Modules

Introduction to Open Science

Overview

This page outlines the four main modules of the course and their associated weeks, topics, and key activities. Use this as a roadmap for the semester and a guide to the detailed readings and assignments posted on the course site.

Module 1: Foundations of Open Science

Weeks: 1–4
Guiding questions: What is open science, why has it emerged, and how does it relate to reproducibility?

Weekly Breakdown

Week 1 – What is Open Science?
- Topics: History and motivations, open vs. closed research, myths about openness.
- Activities: Discussion of exemplar open projects, short diagnostic survey on prior experience.
- Suggested Deliverable: Reflection on your current research workflow.

Week 2 – The Reproducibility Crisis
- Topics: Replication failures, methodological reforms, preregistration and registered reports.
- Activities: Reading discussion on replication case studies, in-class critique of a methods section.
- Suggested Deliverable: Reflection 1 (reproducibility in your field).

Week 3 – Frameworks and Standards
- Topics: FAIR principles, TOP guidelines, data and code availability statements.
- Activities: Group mapping of a research project to FAIR and TOP, discussion of journal policies.
- Suggested Deliverable: Short memo identifying a target journal’s openness policies.

Week 4 – Research Workflows and Project Structure
- Topics: Folder organization, naming conventions, documentation as part of the workflow.
- Activities: Walkthrough of a well-organized open project repository.
- Graded Deliverable: Lab 1 – Project skeleton (directories, README, basic documentation).

Module 2: Tools for Reproducible Research

Weeks: 5–8
Guiding questions: How can we use tools to make our work traceable, repeatable, and automatable?

Weekly Breakdown

Week 5 – Version Control with Git
- Topics: Commits, branches, merging, working locally with Git.
- Activities: Live demo of Git basics, practice committing and reverting changes.
- Graded Deliverable: Lab 2 – Git basics (initialize repo, commit history, branching exercise).

Week 6 – GitHub for Collaboration
- Topics: Remote repositories, pull requests, issues, project boards.
- Activities: Pair activity using pull requests and code review; setting up a course organization or team.
- Suggested Deliverable: Reflection 2 (collaboration norms and practices).

Week 7 – Literate Programming with Quarto
- Topics: Quarto documents, parameters, rendering to HTML/PDF, reproducible reports.
- Activities: Build a simple analysis report from data import to figure and narrative.
- Graded Deliverable: Lab 3 – Reproducible report (Quarto document with code and narrative).

Week 8 – Data Management and Documentation
- Topics: Tidy data, metadata, README files, data dictionaries.
- Activities: Critique and improve an example dataset and its documentation.
- Graded Deliverable: Data & code checklist for your project.

Module 3: Sharing, Collaboration, and Openness

Weeks: 9–11
Guiding questions: How do we share our work responsibly and effectively so that others can reuse and build on it?

Weekly Breakdown

Week 9 – Sharing Data and Code
- Topics: Repositories (GitHub, OSF, Zenodo), DOIs, versioned releases.
- Activities: Evaluate different repository platforms for a sample project.
- Suggested Deliverable: Reflection 3 (where and how you will share your work).

Week 10 – Licensing and Attribution
- Topics: Creative Commons licenses, software licenses (MIT, GPL, etc.), citation and credit.
- Activities: License selection exercise for sample projects and materials.
- Graded Deliverable: Lab 4 – Licensing plan for your open project.

Week 11 – Open Peer Review and Feedback
- Topics: Peer review models, open reports, constructive feedback practices.
- Activities: In-class peer review workshop using project drafts.
- Graded Deliverable: Peer review of a classmate’s repository and report.

Module 4: Applications, Ethics, and Project Synthesis

Weeks: 12–14
Guiding questions: How can open science be practiced ethically and equitably, and how will you apply it in your own work?

Weekly Breakdown

Week 12 – Ethics, Equity, and Inclusion in Open Science
- Topics: Power and access, data justice, risks of openness, community-engaged research.
- Activities: Case study discussions on ethical dilemmas in sharing data and code.
- Suggested Deliverable: Reflection 4 (ethical considerations in your project).

Week 13 – Open Science in Practice
- Topics: Case studies across disciplines, institutional and funder policies, career implications.
- Activities: Guest speaker(s), panel discussion, project troubleshooting clinic.
- Graded Deliverable: Lab 5 – Project refinement checklist and action plan.

Week 14 – Project Presentations and Course Reflection
- Topics: Communicating your open project, lessons learned, next steps.
- Activities: Short presentations or lightning talks; group reflection on open science practices.
- Graded Deliverable: Final open project due (repository, documentation, and rendered report/site).

How to Use This Page

  • Use the modules as a high-level roadmap; consult the Assignments and Syllabus pages for detailed requirements and grading.
  • Links to readings, slides, and datasets will be added to each week’s section as they are finalized.
  • This outline is tentative and may be updated during the semester; any changes will be announced in class and on the course home page.