dasaderi/python_neurobootcamp

python_neurobootcamp's Issues

Day 3 (electrophys data)

Switch with Day 3.

• Move functions and loops to top
• Make electrophys section more didactic
• Move plotting over to Seaborne
• Move file loading into Appendix section

Eliminate discussion of differences between Python 2 and Python 3 in day1

As suggested, I would just mention that there are some key differences between Python 2 and Python 3 and that students need to make sure they're working with Python 3 when writing code.

All Days

Make sure to:

1. Number the sections for each day (i.e., 1.1,1.2,1.3 for day 1, etc)
2. If you refer to another day, use their section number

Day 4

• Add more exercises
• Think about a dataset to use for day 5 (maybe pull stats files for multiple stains, and do some aggregate visualization across stains)

Finalize syllabus by December 14

We need to provide students who enroll with a syllabus. Ted and I drafted one, but it needs more polishing. Please take a look at it here.
Thanks!

Switch Day 3 to Day 2

We will switch day 3 (pandas, electrophys) and day 2 (pandas, imaris) to ramp up in complexity.

Also, we will add to day 2 (pandas, imaris)
[ ] Paths
[ ] Pandas intro
[ ] Intro to Functions
[ ] Import statements

changes made to day 2 based on Zack's comments

the only comment I didn't address yet was:

"What do the ".loc" and ".iloc" methods do? Why are they necessary to select particular rows and columns? I found the first exercise difficult until I realized that I was not indexing directly into the data frame rather than using one of these these methods, then indexing."

I just wasn't sure what level of detail we wanted to get into to explain with using loc() is optimal

Day 5 - Skeletal Notebook

General task for final evaluation:

1. Take a folder full of files (either different electrophys files, or stats for different dyes for imaging)
2. Load files and combine them into a single DataFrame
3. Do aggregate measure across experiment (i.e., average intensity for each file, to look for batch effects).

Ted to do:

1. Start day 5 folder and simple outline for the files

Lisa to do:

1. Copy installation notes to day 5 folder

Decide what to do on Day #5

We have not yet defined what it will happen on Day #5. @bburan proposed we leave it open to questions from the students. I think that is a good idea, but we might need to have it a bit structured.

For instance, we could ask students to bring in their own data (if they have it) and help them load into a notebook where they could do some simple manipulations. If students don't have datasets, they can pair up or form small groups.

More/better ideas?

Set up the Jupyter Hub

Stephen will set up the Jupyter Hub using our AWS account.

We will need everyone to help test this out whenever it's set up.

Day 3

I'm just going to document our progress/timeline about Day 3 here.

Timeline

January 10: final deadline
January 1: Ready for final testing/walkthrough
December 11: First Draft for testing
December 3: get started, look at Data
November 26: have data ready (Ted)

Testing Notebooks and Jupyter Hub

Zack to start testing December 19.

Stephen, we'll need to test out the jupyter hub, so Zack should probably do all testing through the hub and identify any issues.