi: 10.1093/bioinformatics/bty646. PubMed DOI PMC

Brancotte B, et al. A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. J Open Source Software. 2018;3(27):698. doi: 10.21105/joss.00698. DOI

Doppelt-Azeroual, Olivia, et al. “ReGaTE: registration of galaxy tools in elixir.” GigaScience, vol. 6, no. 6, 2017, doi:10.1093/gigascience/gix022. PubMed PMC

da Veiga Leprevost Felipe, Grüning Björn A, Alves Aflitos Saulo, Röst Hannes L, Uszkoreit Julian, Barsnes Harald, Vaudel Marc, Moreno Pablo, Gatto Laurent, Weber Jonas, Bai Mingze, Jimenez Rafael C, Sachsenberg Timo, Pfeuffer Julianus, Vera Alvarez Roberto, Griss Johannes, Nesvizhskii Alexey I, Perez-Riverol Yasset. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017;33(16):2580–2582. doi: 10.1093/bioinformatics/btx192. PubMed DOI PMC

Willighagen, Egon, and Jonathan Mélius. “Automatic OpenAPI to bio.tools Conversion.” 2017, Preprint at doi:10.1101/170274.

Hillion K-H, et al. Using bio.tools to generate and annotate workbench tool descriptions. F1000Research. 2017;6:2074. doi: 10.12688/f1000research.12974.1. PubMed DOI PMC

Afgan Enis, Baker Dannon, Batut Bérénice, van den Beek Marius, Bouvier Dave, Čech Martin, Chilton John, Clements Dave, Coraor Nate, Grüning Björn A, Guerler Aysam, Hillman-Jackson Jennifer, Hiltemann Saskia, Jalili Vahid, Rasche Helena, Soranzo Nicola, Goecks Jeremy, Taylor James, Nekrutenko Anton, Blankenberg Daniel. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Research. 2018;46(W1):W537–W544. doi: 10.1093/nar/gky379. PubMed DOI PMC

Linden M, et al. Common ELIXIR Service for Researcher Authentication and Authorisation. F1000Res. 2018;7:1199. doi: 10.12688/f1000research.15161.1. PubMed DOI PMC

Larcombe L, et al. ELIXIR-UK role in bioinformatics training at the National Level and across ELIXIR. F1000Research. 2017;6:952. doi: 10.12688/f1000research.11837.1. PubMed DOI PMC

McQuilton Peter, Gonzalez-Beltran Alejandra, Rocca-Serra Philippe, Thurston Milo, Lister Allyson, Maguire Eamonn, Sansone Susanna-Assunta. BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. Database. 2016;2016:baw075. doi: 10.1093/database/baw075. PubMed DOI PMC

Ison J, et al. The bio.tools registry of software tools and data resources for the life sciences. Github repository. 2019. https://github.com/bio-tools/biotoolsRegistry. Accessed Aug 2019. PubMed PMC

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