9.401 | Fall 2022 | Graduate

Tools for Robust Science

Week 5 Tool: Dynamic Executable Papers and Fair Open-Source Processing Pipelines

The Tool

Practical skills assignment

  1. Use a tool for making a dynamic executable document (R Markdown; Jupiter Notebook; Matlab Notebook) to write this week’s assignment. In your executable document, use your own data (or data from another paper) to make at least one reproducible figure. 
  2. Zotero has partnered with Retraction Watch to automatically flag retracted papers in a user’s repository. Download Zotero if you do not already have it, and either import a repository from your current citation manager or manually import a few papers of your choice if you do not use a citation manager. Look through one of your repositories, and see if any papers are flagged as retracted. If not, add a retracted paper (you can find many on Retraction Watch’s database) to the repository. Is it correctly flagged as retracted? Do you think this flag is noticeable enough to be a useful tool in preventing the use of retracted papers?

In part 2 of your response paper, describe what you did in fulfilling this activity. What snags did you hit? What made this process easier or more difficult? Did you find any errors?

Dynamic documents: Sharing data and the code to make the figures all at once:

Detecting and responding to mistakes and fraud:

Course Info

As Taught In
Fall 2022
Learning Resource Types
Written Assignments