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.

Table 1: Tentative timetable for the EEB603 Reproducible Science course during the 2023 Fall semester.
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