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Packaging and containerization of computational methods.
Alser, Mohammed; Lawlor, Brendan; Abdill, Richard J; Waymost, Sharon; Ayyala, Ram; Rajkumar, Neha; LaPierre, Nathan; Brito, Jaqueline; Ribeiro-Dos-Santos, André M; Almadhoun, Nour; Sarwal, Varuni; Firtina, Can; Osinski, Tomasz; Eskin, Eleazar; Hu, Qiyang; Strong, Derek; Kim, Byoung-Do B D; Abedalthagafi, Malak S; Mutlu, Onur; Mangul, Serghei.
Afiliação
  • Alser M; Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland.
  • Lawlor B; Department of Computer Science, Munster Technological University, Cork, Ireland.
  • Abdill RJ; Department of Biological Sciences, Munster Technological University, Cork, Ireland.
  • Waymost S; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
  • Ayyala R; Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.
  • Rajkumar N; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
  • LaPierre N; Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
  • Brito J; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA.
  • Ribeiro-Dos-Santos AM; Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.
  • Almadhoun N; Department of Human Genetics, University of Chicago, Chicago, IL, USA.
  • Sarwal V; Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
  • Firtina C; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA.
  • Osinski T; Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland.
  • Eskin E; Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.
  • Hu Q; Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland.
  • Strong D; Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA.
  • Kim BBD; Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.
  • Abedalthagafi MS; Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
  • Mutlu O; Department of Human Genetics, University of California, Los Angeles, CA, USA.
  • Mangul S; Office of Advanced Research Computing, University of California, Los Angeles, CA, USA.
Nat Protoc ; 19(9): 2529-2539, 2024 Sep.
Article em En | MEDLINE | ID: mdl-38565959
ABSTRACT
Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Biologia Computacional Limite: Humans Idioma: En Revista: Nat Protoc Ano de publicação: 2024 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Biologia Computacional Limite: Humans Idioma: En Revista: Nat Protoc Ano de publicação: 2024 Tipo de documento: Article