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Recommendations to enhance rigor and reproducibility in biomedical research.

ABSTRACT: Biomedical research depends increasingly on computational tools, but mechanisms ensuring open data, open software, and reproducibility are variably enforced by academic institutions, funders, and publishers. Publications may present software for which source code or documentation are or become unavailable; this compromises the role of peer review in evaluating technical strength and scientific contribution. Incomplete ancillary information for an academic software package may bias or limit subsequent work. We provide 8 recommendations to improve reproducibility, transparency, and rigor in computational biology-precisely the values that should be emphasized in life science curricula. Our recommendations for improving software availability, usability, and archival stability aim to foster a sustainable data science ecosystem in life science research.

SUBMITTER: Brito JJ

PROVIDER: S-EPMC7263079 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Recommendations to enhance rigor and reproducibility in biomedical research.

Brito Jaqueline J JJ Li Jun J Moore Jason H JH Greene Casey S CS Nogoy Nicole A NA Garmire Lana X LX Mangul Serghei S

GigaScience 20200601 6

Biomedical research depends increasingly on computational tools, but mechanisms ensuring open data, open software, and reproducibility are variably enforced by academic institutions, funders, and publishers. Publications may present software for which source code or documentation are or become unavailable; this compromises the role of peer review in evaluating technical strength and scientific contribution. Incomplete ancillary information for an academic software package may bias or limit subse ...[more]

PMID: 32479592

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Project description:In the Spring of 2020, we launched a rigor and reproducibility curriculum for medical students in research training programs. This required class consisted of eight, 2-h sessions, which transitioned to remote learning in response to the coronavirus disease 2019 (COVID-19) epidemic. The class was graded as pass/fail. Flipped classroom techniques, with multiple hands-on exercises, were developed for first-year medical students (MD/PhD [n = 9], Clinical and Translational Research Pathway (CTRP) students [n = 9]). Four focus groups (n = 13 students) and individual interviews with the two instructors were conducted in May 2020. From individual interviews with instructors and focus groups with medical students, the course and its components were favorably reviewed. Students thought the course was novel, important, relevant, and practical-and teaching strategies were effective (e.g., short lectures, interactive small group exercises, and projects). Most students expressed concerns about lack of time for course preparation. Sharper focus and streamlining of preparation work may be required. Pre- and post-student self-assessments of rigor and reproducibility competencies showed average post-scores ranging from high/moderate to strong understanding (n = 11). We conclude that rigor and reproducibility can be taught to first-year medical students in research pathways programs in a highly interactive and remote format. Study Highlights WHAT IS THE CURRENT KNOWLEDGE ON THE TOPIC? The rigor and reproducibility crisis calls for robust training of scientists in best practices for enhancing the research rigor. WHAT QUESTION DID THIS STUDY ADDRESS? We evaluated a curriculum to develop physician-scientists skilled at documenting research workflow from idea generation to publication with reproducibility in mind. WHAT DOES THIS STUDY ADD TO OUR KNOWLEDGE? Highly interactive exercises, coupled with a hands-on replication group project provide a pathway for students to gain competencies important to the improvement of rigor and reproducibility in scientific research. Rigor and reproducibility can be taught in a highly interactive format and using a remote format. HOW MIGHT THIS CHANGE CLINICAL PHARMACOLOGY OR TRANSLATIONAL SCIENCE? Formal training is needed to raise awareness of the reproducibility crisis and improve the rigor of research conducted. If techniques taught are used, the transparency and reproducibility of clinical and translational science will be improved.

Project description:The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research.

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Recommendations to enhance rigor and reproducibility in biomedical research.

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Recommendations to enhance rigor and reproducibility in biomedical research.

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