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Student course material for the Applied Bioinformatics course at Scripps Research

Jupyter Notebook 100.00%

applied-bioinformatics's Introduction

Applied Bioinformatics

Welcome to the Applied Bioinformatics course offered at The Scripps Research Institute.

Instructors: Dr. Andrew I Su (@andrewsu)
Teaching Assistants (TAs):

Kai-Yu Chen (@chvbs2000)
Carolina Gonzalez (@Carolina1396)
Shashank Nagaraja (@dapluggg)
Roger Tu (@turoger)

This course is available in 2 parts and operates under the Computational Biology & Bioinformatics (CBB) core track:

Fundamentals of Scientific Computing, 4 weeks (1 credit)
1. Learn how to use RStudio and R
2. Learn basics of data visualization and exploratory data analysis
3. Learn to use R Notebooks
Applied Bioinformatics and Computational Biology (ABCB), 8 weeks (2 credits)
1. Learn the fundamentals of exploratory analysis of RNA-seq data, including PCA and clustering
2. Learn the fundamentals of differential expression analysis, enrichment analysis, and visualization
3. Practice and present on learned R skillset through published data via Capstone project.

Prerequisites

A recent computer running Windows 10/11, MacOS, or Linux (inform instructors if you have any concerns)
Software installation prior to first class (instructions)

Course Materials

This section will be updated as the course progresses.

Tuesday 2022-09-06: Course intro
- slides
- Homework due Monday 2022-09-12 3PM PT
Thursday 2022-09-08: Data visualization
- slides
- Homework due Monday 2022-09-19 3PM PT
Tuesday 2022-09-13:
- slides
- Homework due Monday 2022-09-19 3PM PT
Thursday 2022-09-15:
- slides (to be posted)
- Homework due Monday 2022-09-26 3PM PT

Credit to past instructors and TAs: Dr. Sabah Ul-Hasan (@sabahzero), Dr. Huitian Yolanda Diao (@Huitian), Dr. Karthik Gangavarapu (@gkarthik), Shang-Fu Chen (@ShaunFChen), Jerry Zak (@trebbiano)

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applied-bioinformatics's Issues

Lecture Materials: Updates Needed

A1.a: Slides 3, 4 (Jupyter vs colab, order of git), 11-16, 25-27
A1.b: Slide 10 (where are files for this slide?) update path for files and homework, unclear if we need all bash .md files (3) for Unit A

Record Lectures on Zoom for Canvas and Su Lab YouTube

Long-term interest in flipping classroom
Note YouTube links can be embedded in README on Github (Scripps Research YouTube channel)

HW5 notebook with the answer

HW5-Key uploaded now doesn't include any answer. Could you upload the notebook with the answer (Q3 and Q5-Q10) for us to review by ourselves?

Error message on jupyter notebook

Hi...I saved and restarted the kernel as the update comment suggested, then I tried to validate the homework running "validate", I'm getting this error message, and I found this resource (jupyter/nbgrader#883), but I'm not sure if I have the ability to fix the problem on my side:
There was an error running the validate command:

Traceback (most recent call last):
File "/opt/applications/python/3.6.3/gnu/lib/python3.6/site-packages/nbgrader/server_extensions/validate_assignment/handlers.py", line 46, in validate_notebook
result = validator.validate(fullpath)
File "/opt/applications/python/3.6.3/gnu/lib/python3.6/site-packages/nbgrader/validator.py", line 311, in validate
nb = self._preprocess(nb)
File "/opt/applications/python/3.6.3/gnu/lib/python3.6/site-packages/nbgrader/validator.py", line 290, in _preprocess
nb, resources = pp.preprocess(nb, resources)
File "/opt/applications/python/3.6.3/gnu/lib/python3.6/site-packages/nbgrader/preprocessors/checkcellmetadata.py", line 16, in preprocess
raise ValidationError(msg)
jsonschema.exceptions.ValidationError: Notebook failed to validate; the nbgrader metadata may be corrupted.