MIIM-620S Blackboard (Bb) Learn course site
Recent advances in molecular biology and computational achievements have generated an explosion of data that surveys biological processes on a massive scale. Collectively referred to as ‘omics scale data, these techniques have revolutionized our ability to explore complex phenotypes in microbiology & immunology. This course covers the history, application, and computational analysis of ‘omics scale data and provides hands-on analysis experience.
- Recognize popular next-generation sequencing technologies and distinguish their appropriate uses.
- Recognize how to apply OMICS scale techniques to multiple facets of microbiology and immunology.
- Design OMICS scale experiments to inspect biological functions across DNA, RNA, and proteins.
- Perform basic terminal activities such as moving, copying, inspecting files, and calling installed tools as well as employ pipes to chain small functions together to create complex analyses.
- Utilize Jupyter Notebooks to perform data analysis and visualization of OMICS scale data.
- Practice presenting OMICS scale data analysis to both traditional & computational biological audiences.
| Instructor | ABC | Role |
|---|---|---|
| Dr. Will Dampier | WND | Co-Director, Instructor |
| Dr. Joshua Earl | JPE | Instructor |
| Dr. Katherine Innamorati | KAI | Instructor |
| Dr. DV Klopfenstein | DVK | Instructor |
| Dr. Joshua Chang Mell | JCM | Co-Director, Instructor |
| Name | Grade | Description |
|---|---|---|
| Class Participation | 25% | Participation in weekly lecture and in-class learning activities. |
| Weekly Assignment | 50% | Completing weekly assignments |
| Project | 25% | Weekly analysis of your own dataset |
This repository contains all of the learning content for the course and will be the way you submit all assignments.
The content folder contains the learning content organized by week.
You will pull this from the main repository each week.
Within each week's assignment you will be asked to create a notes_{github-user}.md file as you complete the assignments in each week's folder.
As you complete the assignment you will commit these notes and when complete, make PRs to the main repository.
This is how you will submit assignments.
The projects folder contains information about the ongoing project and is where you will keep information and notes.
| Week | Date | Module | Topic | Instructors | Status |
|---|---|---|---|---|---|
| 1 | 08/22/2023 | Hello World | Course intro, git, & JupyterHub | DVK, KAI | released |
| 2 | 08/29/2023 | Hello World | Terminal + git: push & "Pull Requests" | DVK, KAI | released |
| 3 | 09/05/2023 | Hello World | Sequencing datasets & terminal analysis | WND, JCM | released |
| 4 | 09/12/2023 | Align all the things | NGS read alignment | WND, JCM | released |
| 5 | 09/19/2023 | Align all the things | Counting aligned reads | WND, JCM | released |
| 6 | 09/26/2023 | Align all the things | Variant calling | WND, JCM | released |
| 7 | 10/03/2023 | Align all the things | Interpreting variant effects | WND, JCM | released |
| 8 | 10/10/2023 | OMICS as count table | Transcriptomics | WND, JCM | released |
| 9 | 10/17/2023 | OMICS as count table | Statistical Analysis of Count-Data | WND, JCM | released |
| 10 | 10/24/2023 | OMICS as count table | Introduction to the powerful vim editor | DVK | released |
| 11 | 10/31/2023 | OMICS as count table | Gene Ontology Enrichment Analysis | DVK | released |
| 12 | 11/07/2023 | OMICS as count table | Peak analysis in OMICS data (ChIP-Seq) | WND, JCM | unreleased |
| 13 | 11/14/2023 | Genome Comparisons | Microbiome creation | JPE, KAI | unreleased |
| 14 | 11/21/2023 | Genome Comparisons | Microbiome analysis | JPE, KAI | unreleased |
| 15 | 11/28/2023 | Genome Comparisons | Microbiome metrics | JPI, KAI | unreleased |
| 16 | 12/05/2023 | Future directions in OMICS | Everyone | unreleased |
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