Final Project 2: progress report

Author

Affiliations

Jelmer Poelstra

CFAES Bioinformatics Core, Ohio State University

Dept. of Plant Pathology, Ohio State University

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Minor changes to this document may still be made. We’re sharing it now to give you an idea of what to expect.

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Overview

The second Final Project checkpoint is to submit the current version of your Final Project repository, including a report on your progress. This is worth 10 points.

Directions and grading

Submission expectations

• Deadline: Sunday Nov 29^th at 11:59 pm.
• Submission: Submit your assignment by tagging @kstarr791 and @jelmerp in a new Issue in your GitHub repo.

Academic integrity

	Use of generative AI Tools is permitted.
	Open-book research for the assignment is permitted.
	Getting help on the assignment is not permitted, except from the instructors.
	Collaborating, or completing the assignment with others, is not permitted.
	Copying or reusing previous work is not permitted, except as described on the general info page.
	APA Citations and/or formatting for this assignment are not required.

Rubric

You can earn a total of 10 points as follows:

Item	Points
1. Scripts	4
2. Directory structure, README, and protocol	2
3a. Overview of scripts	1
3b. To-do list	1
3c. Response to proposal feedback	1
Git commits	1

Detailed steps

Make sure you have the following in your Final Project’s GitHub repository:

1. One or more (Bash/R/Quarto) scripts with a significant amount of code.
   The scripts do not need to be complete or functioning yet, but make sure we can understand what you are trying to do, and what the general purpose of each script is. You can earn as many points with clarity of purpose and documentation (use comments!) as with the code itself.

2. A sensible directory structure, a README, and a draft protocol.
   Your project should already be organized the way you intend to keep it, and your README.md should briefly describe the project’s goals. Also start the protocol Markdown file for your project (see week 10): include the actual commands for the steps you have scripts for so far, and for later steps, just a heading with a one-line description.

3. A file doc/progress-report.md, with the following sections:

   1. An overview of all the scripts you envision writing, and what each one does.
      This is essentially a more fully worked-out version of the workflow steps in your proposal (some remaining uncertainties are fine!).

   2. A to-do list.
      This could be a separate list, or it could be integrated with the overview of scripts mentioned above.

   3. How you have addressed the feedback on your proposal.
      Briefly describe what you changed based on our discussion of your proposal — or what you decided not to change, and why.

   4. Optionally, you can explicitly request feedback or advice on certain aspects of your project, or point us to files to look at or to ignore.

Finally, note that we will also look at your Git commits and associated commit messages.