CS 4980 Schedule, Spring 2025

CS 4980, Developing an AI Tool to Enhance Research in Health / STEM, Spring 2025

Class Schedule

WK Class/Date Topic Readings Links

1 Week of 1/29 Prep / Set-up / Student recruitment

2 Week of 2/3 Prep / Set-up / Student recruitment

3 Week of 2/10

4 Week of 2/17

5 Week of 2/24 Complete 'All of Us' training:
How to Register as an All of Us Researcher.
Instructions from Dr. Youngblom below -- read before you start the training.

6 Week of 3/3 Watch videos about how to access All of Us platform.
Go through code base in github, using API keys RY will supply. Test code.
Test command line version of the program to see how it work. RY will supply sample "research questions".
Get the code from Anthropic to "answer the question" and see if you can use that code to get answers from All of Us.
Meet RY Monday morning at 9 - 9:30am.
Explore data browser at https://databrowser.researchallofus.org/. Get a feel for the data, and the questions biologists are interested in.

7 Week of 3/10 Tasks for students:
Make notes on control flow improvements. (Make program run smoother.)
Make notes on improvements for testing user inputs.
Continue to take notes on needed fixes; put as 'issues' in git.
Come up with plan for a small program that uses the Anthropic/Claude API. Program interaction with Claude cannot be "one off" - must ask, take response, do something, feed prior response back to Claude... Send plan to RY by Monday.
Watch Tkinter video; link sent by RY.
Make 3-5 questions for RY, JY, MT.

8 Week of 3/17

9 Week of 3/24

10 Week of 3/31 School Holiday: Cesar Chavez Day / Spring Break

11 Week of 4/7

12 Week of 4/14

13 Week of 4/21

14 Week of 4/28

15 Week of 5/5

16 Week of 5/12

17 Final Exam Week

Assignments

Week of 2/24: "The link below explains how to create an account and register for the training through All of Us: https://www.researchallofus.org/register/
For step 1, our University already has a DURA agreement with All of Us, so you can start with step 2 (create an account and verify your identity). Let me know anytime you have any question at all about anything.
1) get registered through All of Us. Go through the "Registered tier" training. You need clearance through the Controlled tier to get access to the genomic data. I don't know if we will be able to get to using the genomic data this semester, but it may be worthwhile for you to see what some of the data looks like. The Controlled tier is a harder quiz than the Registered tier and students often need more than one chance to pass it, so don't get upset if you need to take it again."

Links

Follow the link on this page to the O'Reilly library. If you are off-campus, this link will connect to campus so you can log into Safari TechBooks using your student ID and login.

https://library.csustan.edu/computerscience/articles

Google's Style Guide for Python Code

Python GUI Programming with Tkinter - Second Edition by Alan D. Moore. (The link may not work. You may be required to go to the CSUS Library, click on their Safari TechBooks link, authenticate yourself, then search for the book.) I found this book on a couple "best Tkinter books" lists.

Learning Git by Anna Skoulikari (From O'Reilly's own publishing wing). There is also a Head-First Git book available.

Anthropic's Quickstarts

WK	Class/Date	Topic
1	Week of 1/29	Prep / Set-up / Student recruitment
2	Week of 2/3	Prep / Set-up / Student recruitment
3	Week of 2/10
4	Week of 2/17
5	Week of 2/24	Complete 'All of Us' training: How to Register as an All of Us Researcher. Instructions from Dr. Youngblom below -- read before you start the training.
6	Week of 3/3	Watch videos about how to access All of Us platform. Go through code base in github, using API keys RY will supply. Test code. Test command line version of the program to see how it work. RY will supply sample "research questions". Get the code from Anthropic to "answer the question" and see if you can use that code to get answers from All of Us. Meet RY Monday morning at 9 - 9:30am. Explore data browser at https://databrowser.researchallofus.org/. Get a feel for the data, and the questions biologists are interested in.
7	Week of 3/10	Tasks for students: Make notes on control flow improvements. (Make program run smoother.) Make notes on improvements for testing user inputs. Continue to take notes on needed fixes; put as 'issues' in git. Come up with plan for a small program that uses the Anthropic/Claude API. Program interaction with Claude cannot be "one off" - must ask, take response, do something, feed prior response back to Claude... Send plan to RY by Monday. Watch Tkinter video; link sent by RY. Make 3-5 questions for RY, JY, MT.
8	Week of 3/17
9	Week of 3/24
10	Week of 3/31	School Holiday: Cesar Chavez Day / Spring Break
11	Week of 4/7
12	Week of 4/14
13	Week of 4/21
14	Week of 4/28
15	Week of 5/5
16	Week of 5/12
17		Final Exam Week