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BioContainers: an open-source and community-driven framework for software standardization.
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.
Afiliação
  • da Veiga Leprevost F; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
  • Grüning BA; Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
  • Alves Aflitos S; Albert-Ludwigs-University, Department of Computer Science, Bioinformatics Group, Freiburg, Baden-Württemberg, 79110 Freiburg, Freiburg.
  • Röst HL; Wageningen Plant Research, Cluster Bioinformatics, Wageningen, 6700 AD, Gelderland, Netherlands.
  • Uszkoreit J; Department of Genetics, Stanford University, USA.
  • Barsnes H; Medizinisches Proteom-Center, Ruhr-University Bochum, Germany, 44801.
  • Vaudel M; Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.
  • Moreno P; Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway.
  • Gatto L; KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway.
  • Weber J; (I) KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway, 5020; (II) Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway, 5020.
  • Bai M; EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
  • Jimenez RC; Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
  • Sachsenberg T; Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
  • Pfeuffer J; EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
  • Vera Alvarez R; EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
  • Griss J; Universität Tübingen, Wilhelm Schickard Institut für Informatik, Applied Bioinformatics Group,D-72076 Tübingen, Germany.
  • Nesvizhskii AI; Eberhard-Karls-Universität Tübingen, Department of Computer Science, Applied bioinformatics, 72076 Tübingen.
  • Perez-Riverol Y; Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
Bioinformatics ; 33(16): 2580-2582, 2017 Aug 15.
Article em En | MEDLINE | ID: mdl-28379341
ABSTRACT
MOTIVATION BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). AVAILABILITY AND IMPLEMENTATION The software is freely available at github.com/BioContainers/. CONTACT yperez@ebi.ac.uk.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Biologia Computacional Idioma: En Ano de publicação: 2017 Tipo de documento: Article
Texto completo
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XML
PubMed Links
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Biologia Computacional Idioma: En Ano de publicação: 2017 Tipo de documento: Article