The tentative schedule for this course is provided in Table 1. Please note that the instructor may adjust our schedule to accommodate the course’s progress and students’ needs. Any changes will be communicated to enrolled students in a timely manner.
| WeekID | Date | Weekday | Topic | Homework | Deadline | |
|---|---|---|---|---|---|---|
| 1 | 2025-08-26 | Tuesday | Syllabus | |||
| 1 | 2025-08-28 | Thursday | Chapt. 1 - part A | Read the syllabus carefully and ask questions if you need any clarification | ||
| 2 | 2025-09-02 | Tuesday | Chapt. 1 - part A | Read your assigned publication for Chapter 1 - part A and identify its reproducibility challenges | ||
| 2 | 2025-09-04 | Thursday | Chapt. 1 - part B | Read Baker (2016) and Summary (pages 5-19) of the Reproducibility and replicability in science report (from The National Academies Press) | ||
| 3 | 2025-09-09 | Tuesday | Chap. 2 - part A: Learning the basics | Install software and Sign up for bioinformatics tutorial (see Syllabus ) | ||
| 3 | 2025-09-11 | Thursday | Review Chap. 2 - part A and Chap. 2 - part B: Setting Your R Markdown Document | Complete Chapter 2 - part A | ||
| 4 | 2025-09-16 | Tuesday | Complete Chap. 2 - Part B: Setting Your R Markdown Document (we will start at the “Install R Dependencies and Load Packages” section) | Complete the sections of Chapter 2 – Part B up to the end of the “YAML Metadata Section.” Read the “Install R Dependencies and Load Packages” section to familiarize yourself with its content and purpose | ||
| 4 | 2025-09-18 | Thursday | Start Chap. 2 - Part C: Tables, Figures, and References and complete it until the end of the “Cross-reference Tables and Figures in the Text” section | Make sure that your “Chapter2_partB.Rmd” file knits successfully and includes all the material from Chapter 2 - Part B | ||
| 5 | 2025-09-23 | Tuesday | Complete Chap. 2 - part C: Tables, Figures and References (we will start at section 3.4.7 “Cite References in the Text”) |
Make sure that your Chapter2_partC.Rmd file knits successfully and includes all the material up to the end of section 3.4.6 “Cross-reference Tables and Figures in the Text”. Refer to section 3.4.4.2 “Double Table in Caption” for guidance on how to debug this issue if needed
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| 5 | 2025-09-25 | Thursday | Chap. 2 - part D: Advanced R and R Markdown settings | Complete Chap. 2 - part C: Tables, Figures and References | ||
| 6 | 2025-09-30 | Tuesday | Chap. 2 - part E: User-Defined Functions in R | Read material presented in Chap. 2 - part E: User-Defined Functions in R | ||
| 6 | 2025-10-02 | Thursday | Complete Chap. 2 - part E: User-Defined Functions in R (we will start at section 3.6.8 Create, Name, and Access Elements of a List in R) | Complete Chap. 2 - part E up to section 3.6.8 Create, Name, and Access Elements of a List in R | ||
| 7 | 2025-10-07 | Tuesday | Chap. 3: A roadmap to implement reproducible science | Read material presented in Chapter 3 | ||
| 7 | 2025-10-09 | Thursday | Chap. 4: Open science and CARE principles | Read material presented in Chapter 4 | ||
| 8 | 2025-10-14 | Tuesday | Complete Chap. 4 (group activities on CARE Principles and comparing FAIR & CARE Principles) and Chap. 5: Data Management | Read material presented in Chapter 5 - Data Management | Turn in tutorial for Chap. 7 | |
| 8 | 2025-10-16 | Thursday | Chap. 5: Reproducible Code | Read material presented in Chapter 5 - Reproducible Code | Upload tutorial of Chap. 7 on Google Drive | |
| 9 | 2025-10-21 | Tuesday | Chap. 6: Getting published & Writing papers in R Markdown | Read material presented in Chapter 6 | Turn in tutorial for Chap. 8 | |
| 9 | 2025-10-23 | Thursday | Bioinfo. tutorial - Chap. 7 | Students work on bioinformatics tutorials and their individual projects | Upload tutorial of Chap. 8 on Google Drive | |
| 10 | 2025-10-28 | Tuesday | Bioinfo. tutorial - Chap. 8 | Students work on bioinformatics tutorials and their individual projects | Turn in tutorial for Chap. 9 | |
| 10 | 2025-10-30 | Thursday | Bioinfo. tutorial - Chap. 8 | Students work on bioinformatics tutorials and their individual projects | Upload tutorial of Chap. 9 on Google Drive | |
| 11 | 2025-11-04 | Tuesday | Bioinfo. tutorial - Chap. 9 | Students work on bioinformatics tutorials and their individual projects | Turn in tutorial for Chap. 10 | |
| 11 | 2025-11-06 | Thursday | Bioinfo. tutorial - Chap. 9 | Students work on bioinformatics tutorials and their individual projects | Upload tutorial of Chap. 10 on Google Drive | |
| 12 | 2025-11-11 | Tuesday | Bioinfo. tutorial - Chap. 10 | Students work on bioinformatics tutorials and their individual projects | Turn in tutorial for Chap. 11 | |
| 12 | 2025-11-13 | Thursday | Bioinfo. tutorial - Chap. 10 | Students work on bioinformatics tutorials and their individual projects | Upload tutorial of Chap. 11 on Google Drive | |
| 13 | 2025-11-18 | Tuesday | Bioinfo. tutorial - Chap. 11 | Students work on bioinformatics tutorials and their individual projects | Turn in tutorial for Chap. 12 | |
| 13 | 2025-11-20 | Thursday | Bioinfo. tutorial - Chap. 11 | Students work on bioinformatics tutorials and their individual projects | Upload tutorial of Chap. 12 on Google Drive | |
| 15 | 2025-12-02 | Tuesday | Bioinfo. tutorial - Chap. 12 | Students work on bioinformatics tutorials and their individual projects | ||
| 15 | 2025-12-04 | Thursday | Bioinfo. tutorial - Chap. 12 | Students work on bioinformatics tutorials and their individual projects | ||
| 16 | 2025-12-09 | Tuesday | Individual projects - Q&A | Students work on bioinformatics tutorials and their individual projects | ||
| 16 | 2025-12-11 | Thursday | Individual projects - Q&A | Upload slides of individual projects (on Google Drive) | Turn in ind. projects (on Google Drive) | |
| 17 | 2025-12-16 | Tuesday | Oral presentations of individual projects | |||
| 17 | 2025-12-18 | Thursday | Oral presentations of individual projects |