Technology enhanced learning (TEL) for genomics
Teach genomics with the tools researchers use
These guides are for educators who want to use research tools in their genomics teaching, and for developers who build teaching websites. They cover genome browsers, alignments, 3D structures, networks, Galaxy, R and Python in the browser, phylogenetic trees and charts, and every topic comes with live examples whose code you can copy.
The sequence reads ATG GTG CAT CTG ACT CCT GAG GAG AAG TCT GCC GTT ACT GCC CTG TGG GGC AAG GTG AAC GTG GAT GAA GTT GGT GGT GAG GCC CTG GGC.
Codon 7 reads GAG, which codes for glutamate.
Follow this gene through the site: in a genome browser, in an alignment of eight species and in the haemoglobin structure.
What the guides cover
The site covers eight topics, and each has two pages. The page for educators is about using the tool in class: what it is good for, and how to run an activity with it. The page for developers is about building the tool into a web page. Each page links to the other, so you can move between them.
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Genome browsers
For educators Show students where a gene or variant sits, what lies around it, and how the evidence for it builds up track by track. (Teaching with genome browsers) For developers Put igv.js or JBrowse 2 in a page, load your own tracks, and link to UCSC and Ensembl. (Embedding genome browsers) -
Sequences and alignments
For educators Help students read sequences, compare them across species, and see why some positions never change. (Teaching with sequences and alignments) For developers Show sequences and multiple alignments with Nightingale, or in a few lines of SVG. (Showing sequences and alignments) -
3D structures
For educators Find a variant in the folded protein, and learn how far an AlphaFold model can be trusted. (Teaching with 3D structures) For developers Embed Mol*, 3Dmol.js or NGL, load PDB and AlphaFold models, and highlight residues. (Embedding 3D structure viewers) -
Networks
For educators Explore interactions and pathways, without reading too much into where each molecule happens to be drawn. (Teaching with networks) For developers Draw interactive networks with Cytoscape.js and load them from STRING or Cytoscape. (Drawing networks with Cytoscape.js) -
Galaxy
For educators Run real analyses in class with nothing to install, and keep a record of every step. (Teaching with Galaxy) For developers Link into Galaxy, list training tutorials live, and set up a class with BioBlend. (Working with Galaxy) -
R and Python in the browser
For educators Let students write and run code from the first minute, on any computer. (Teaching with R and Python in the browser) For developers Run R with webR and Python with Pyodide in a page, or publish a JupyterLite site. (Running R and Python in a page) -
Phylogenetic trees
For educators Teach students to read a tree by its branching, not by the order of its tips. (Teaching with phylogenetic trees) For developers Draw trees from Newick files with phylotree.js or d3, and link to Nextstrain. (Drawing phylogenetic trees) -
Charts of genomic data
For educators Help students read Manhattan plots, volcano plots and heatmaps, and understand the thresholds drawn on them. (Teaching with charts of genomic data) For developers Make interactive Manhattan plots, volcano plots and heatmaps with Vega-Lite. (Charting genomic data)
Before you start
For educators
For developers
Teaching sites we have made
All of them run in a web browser, so students have nothing to install. You can find the rest, with our course materials and code, on Our sites.
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How aligners work
An interactive tutorial on the algorithms inside sequence aligners and read mappers, from hashing and the Burrows–Wheeler transform to BLAST, multiple alignment and hidden Markov models, with exercises in every chapter.
comparativechrono.github.io/how-aligners-work/Code on GitHub for How aligners work
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R workbench
R running in the browser, built as a base for practicals. The R console, an RStudio-style editor (with R Markdown, Quarto and Shiny), Jupyter-style notebooks and a terminal sit next to the practical's instructions.
comparativechrono.github.io/R-workbench/Code on GitHub for R workbench
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Bioinformatics workbench
Real bioinformatics programs, such as fastp, minimap2, BWA, samtools, bcftools, Salmon and PLINK 2, compiled to run in the browser. Python and R notebooks, a genome browser, a 3D structure viewer and a network viewer sit alongside them.
comparativechrono.github.io/bioinformatics-workbench/Code on GitHub for Bioinformatics workbench
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Genomic variant analysis practicals
Two practicals and a coursework workbench. Students take raw exome reads to a variant that matters in the clinic, CYP2C19*2, then annotate, filter and interpret variants, and finally analyse a patient's exome for their coursework.
comparativechrono.github.io/variant-practicals/Code on GitHub for Genomic variant analysis practicals
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AI agents for bioinformatics
A two-hour practical on AI assistants and AI agents. Students answer one question, which genotype NA12878 has at CYP2C19*2, with an assistant that writes commands and with an agent that runs them, and then turn the agent's run into an analysis they can repeat.
comparativechrono.github.io/ai-agents-practical/Code on GitHub for AI agents for bioinformatics
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Bioinformatics algorithms in Python
A three-hour practical in which students write Python in the browser and use it to look inside alignment, BLAST, trees and networks, with exercises that check themselves.
comparativechrono.github.io/bioinformatics-algorithms-python/Code on GitHub for Bioinformatics algorithms in Python