Welcome to the central hub for course organization in EEB 603 – Reproducible Science. This webpage consolidates all essential information related to assignment deadlines (they are not posted in Canvas), and the weekly schedule.
Here you will find:
This page serves as a single reference point to help you plan your semester, stay on top of coursework, and engage fully with both theoretical and applied aspects of reproducible science.
To facilitate communication and help you plan your work, deadlines and point allocations for all assessments are provided in Table 2.1.
The bioinformatics tutorials are taught on a rolling basis, so their deadlines depend on the chapter you sign up to teach. These deadlines are listed separately in Table 2.2. You must sign up for a chapter by 2026-09-08, using the Google Sheet and respecting the number of students indicated for each chapter. Once you have signed up, find your chapter in Table 2.2 and note the two deadlines that apply to you. Everything else in your tutorial timeline follows from that choice, which is why this is the first deadline of the semester.
This year I am teaching Chapter 7 and 8 myself, given the size of the cohort. Those sessions still run as scheduled below, but they are not available to sign up for and carry no student deadlines, so they do not appear in Table 2.2.
Please also read the Late Work Policy in the syllabus. In particular, your bioinformatics tutorial must be submitted one week before you teach it. This is a firm deadline, and extensions are not available. The individual report may be submitted up to one week late, but late submissions are subject to the consequences described in the Late Work Policy. I strongly recommend submitting your report by the deadline whenever possible.
| Assessment | Points | Date | Time | Evaluation form |
|---|---|---|---|---|
| Sign up for a bioinformatics tutorial chapter | – | 2026-09-08 | before class | – |
| Individual project – proposal | 50 | 2026-10-08 | 5 PM MT | Rubric |
| Bioinformatics tutorial (written) | 150 | varies by chapter – see Table 2 | 5 PM MT | Rubric |
| Teaching your bioinformatics tutorial | 100 | varies by chapter – see schedule below | in class | Rubric |
| Participation and engagement (PARTS 1 & 2) | 50 | throughout PARTS 1 and 2 | – | Syllabus |
| Individual project – final report | 150 | 2026-12-03 | 5 PM MT | Rubric |
| Oral presentation – slides | – | 2026-12-10 | 5 PM MT | – |
| Oral presentation | 100 | 2026-12-15 & 2026-12-17 | in class | Rubric |
| TOTAL | 600 |
| Chapter | Submit to me for review | Upload to Google Drive | Taught in class |
|---|---|---|---|
| Chapter 9 | 2026-10-27 | 2026-10-29 | Nov 03 & Nov 05 |
| Chapter 10 | 2026-11-03 | 2026-11-05 | Nov 10 & Nov 12 |
| Chapter 11 | 2026-11-10 | 2026-11-12 | Nov 17 & Nov 19 |
| Chapter 12 | 2026-11-17 | 2026-11-19 | Dec 01 & Dec 03 |
The full session-by-session schedule follows in Table 3.1. I may adjust the schedule to accommodate the course’s progress and your needs; if I do, I will let everyone enrolled know in good time and update this page, which is always the current version.
Our classes run for 75 minutes, and roughly halfway through I will call a five-minute break. I aim for a natural pause in the material rather than a fixed time on the clock, so it may fall a little either side of the midpoint.
| Week | Date | Weekday | Topic | Homework | Completed | |
|---|---|---|---|---|---|---|
| 1 | 2026-08-25 | Tuesday | Syllabus | ✔ | ||
| 1 | 2026-08-27 | Thursday | Chapt. 1 - part A | Read the syllabus carefully and ask questions if you need any clarification | ✔ | |
| 2 | 2026-09-01 | Tuesday | Chapt. 1 - part A: start at section 2.4.3 (Case Studies and Challenges) | Read your assigned publication for Chapter 1 - part A and identify its reproducibility challenges. These articles are available on Google Drive. | ✔ | |
| 2 | 2026-09-03 | Thursday | Complete Chapt. 1 - part A: start at section 2.4.5 (Wrap-up and Future Directions) and 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). These articles are available on Google Drive. | ✔ | |
| 3 | 2026-09-08 | Tuesday | Complete Chapt. 1 - part B and start Chap. 2 - part A: Learning the basics |
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✔ | |
| 3 | 2026-09-10 | Thursday | Complete Chapt. 1 - Part B (starting at section 2.5.5.7 Revise and Commit) and start Chap. 2 - Part A: Learning the Basics |
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✔ | |
| 4 | 2026-09-15 | Tuesday | Complete Chap. 2 - Part A: Learning the Basics |
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| 4 | 2026-09-17 | Thursday | Chap. 2 - Part B: Setting Your R Markdown Document | Make sure that your “Chapter2_partB.Rmd” file knits successfully and includes all the material from Chapter 2 - Part B | ||
| 5 | 2026-09-22 | Tuesday | Chap. 2 - part C: Tables, Figures and References |
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 | 2026-09-24 | Thursday | Individual project workshop: develop your project and proposal with feedback from me | Bring your scientific question, your candidate dataset (yours or a publication), and anything you have already drafted or coded. Read the Project Proposal rubric before class. | ||
| 6 | 2026-09-29 | Tuesday | Chap. 2 - part D: Advanced R and R Markdown settings | Complete Chap. 2 - part C: Tables, Figures and References | ||
| 6 | 2026-10-01 | Thursday | Chap. 2 - part E: User-Defined Functions in R | Read material presented in Chap. 2 - part E: User-Defined Functions in R. Start drafting your individual project proposal | ||
| 7 | 2026-10-06 | Tuesday | 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. Continue working on your project proposal | ||
| 7 | 2026-10-08 | Thursday | Chap. 3: A roadmap to implement reproducible science | Read material presented in Chapter 3. Finalise your project proposal (due next session) | ||
| 8 | 2026-10-13 | Tuesday | Chap. 4: Open science and CARE principles | Read material presented in Chapter 4 and in Chapter 5 - Data Management | ||
| 8 | 2026-10-15 | Thursday | Complete Chap. 4 (group activities on CARE Principles and comparing FAIR & CARE Principles) and introduction to Chap. 5: Data Management | Read material presented in Chapter 5 - Reproducible Code | ||
| 9 | 2026-10-20 | Tuesday | Complete Chap. 5: Data Management and Chap. 5: Reproducible Code | Read material presented in Chapter 6. | ||
| 9 | 2026-10-22 | Thursday | Chap. 6: Getting published & Peer review | Work through the Chap. 7 tutorial materials uploaded to the shared Google Drive and install any R packages they require, so that you are ready for the laboratory on Tuesday. Collect my feedback on your project proposal and start building your workflow | ||
| 10 | 2026-10-27 | Tuesday | Bioinfo. tutorial - Chap. 7 | Students work on bioinformatics tutorials and their individual projects | ||
| 10 | 2026-10-29 | Thursday | Bioinfo. tutorial - Chap. 8 | Students work on bioinformatics tutorials and their individual projects | ||
| 11 | 2026-11-03 | Tuesday | Bioinfo. tutorial - Chap. 9 | Students work on bioinformatics tutorials and their individual projects | ||
| 11 | 2026-11-05 | Thursday | Bioinfo. tutorial - Chap. 9 | Students work on bioinformatics tutorials and their individual projects | ||
| 12 | 2026-11-10 | Tuesday | Bioinfo. tutorial - Chap. 10 | Students work on bioinformatics tutorials and their individual projects | ||
| 12 | 2026-11-12 | Thursday | Bioinfo. tutorial - Chap. 10 | Students work on bioinformatics tutorials and their individual projects | ||
| 13 | 2026-11-17 | Tuesday | Bioinfo. tutorial - Chap. 11 | Students work on bioinformatics tutorials and their individual projects | ||
| 13 | 2026-11-19 | Thursday | Bioinfo. tutorial - Chap. 11 | Students work on bioinformatics tutorials and their individual projects | ||
| 15 | 2026-12-01 | Tuesday | Bioinfo. tutorial - Chap. 12 | Students work on bioinformatics tutorials and their individual projects | ||
| 15 | 2026-12-03 | Thursday | Bioinfo. tutorial - Chap. 12 | Students work on bioinformatics tutorials and their individual projects | ||
| 16 | 2026-12-08 | Tuesday | Individual projects - feedback & Q&A | Revise your report using my feedback; prepare your presentation | ||
| 16 | 2026-12-10 | Thursday | Individual projects - feedback & Q&A | Finalise your presentation | ||
| 17 | 2026-12-15 | Tuesday | Oral presentations of individual projects | |||
| 17 | 2026-12-17 | Thursday | Oral presentations of individual projects |