Many biomedical research graduate programs have been compelled to “go online” with little or no notice due to the COVID-19 pandemic. Since many professors are distinctly uncomfortable in front of a camera, students may not get exposure to some of the topics that they might have expected. Since my move to South Africa in 2015, I have tried to deposit video on YouTube (and PDFs of the slides to Google Drive) every time I have delivered a lecture for students. Since I teach a fairly broad range of coursework, the catalog of topics may be useful for students working from home or for departments that are trying to ensure their students get the training they need. This page indexes the series of lectures I have made available. I hope you enjoy watching them as much as I have enjoyed creating them! (Please see the note about copyright and attribution at the bottom.)
I would like to start with the core part of my curriculum. Most of the researchers I train need help to analyze the reams of data coming from massively parallel sequencing experiments. I have delivered these five lectures in a variety of revisions at three different universities in the Western Cape. This year I chose a new structure to put mapping and assembly right up front and to give myself a bit more room for some of the other topics. The amplicon lecture started at the University of the Western Cape but now has evolved strongly enough in the microbiome direction that it will be taught at my own campus, as well.
|Sequencing, Mapping, and Assembly||1:29:58|
|Gene-Finding and Sequence Alignment||1:30:00|
|Genetic Variants, Phenotype, and GWAS||1:08:20|
|Gene Expression and Differentiation||1:20:14|
|Amplicon and Microbiome Informatics||1:15:28|
|A Quick Tour of Oligo7 Primer Design Software||none||0:06:01|
Bioinformatics Beyond Sequences
Of course, bioinformatics is critical for producing information from all kinds of data, not just those from sequencers. I feel it is important for bioinformatics students to learn about basics like ASCII and the representation of image data in memory. An emphasis on the essentials of biological pathways always finds its way into my teaching line-up; I feel grateful that my colleague Bing Zhang was willing to explain so much of this topic to me!
|Computer Science Concepts in Bioinformatics||1:14:21|
|Image Analysis and Flow Cytometry||0:55:34|
|Relational Databases and Repositories||0:52:43|
|What does this gene do?||0:49:33|
|Biological Pathways and Networks||1:16:48|
For twenty years, I have been publishing in the field of proteomics, and its rich informatics is something I want to share with every student! Frequently, though, I find that proteomics content is reduced to just a single lecture for our division’s B.Sc. Honours students. I was pleased as I looked back through my YouTube channel to discover lectures on a much broader range of subjects. The identification of MS/MS to peptide sequences continues to be my “wheelhouse,” but many aspects of this field fascinate me just as much today as they did a decade ago. I have highlighted the lectures designed for classrooms.
|Why Bother with Proteomics?||0:28:03|
|Fundamentals of Biological Mass Spectrometry||planned||0:00:00|
|Peptide and Protein Identification from MS/MS Data||1:27:14|
|Hands On: MSFragger Database Search with IDPicker Protein Assembly||none||1:10:16|
|Hands On: MSFragger Database Search with Philosopher Protein Assembly||none||0:42:08|
|Identification of Post-Translational Modifications||0:58:14|
|Proteomics in biofluids||planned||0:00:00|
|Fractionation Strategies in Proteomics||planned||0:00:00|
|Proteomic Quality Control||1:49:35|
|Adventures at the Proteome-Genome Boundary||0:46:02|
|Proteogenomics in Mycobacteria||0:48:13|
|The Secret Lives of Amino Acids||none||0:42:34|
|Protein Structure Determination and Estimation||1:00:04|
I am definitely a visitor in the field of metabolomics, but only recently have enough researchers been available in this field that departments who want this emphasis can hire a professor in the space. In my final year at Vanderbilt University (2015), I organized a course demonstrating two of the most widely used tools in the field: XCMS and METLIN. From what I have read in metabolomics papers, 2015 is essentially before the last ice age. Still, I felt these lectures could be useful to newcomers in the field.
|The Origin and Tools of the ProteoWizard Project||0:40:46|
|Advanced Options in ProteoWizard msConvert||0:40:30|
|XCMS Feature Finding and Retention Time Warping||0:41:30|
|Statistics of differentiation||0:35:55|
|METLIN and MassBank||0:46:55|
|Lipid Identification with Greazy and LipidLama||0:32:51|
The Department of Biotechnology at University of the Western Cape sought to broaden the medical content available in their B.Sc. Honours curriculum, so I teamed with talented post-doc Dr. Caroline Beltran to create a module. 2020 will represent the third year the course is presented; in 2019, when this was filmed, Dr. Byron Reeve assisted by teaching the gene expression segment.
|Introduction to Biomarker Research||0:48:14|
|Proteomics for Biomarker Discovery||0:47:46|
|Luminex Data Analysis||0:48:36|
|Inborn and Acquired Genetic Predisposition Biomarkers||Planned||0:00:00|
|Gene Expression Biomarkers||1:02:31|
|Receiver Operating Characteristic Curves||0:47:27|
|Introduction to Machine Learning||1:08:59|
Many students experience statistics as a very dry topic. When the University of the Western Cape asked me in 2017 to assemble a course in biostatistics, I decided it was a good opportunity to “decolonize” the subject. Many of the great advances in statistics came from researchers who had strong ties to the burgeoning eugenics movement. As I felt more comfortable at the helm over the twelve-week course, I incorporated more and more of the social context in which these researchers were laboring. Source scripts can be found in Google Drive.
|Measurements and Distributions||1:03:14|
|Spread and Conformance||0:51:12|
|Correlation is not Causation||0:50:11|
|ANOVA and the Tukey HSD Test||0:58:33|
|Two-way ANOVA and Repeated Measures||1:01:46|
|Dimensionality Reduction and Principal Components Analysis||0:57:44|
|Agglomerative and Divisive Hierarchical Clustering||1:00:08|
|Multiple Testing Correction||1:07:40|
|Bonus: Create a Histogram and Boxplot in Excel||Inputs||0:25:06|
|Bonus: Create a Histogram and Boxplot in GraphPad Prism||Inputs||0:14:42|
|Bonus: Create a Histogram and Boxplot in R||Inputs||0:15:45|
Introduction to R Statistical Environment
The free R language has become one of the most commonly used for biostatistics because of its inherent parallelism and ability to incorporate libraries of advanced functionality, particularly the “Tidyverse.” This five-part series is designed to teach the “first rung of the ladder” to newcomers. The scripts to support the class can be found in Google Drive.
|Why bother learning R? and basics||1:06:42|
|Reading and Writing Files||0:39:34|
|Conditional Execution, Looping, and Functions||0:45:33|
|Visualizing Data with GGPlot2 Library||0:43:38|
|Interpreting Difference Tests||0:51:48|
Introduction to Python for Bioinformatics
Python is still quite a new language for me, but it clearly has a lot of momentum on its side! For students who want to create software of broader capability than what R can support, Python is a great choice. I decided to build my six-session workshop on the project of reading a FASTA file and evaluating and visualizing the frequencies of amino acids. It’s a helpful way to get started with the basics of this very powerful language! The Python code can be found in Google Drive.
|Why Python? and Essential Concepts||0:47:41|
|Sets and Iterating Loops||0:42:00|
|Exceptions and the Collections Data Structure||0:40:28|
|Data Structures and Plotting||0:43:22|
|BioPython and NumPy||0:42:06|
Careers in Research
From time to time, I get the chance to help graduate students with some of the essential skills of being a scientist. Perhaps my favorite of these talks is the first, which explains that going to graduate school is not a mistake, even for someone who decides that they will not stay in biomedical research afterwards! Researchers can really benefit from encouragement, just like anybody else.
|Research Skills for a Stronger South Africa||0:38:36|
|The Unholy Trinity of Research Ethics||0:43:59|
|Creating a solid research poster||0:37:13|
|Zotero Citation Manager||none||0:49:48|
|Social Media for Scientists||none||0:45:36|
Copyright and Usage Information
If you are a professor using these lectures as part of a class, you are welcome! Please let me know that you are using them by email (I am dtabb over at sun.ac.za) or by a comment below. If you need to use a slide or two from my presentations, I am willing to send you the PPTX rather than leaving you to copy images from the PDF.
I choose to license these materials as Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0), meaning “You are free to:
Share — copy and redistribute the material in any medium or format
Adapt — remix, transform, and build upon the material
The licensor cannot revoke these freedoms as long as you follow the license terms.”