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Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.
Koehler Leman, Julia; Lyskov, Sergey; Lewis, Steven M; Adolf-Bryfogle, Jared; Alford, Rebecca F; Barlow, Kyle; Ben-Aharon, Ziv; Farrell, Daniel; Fell, Jason; Hansen, William A; Harmalkar, Ameya; Jeliazkov, Jeliazko; Kuenze, Georg; Krys, Justyna D; Ljubetic, Ajasja; Loshbaugh, Amanda L; Maguire, Jack; Moretti, Rocco; Mulligan, Vikram Khipple; Nance, Morgan L; Nguyen, Phuong T; Ó Conchúir, Shane; Roy Burman, Shourya S; Samanta, Rituparna; Smith, Shannon T; Teets, Frank; Tiemann, Johanna K S; Watkins, Andrew; Woods, Hope; Yachnin, Brahm J; Bahl, Christopher D; Bailey-Kellogg, Chris; Baker, David; Das, Rhiju; DiMaio, Frank; Khare, Sagar D; Kortemme, Tanja; Labonte, Jason W; Lindorff-Larsen, Kresten; Meiler, Jens; Schief, William; Schueler-Furman, Ora; Siegel, Justin B; Stein, Amelie; Yarov-Yarovoy, Vladimir; Kuhlman, Brian; Leaver-Fay, Andrew; Gront, Dominik; Gray, Jeffrey J; Bonneau, Richard.
Afiliação
  • Koehler Leman J; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA. julia.koehler.leman@gmail.com.
  • Lyskov S; Department of Biology, New York University, New York, NY, 10003, USA. julia.koehler.leman@gmail.com.
  • Lewis SM; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Adolf-Bryfogle J; Cyrus Biotechnology, 1201 Second Ave, Suite 900, Seattle, WA, 98101, USA.
  • Alford RF; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA.
  • Barlow K; IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, 92037, USA.
  • Ben-Aharon Z; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Farrell D; Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, 94158, USA.
  • Fell J; Department of Microbiology and Molecular Genetics, Hebrew University, Hadassah Medical School, POB 12272, Jerusalem, 91120, Israel.
  • Hansen WA; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
  • Harmalkar A; Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
  • Jeliazkov J; Genome Center, University of California, Davis, CA, 95616, USA.
  • Kuenze G; Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, 95616, USA.
  • Krys JD; Department of Chemistry, University of California, Davis, CA, 95616, USA.
  • Ljubetic A; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA.
  • Loshbaugh AL; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA.
  • Maguire J; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Moretti R; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Mulligan VK; Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
  • Nance ML; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.
  • Nguyen PT; Institute for Drug Discovery, Medical School, Leipzig University, 04103, Leipzig, Germany.
  • Ó Conchúir S; Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
  • Roy Burman SS; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
  • Samanta R; Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
  • Smith ST; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
  • Teets F; Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA.
  • Tiemann JKS; Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
  • Watkins A; Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
  • Woods H; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.
  • Yachnin BJ; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA.
  • Bahl CD; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Bailey-Kellogg C; Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, 95616, USA.
  • Baker D; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
  • Das R; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • DiMaio F; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Khare SD; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.
  • Kortemme T; Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, 37235, USA.
  • Labonte JW; Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA.
  • Lindorff-Larsen K; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark.
  • Meiler J; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.
  • Schief W; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.
  • Schueler-Furman O; Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, 37235, USA.
  • Siegel JB; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA.
  • Stein A; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA.
  • Yarov-Yarovoy V; Institute for Protein Innovation, Boston, MA, 02115, USA.
  • Kuhlman B; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA.
  • Leaver-Fay A; Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
  • Gront D; Department of Computer Science, Dartmouth, Hanover, NH, 03755, USA.
  • Gray JJ; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
  • Bonneau R; Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
Nat Commun ; 12(1): 6947, 2021 11 29.
Article em En | MEDLINE | ID: mdl-34845212
ABSTRACT
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Proteínas / Substâncias Macromoleculares / Simulação de Acoplamento Molecular Tipo de estudo: Guideline / Prognostic_studies Limite: Humans Idioma: En Revista: Nat Commun Assunto da revista: BIOLOGIA / CIENCIA Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Proteínas / Substâncias Macromoleculares / Simulação de Acoplamento Molecular Tipo de estudo: Guideline / Prognostic_studies Limite: Humans Idioma: En Revista: Nat Commun Assunto da revista: BIOLOGIA / CIENCIA Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos