Course Description
Introduction to the principles and practices of rigor and reproducibility spanning the breadth of research in genetics. Students will learn the core pillars of rigor and reproducibility in genetics research and be exposed to the diversity of approaches for executing rigorous and reproducible research across subfields of modern genetics.
Athena Title
Rigor and Reproducibility Gene
Prerequisite
Permission of department
Semester Course Offered
Offered spring
Grading System
S/U (Satisfactory/Unsatisfactory)
Course Objectives
Students will understand the principles of rigor and reproducibility in genetics research and be exposed to numerous case studies. As a result, they will become more effective at designing, executing, and evaluating rigorous and reproducible research in genetics.
Topical Outline
This topical outline is the general plan for the course; the exact order and specific content of each class will vary from instructor to instructor. 1. Overview of the reproducibility crisis 2. Reproducibility vs. replication 3. Rigor and Reproducibility (R&R) vs. Responsible Conduct of Research (RCR) 4. Journal and funding agency guidelines for R&R 5. Role of experimental design in R&R 6. Replication vs. pseudo-replication 7. Batch effects 8. Pet hypotheses and strong inference 9. Effect sizes, power, and appropriate choice of statistical tests 10. P-hacking 11. Variation in biological strains and reagents 12. Choosing appropriate software and data sets 13. Use of notebooks/electronic notebooks 14. Data and metadata management 15. Differences between raw and processed data 16. Version control, storage, and backups 17. Publishing standards for R&R 18. Cherry picking data and over-stating conclusions 19. Responsible image processing and presentation 20. Submitting data and code to public repositories 21. Subdiscipline-specific approaches to R&R in genetics
Syllabus
Public CV