1 Course Information Hub

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.

2 Assignment Deadlines

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.

The project proposal may be revised and resubmitted for up to the full 50 points. This is optional and open to everyone, and the deadline is in Table 2.1 below. See Revise and Resubmit on the Assignments page for what to hand in.

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.

Table 2.1: Deadlines, point allocations and evaluation rubrics for EEB603, Fall 2026. The first row is not graded, but signing up on time is what sets your tutorial deadlines in Table 2. Times are Mountain Time. Every rubric is also on the Assignments page.
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
Individual project – proposal, optional revision – 2026-10-22 5 PM MT Rubric (self-evaluation)
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
Table 2.2: Bioinformatics tutorial deadlines by chapter, for the chapters taught by student groups. Find the chapter you signed up for and note your dates. Submitting to me one week before you teach is a firm deadline: your peers need that week to prepare.
Chapter Submit to me for review Upload to Google Drive Taught in class
Chapter 9 2026-11-03 2026-11-05 2026-11-10 & 2026-11-12
Chapter 10 2026-11-10 2026-11-12 2026-11-17 & 2026-11-19
Chapter 12 2026-11-17 2026-11-19 2026-12-01 & 2026-12-03
Chapter 11 2026-12-01 2026-12-03 2026-12-08 & 2026-12-10

3 Schedule

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.

Homework shown as a bulleted list is confirmed. Plain-text entries further down the table are provisional: they describe what I expect to set, and I will itemise them as each session approaches. If in doubt about what is actually due, work from the bulleted entries and from the deadlines in Table 2.1 above.

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.

Table 3.1: Tentative schedule for EEB603 Reproducible Science, Fall 2026 semester.
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
  • Note any questions you have, and ask them in class
✔
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 (on Google Drive)
  • Identify its reproducibility challenges, ready to discuss them with your group
✔
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) (on Google Drive)
  • Read the Summary (pages 5-19) of the Reproducibility and Replicability in Science report, from The National Academies Press (on Google Drive)
✔
3 2026-09-08 Tuesday Complete Chapt. 1 - part B and start Chap. 2 - part A: Learning the basics ✔
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 ✔
4 2026-09-15 Tuesday Complete Chap. 2 - Part A: Learning the Basics ✔
4 2026-09-17 Thursday Chap. 2 - Part B: Setting Your R Markdown Document (up to the end of Install R Dependencies and Load Packages) ✔
5 2026-09-22 Tuesday Complete Chap. 2 - Part B (starting at Generate a Citation File of R Packages Used) and start Chap. 2 - Part C: Tables, Figures and References ✔
5 2026-09-24 Thursday Individual project workshop: develop your project and proposal with feedback from me ✔
6 2026-09-29 Tuesday Review Chap. 2 - Part C: Tables, Figures and References, then Chap. 2 - Part D: Advanced R and R Markdown Settings ✔
6 2026-10-01 Thursday Insert a Figure from an Image File: a 20-minute challenge filling a gap in Part C, then Chap. 2 - Part E: User-Defined Functions in R: what a function is, and your first UDF ✔
7 2026-10-06 Tuesday Complete Chap. 2 - Part E: User-Defined Functions in R, starting at Create, Name, and Access Elements of a List in R
  • Finish UDFs That Return a Single Value: implement square_number.R and apply it, then check your work against that section’s Checkpoint
  • Your individual project proposal is due by 5 PM on Thursday, 8 October. It must be an R Markdown source that knits — not a PDF or a Word file — so leave time to check that it does. Bring any questions to Tuesday’s class: it is your last chance to ask before you submit
✔
7 2026-10-08 Thursday Complete Chap. 2 - Part E in full: pairs present their code for UDFs that Return Multiple Values at the whiteboard, then Logical Operators, Defensive Programming and Use Your UDFs in an R Markdown Document. We then start Chap. 3: A Roadmap for Reproducible Science: the steps of the scientific process and the threats to it
  • Make sure you have completed Develop, Implement, and Apply UDFs that Return Multiple Values: your pair presents its plan and its code at the whiteboard at the start of class, so the function needs to be written and tested
  • Finalise and submit your individual project proposal by 5 PM. Hand in a folder named with your first and last name (for example Jane_Doe) containing the .Rmd source and everything needed to knit it: the .bib, the .csl, any data and any images. See How to Submit It. Before you submit, check that it knits without error, contains at least one code chunk that runs, and manages its citations through a bibliography file. A PDF or Word file cannot earn the marks reserved for a working reproducible document
✔
8 2026-10-13 Tuesday Chap. 3: a 15-minute synthesis of the steps of the scientific process and the threats to it from the slides, then the group activities Do Your Standards Hold? and Score Your Charter Against TOP, with the TOP Guidelines in between ✔
8 2026-10-15 Thursday Complete Chap. 3 with the presentations of both group activities in the first 10 minutes, then Chap. 4: Open Science and CARE Principles
  • Finish updating your charter from the Do Your Standards Hold? activity: every threat tested, the clauses written, and the remaining gaps recorded as dated to-dos
  • Complete the journal comparison: each member takes a different journal they might realistically publish in and finds its TOP policy, noting one place it is stricter than your charter and one place your charter is stricter than it
  • Prepare a five-minute group presentation for the start of class, covering both Chapter 3 activities: the threat your charter handled best, the gap that surprised you most and the clause you wrote, your highest and lowest TOP standards, and what the journal comparison showed
  • Pre-read the two frameworks the activities use: FAIR Data, The CARE Principles for Indigenous Data Governance and Data Sovereignty. The three activities done in class apply these rather than introduce them, so a pair arriving without them spends its fifteen minutes looking up definitions instead of thinking
✔
9 2026-10-20 Tuesday Complete Chap. 4 with the FAIR pairs’ report and the CARE Principles activity, then Chap. 5 - PART A: Data Management
  • Pre-read the seven stages of the data life cycle: Planning, Creating, Processing, Documenting, Preserving, Sharing and Reusing data. My pass over them in class is a synthesis, not your first contact with them
  • Complete the Before Class Activity: create a Chapter_5 folder in your Chapters folder, beside Chapter_2, start a script named Chapter_5_data_management.R, and use it to download and unzip Messy_Project.zip. Do not tidy the project up: its state is the exercise. Bring your laptop
✔
9 2026-10-22 Thursday Complete Chap. 5 - PART A with Steps 2, 3 and 4: open a csv, build the Defect_log and the metadata, and start diagnosing the area your pair owns ✔
10 2026-10-27 Tuesday 💻 On Zoom. Chap. 5 - PART B: Reproducible Code, first of two classes: the One Pass Over the Workflow, then Step 1: Try to Run It and Step 2: Diagnose the Area Your Pair Owns. The reporting round, which also closes PART A, moves to the next class ✔
10 2026-10-29 Thursday 💻 On Zoom. Chap. 5 - PART B group activity: Step 3: report your data and code defects together, then Step 4: write the clauses, one for the data and one for the code. Step 5: merge the eight clauses into your charter is homework, and we go over the charters briefly at the start of the next class ✔
11 2026-11-03 Tuesday A short pass over the clauses you wrote into your charters, then Open Access, Creative Commons Licenses and Software Licenses, the licences on the article, the data and the code. Then a work session on your bioinformatics tutorials: bring your tutorial in progress; I am there to give feedback as you build it
11 2026-11-05 Thursday Work session: individual projects. I am away this day, so use the class time to build your report. Bring anything you want me to look at to the following class
  • Use the session to write. The final report is due 3 December, and this is protected time for it
  • Keep working on your bioinformatics tutorial
12 2026-11-10 Tuesday Bioinfo. tutorial - Chap. 9: get the material here and work through it before class Students work on bioinformatics tutorials and their individual projects
12 2026-11-12 Thursday Bioinfo. tutorial - Chap. 9: get the material here and work through it before class Students work on bioinformatics tutorials and their individual projects
13 2026-11-17 Tuesday Bioinfo. tutorial - Chap. 10: get the material here and work through it before class Students work on bioinformatics tutorials and their individual projects
13 2026-11-19 Thursday Bioinfo. tutorial - Chap. 10: get the material here and work through it before class Students work on bioinformatics tutorials and their individual projects
15 2026-12-01 Tuesday Bioinfo. tutorial - Chap. 12: get the material here and work through it before class Students work on bioinformatics tutorials and their individual projects
15 2026-12-03 Thursday Bioinfo. tutorial - Chap. 12: get the material here and work through it before class Students work on bioinformatics tutorials and their individual projects
16 2026-12-08 Tuesday Bioinfo. tutorial - Chap. 11: get the material here and work through it before class Revise your report using my feedback; prepare your presentation
16 2026-12-10 Thursday Bioinfo. tutorial - Chap. 11: get the material here and work through it before class Finalise your presentation
17 2026-12-15 Tuesday Oral presentations of individual projects
17 2026-12-17 Thursday Oral presentations of individual projects