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Challenges and recommendations to improve the installability and archival stability of omics computational tools.
Mangul, Serghei; Mosqueiro, Thiago; Abdill, Richard J; Duong, Dat; Mitchell, Keith; Sarwal, Varuni; Hill, Brian; Brito, Jaqueline; Littman, Russell Jared; Statz, Benjamin; Lam, Angela Ka-Mei; Dayama, Gargi; Grieneisen, Laura; Martin, Lana S; Flint, Jonathan; Eskin, Eleazar; Blekhman, Ran.
Afiliación
  • Mangul S; Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America.
  • Mosqueiro T; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, California, United States of America.
  • Abdill RJ; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, California, United States of America.
  • Duong D; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America.
  • Mitchell K; Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America.
  • Sarwal V; Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America.
  • Hill B; Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.
  • Brito J; Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America.
  • Littman RJ; Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil.
  • Statz B; Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America.
  • Lam AK; Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America.
  • Dayama G; Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America.
  • Grieneisen L; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America.
  • Martin LS; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America.
  • Flint J; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, California, United States of America.
  • Eskin E; Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America.
  • Blekhman R; Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America.
PLoS Biol ; 17(6): e3000333, 2019 06.
Article en En | MEDLINE | ID: mdl-31220077
Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed "easy to install," and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Almacenamiento y Recuperación de la Información / Biología Computacional / Difusión de la Información Límite: Humans Idioma: En Revista: PLoS Biol Asunto de la revista: BIOLOGIA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Almacenamiento y Recuperación de la Información / Biología Computacional / Difusión de la Información Límite: Humans Idioma: En Revista: PLoS Biol Asunto de la revista: BIOLOGIA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos