المؤلفون: Ison, Jon, Ménager, Hervé, Brancotte, Bryan, Jaaniso, Erik, Salumets, Ahto, Raček, Tomáš, Lamprecht, Anna-Lena, Palmblad, Magnus, Kalaš, Matúš, Chmura, Piotr, Hancock, John M, Schwämmle, Veit, Ienasescu, Hans-Ioan

Relation: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbz075/5560007

الإتاحة: https://hdl.handle.net/1956/22831

المؤلفون: Ison J; National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800 Kongens Lyngby, Denmark., Ménager H; Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France., Brancotte B; Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France., Jaaniso E; ELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia., Salumets A; ELIXIR-EE, Institute of Computer Science, University of Tartu. J Liivi 2, Tartu, Estonia., Raček T; CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.; Faculty of Informatics, Masaryk University, Botanická 68a, 602 00 Brno, Czech Republic., Lamprecht AL; Department of Information and Computing Sciences, Utrecht University, Utrecht, Netherlands., Palmblad M; Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands., Kalaš M; Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway., Chmura P; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen., Hancock JM; ELIXIR-Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom., Schwämmle V; Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark., Ienasescu HI; National Life Science Supercomputing Center, Technical University of Denmark, Building 208, DK-2800 Kongens Lyngby, Denmark.

المصدر: Briefings in bioinformatics [Brief Bioinform] 2020 Sep 25; Vol. 21 (5), pp. 1697-1705.

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

مواضيع طبية MeSH: Community Participation* , Software*, Computational Biology/*methods, Computational Biology/standards ; Database Management Systems ; Europe ; Humans

مستخلص: The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.
(© The Author(s) 2019. Published by Oxford University Press.)

المؤلفون: Palmblad M; Center for Proteomics and Metabolomics, Leiden University Medical Center, RC Leiden, The Netherlands., Lamprecht AL; Department of Information and Computing Sciences, Utrecht University, CC Utrecht, The Netherlands., Ison J; National Life Science Supercomputing Center, Technical University of Denmark, Kongens Lyngby, Denmark., Schwämmle V; Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.

المصدر: Bioinformatics (Oxford, England) [Bioinformatics] 2019 Feb 15; Vol. 35 (4), pp. 656-664.

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

مواضيع طبية MeSH: Mass Spectrometry* , Proteomics* , Workflow*, Computational Biology ; Software

مستخلص: Motivation: Numerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows. Working out which tools and combinations are applicable or optimal in practice is often hard. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.
Results: We provide a toolkit to support researchers in identifying, comparing and benchmarking multiple workflows from individual bioinformatics tools. Automated workflow composition is enabled by the tools' semantic annotation in terms of the EDAM ontology. To demonstrate the practical use of our framework, we created and evaluated a number of logically and semantically equivalent workflows for four use cases representing frequent tasks in MS-based proteomics. Indeed we found that the results computed by the workflows could vary considerably, emphasizing the benefits of a framework that facilitates their systematic exploration.
Availability and Implementation: The project files and workflows are available from https://github.com/bio-tools/biotoolsCompose/tree/master/Automatic-Workflow-Composition.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2018. Published by Oxford University Press.)