The tentative timetable for this course is available in Table 1. The instructor wants to warn students that he might adjust the timetable to accommodate progress and needs. However, in case of changes, the instructor will make sure to contact enrolled students to keep them posted.
| WeekID | Date | Weekday | Topic | Homework | URL | |
|---|---|---|---|---|---|---|
| 1 | 2023-08-22 | Tuesday | Syllabus | Syllabus | ||
| 1 | 2023-08-24 | Thursday | Intro. Chapt. 1 & Chap. 2: The reproducibility crisis | Due to internet outage on campus, we had to change schedule. Read Baker (2016) and prepare for discussing outcome of study | Chapter 1 & Chapter 2 | |
| 2 | 2023-08-29 | Tuesday | Chap. 1 - part A: Learning the basics | Install software | Part A | |
| 2 | 2023-08-31 | Thursday | Chap. 1 - Complete part A & overview of part B: Tables, Figures and References | Read Chapt. 1 - part B (Set your R Markdown environment) | Part A & Part B: Set your R Markdown environment | |
| 3 | 2023-09-05 | Tuesday | Chap. 1 - part B: Tables, Figures and References | Work on bioinfo. tutorials | Part B | |
| 3 | 2023-09-07 | Thursday | Chap. 1 - part B: Tables, Figures and References | Work on bioinfo. tutorials | Part B | |
| 4 | 2023-09-12 | Tuesday | Chap. 1 - Complete part B and part C: Advanced R Markdown settings | 1. Complete material all the way to the end of section 2.3.6; 2. Read sections 2.3.7 and 2.3.8 and make sure that the bibliography file “Bibliography_Reproducible_Science_2.bib” is copied in your working directory; 3. Read section 2.3.9 and make sure that the csl file “AmJBot.csl” is copied in your working directory; 4. Read section 2.4 (Chapter 1 - part C) and get accustomed with the concepts presented in this part. I will be giving a presentation on these concepts and you will be implementing the code. | Part B & Part C | |
| 4 | 2023-09-14 | Thursday | Chap. 1 - part D: User Defined Functions in R | 1. Complete section 2.4.6 of part C and 2. Read part D until the end of section 2.5.8. | Part D | |
| 5 | 2023-09-19 | Tuesday | Chap. 1 - part D: User Defined Functions in R | 1. Complete exercise in section 2.4.7 of part C and 2. Read part D until the end of section 2.5.8. | Part D | |
| 5 | 2023-09-21 | Thursday | Q&A and work on bioinformatic tutorials | 1. Sign up for bioinformatics tutorial (see Syllabus sections 5.1, 6 and 11 ) and 2. Work with your group to organize your bioinformatics tutorial | Publications and Resources for bioinformatic tutorials | |
| 6 | 2023-09-26 | Tuesday | Chap. 3: A roadmap to implement reproducible science in Ecology, Evolution & Behavior | Read material presented in Chapter 3 | Chapter 3 | |
| 6 | 2023-09-28 | Thursday | Chap. 4: Open science and CARE principles | Read material presented in Chapter 4 | Chapter 4 | |
| 7 | 2023-10-03 | Tuesday | Chap. 5: Data management | Read material presented in Chapter 5 - Part A | Chapter 5 - Part A | |
| 7 | 2023-10-05 | Thursday | Complete Chap. 5: Data management and Chap. 5: Reproducible code | Read material presented in Chapter 5 - Part B + Download folder “Project_ID/“ on Google Drive under this path: Reproducible_Science > Exercises > Chapter_5 | Chapter 5 - Part B | |
| 8 | 2023-10-10 | Tuesday | Chap. 6: Getting published | Turn in tutorial for Chap. 7 & start individual reports | Chapter 6 - Part A | |
| 8 | 2023-10-12 | Thursday | Chap. 6: Writing papers in R Markdown (rticles) and Work on bioinformatic tutorials | Upload tutorial of Chap. 7 on Google Drive | Chapter 6 - Part B | |
| 9 | 2023-10-17 | Tuesday | Bioinfo. tutorial - Chap. 7 | Turn in tutorial for Chap. 8 | ||
| 9 | 2023-10-19 | Thursday | Bioinfo. tutorial - Chap. 7 | Upload tutorial of Chap. 8 on Google Drive | ||
| 10 | 2023-10-24 | Tuesday | Bioinfo. tutorial - Chap. 8 | Turn in tutorial for Chap. 9 | ||
| 10 | 2023-10-26 | Thursday | Bioinfo. tutorial - Chap. 8 | Upload tutorial of Chap. 9 on Google Drive | ||
| 11 | 2023-10-31 | Tuesday | Bioinfo. tutorial - Chap. 9 | Turn in tutorial for Chap. 10 | ||
| 11 | 2023-11-02 | Thursday | Bioinfo. tutorial - Chap. 9 | Upload tutorial of Chap. 10 on Google Drive | ||
| 12 | 2023-11-07 | Tuesday | Bioinfo. tutorial - Chap. 10 | Turn in tutorial for Chap. 11 | ||
| 12 | 2023-11-09 | Thursday | Bioinfo. tutorial - Chap. 10 | Upload tutorial of Chap. 11 on Google Drive | ||
| 13 | 2023-11-14 | Tuesday | Bioinfo. tutorial - Chap. 11 | Turn in tutorial for Chap. 12 | ||
| 13 | 2023-11-16 | Thursday | Bioinfo. tutorial - Chap. 11 | Upload tutorial of Chap. 12 on Google Drive | ||
| 15 | 2023-11-28 | Tuesday | Bioinfo. tutorial - Chap. 12 | Students work on ind. projects: Review literature (see Syllabus) | ||
| 15 | 2023-11-30 | Thursday | Bioinfo. tutorial - Chap. 12 | Students work on ind. projects: Data management workflow | ||
| 16 | 2023-12-05 | Tuesday | Individual projects - Q&A | Students work on ind. projects: Data management workflow | ||
| 16 | 2023-12-07 | Thursday | Individual projects - Q&A | Turn in ind. projects (on Google Drive) | ||
| 17 | 2023-12-12 | Tuesday | Oral presentations of individual projects | |||
| 17 | 2023-12-14 | Thursday | Oral presentations of individual projects |