Complete, free Genomics course (Lecture notes, recordings, assignments and tests!)

Published: July 31st, 2022   Last Modified: November 12th, 2022

During the fall of 2020 I had the opportunity to design and teach a Genomics course for 60+ 4th year undergraduate biology students. It was one of the harder (but also most rewarding) things I’ve had to do, especially with 3 months to prepare. I’m proud of the course I delivered and I’d like to share ALL my class materials so that the next person has an easier time than I did 🙂 As well, the field of Genomics moves so fast I don’t want it to be completely out of date before somebody gets some use out of it.

Click read more for links to the rationale behind the design of the course, caveats, credits, etc!

Table of Contents:

Material Links
Course Structure
Course Goals
Course Content
Important Teaching Tips / Considerations
Caveats / Limitations
Credits
Copyright Information

Material Links:

– Course Materials (.zip)
– Course Materials Google Folder
– Lecture Recordings (.zip)
– Lecture Recordings Google Folder
– Assignment 1 Raw Data (Read caveats!)

Course Structure:

– Two 1-hour lectures online lectures per week
– 3 Modules
– 3 Assignments
– 3 Tests
– No final exam
– No textbook

Course Goals:

– Provide 4th year undergraduate students who have had little or no bioinformatics experience with a practical introduction to Genomics
– Prioritize understanding material vs pure memorization
– Focus on reading and understanding current literature from Genomics
– Provide hands on experience of beginner level bioinformatics with assignments
– Deliver course purely online due to covid

Course Content:

Introductory Module
1) Brief History
2) Types of genomes
3) Structural vs Functional vs Comparative Genomics
4) What questions can we answer with Genomics?

Module 1 – Structural Genomics
1) Chromosome structure/number and gene mapping
2) Epigenetics
3) Genome sequencing technologies
4) Assembly of genomes
5) Annotation of genomic DNA
6) Genetic markers and mutations

Assignment 1
– Assemble, annotate and explore a small bacteria genome with Galaxy

Module 2 – Functional Genomics
1) Sequence alignment
2) Annotating protein function with BLAST
3) Methods of determining protein function and interactions
4) Proteomic analysis
5) Transcriptome analysis of gene expression

Assignment 2
– Analyze RNA-Seq data to identify differentially expressed genes in nematode infested Arabidopsis

Module 3 – Comparative Genomics
1) Homologs/paralogs/orthologs
2) Genome wide association studies
3) Genome evolution
4) Phylogenetic analysis

Assignment 3
– Retrieve viral sequences and construct phylogenetic trees to determine evolution of SARS-COV 2

Important Teaching Tips / Considerations:

– Having 60+ students pile onto a single galaxy server wasn’t the best idea for numerous reasons. With only a few months to get the course ready I had to distribute the load between several public servers online. Each server is slightly different in terms of tools available, setup etc. This makes troubleshooting student problems difficult.

– If I were to do this again I would spend the time coordinating with IT to set up a custom galaxy server at the university. SERIOUSLY, consider this before running this type of course!!! 3 months is NOT enough notice for the IT people to set up a custom server for you!!!

***Update*** The official galaxy servers can offer personal instances for you, shoot them an email!

– Don’t be afraid to cut down the size of datasets for analysis. Yeah assembling a few gigabytes is cool but it takes a lot longer for students and can be frustrating if the job crashes.

– Run through all bioinformatics assignments BEFORE you make them live! Tools will break…servers will go down…make sure it works before you send it to students.

– Have students post their questions onto some kind of public forum (Moodle, custom wiki…) instead of emailing you. This significantly cuts down repetitive troubleshooting.

– Be kind and patient with your students! Online learning during covid was hard for everyone, patience goes a long way.

– MOST undergraduate students don’t want to go to grad school or become a research scientist, probably about 1% in a given class do. Accept and respect this early on.

– Dealing with the human element of teaching is one of the hardest parts. You will encounter students who are easy to teach and those that need help or will directly challenge you. You WILL get nasty, frustrated emails. Learn about your university policies and ask other faculty for advice for how to proceed. NEVER reply in anger! If you reply emotionally you lose, even if you’re in the right. Walk away from the computer and come back with a clear head.

– Sometimes your students will stump you with questions. It’s okay! Tell them you’ll revisit their question next class, and don’t forget to follow up.

Caveats / Limitations:

– This was my first time designing a course and delivering it, some professors have decades to perfect their craft, bear with me 🙂

– I have moved on from academia since I taught this course so it is unlikely I will have time to make corrections, the material is provided as is! If you are struggling in some way please leave a comment and I will try to get back to you.

– The intended audience are 4th year undergraduate students who have had little to no exposure to this subject. If you are reading this far in the future you may be teaching bioinformatics in first year in virtual reality!

– Genomics is an enormous field! I tried to do the breadth of it justice but you only have a few hours a week in 4 months to teach the material. There’s only so much you can (and should) say. If I haven’t touched a subject near and dear to your heart, I’m sorry.

– I anonymized the raw data for Assignment 1 so well I lost the original source. Woops! I shared my galaxy history that contains the raw data, but I would recommend adapting the assignment with data you know the source of. Also, who knows when Galaxy will purge the raw data, so download it if you need it!

Credits:

First, my PI, who listened to every one of my lectures and always gave me constructive feedback. I couldn’t have done it without your mentorship, thank you.

Credit to all the authors of the papers I featured.

Credit to the Galaxy bioinformatics team for making software that novices can use.

Credit to the administrators of the American, European and Australian galaxy servers for letting us use your resources!

Credit to Matthew Anthony Escobar, William Morgan, Irina Makarevitch, Sabrina Robertson for their design of a Galaxy based bioinformatics assignment (Tackling “Big Data” with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy) which I adapted for Assignment 2.

!!! I’ve tried to give credit where it’s due but for pictures I snatched off the internet I often do not have a URL. I’ll gladly add you into the credits if you notice something that’s yours. !!!

Copyright Information

– You are free to use any of the materials provided for educational purposes without asking me for permission first.

– You can credit me somewhere if you wish, but I won’t be offended if you don’t.