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 | |
|---|---|---|---|---|---|
| 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 | TBD | |
| 5 | 2025-09-25 | Thursday | Chap. 2 - part D: Advanced R and R Markdown settings | TBD | |
| 6 | 2025-09-30 | Tuesday | Chap. 2 - part E: User-Defined Functions in R | Read material presented in Chapter 3 | |
| 6 | 2025-10-02 | Thursday | Chap. 3: A roadmap to implement reproducible science in Ecology, Evolution & Behavior | Read material presented in Chapter 4 | |
| 7 | 2025-10-07 | Tuesday | Chap. 4: Open science and CARE principles | Read material presented in Chapter 5 - Part A | |
| 7 | 2025-10-09 | Thursday | Chap. 5: Data management | Read material presented in Chapter 5 - Part B + Download folder “Project_ID/“ on Google Drive under this path: Reproducible_Science > Exercises > Chapter_5 | |
| 8 | 2025-10-14 | Tuesday | Chap. 6: Getting published | Turn in tutorial for Chap. 7 & start individual reports | |
| 8 | 2025-10-16 | Thursday | Chap. 6: Writing papers in R Markdown (rticles) and Work on bioinformatic tutorials | Upload tutorial of Chap. 7 on Google Drive | |
| 9 | 2025-10-21 | Tuesday | Bioinfo. tutorial - Chap. 7 | Turn in tutorial for Chap. 8 | |
| 9 | 2025-10-23 | Thursday | Bioinfo. tutorial - Chap. 7 | Upload tutorial of Chap. 8 on Google Drive | |
| 10 | 2025-10-28 | Tuesday | Bioinfo. tutorial - Chap. 8 | Turn in tutorial for Chap. 9 | |
| 10 | 2025-10-30 | Thursday | Bioinfo. tutorial - Chap. 8 | Upload tutorial of Chap. 9 on Google Drive | |
| 11 | 2025-11-04 | Tuesday | Bioinfo. tutorial - Chap. 9 | Turn in tutorial for Chap. 10 | |
| 11 | 2025-11-06 | Thursday | Bioinfo. tutorial - Chap. 9 | Upload tutorial of Chap. 10 on Google Drive | |
| 12 | 2025-11-11 | Tuesday | Bioinfo. tutorial - Chap. 10 | Turn in tutorial for Chap. 11 | |
| 12 | 2025-11-13 | Thursday | Bioinfo. tutorial - Chap. 10 | Upload tutorial of Chap. 11 on Google Drive | |
| 13 | 2025-11-18 | Tuesday | Bioinfo. tutorial - Chap. 11 | Turn in tutorial for Chap. 12 | |
| 13 | 2025-11-20 | Thursday | Bioinfo. tutorial - Chap. 11 | Upload tutorial of Chap. 12 on Google Drive | |
| 15 | 2025-12-02 | Tuesday | Bioinfo. tutorial - Chap. 12 | Students work on ind. projects: Review literature (see Syllabus) | |
| 15 | 2025-12-04 | Thursday | Bioinfo. tutorial - Chap. 12 | Students work on ind. projects: Data management workflow | |
| 16 | 2025-12-09 | Tuesday | Individual projects - Q&A | Students work on ind. projects: Data management workflow | |
| 16 | 2025-12-11 | Thursday | Individual projects - Q&A | 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 |