From FASTA to a gene and its protein
Trace real HBB and HBD transcripts through their annotated coding regions, then verify translation against RefSeq.
numpy · pandas · matplotlib · IPython
BIOINFORMATICS / 01–08
Bioinformatics
8 independent, runnable lessons connecting questions, traceable inputs, transparent methods and interpretation. One notebook download starts each workflow.
Sequence path 01 → 02 → 06; expression path 03 → 04 → 05; drug structures 06 → 07 → 08
Download this discipline in both languages8 recipes
Align the beta- and delta-globin genes
Build affine-gap global and local alignment, follow the traceback, and explain exactly what identity and coverage measure.
numpy · pandas · matplotlib · IPython
Explore a paired RNA-seq experiment
Inspect 63,677 genes across eight airway samples; normalize depth, distinguish donor from treatment, and inspect paired responses.
numpy · pandas · matplotlib · IPython
Test pathway overrepresentation
Define a measured gene universe, test real Reactome pathways with a hypergeometric model, and correct the entire test family.
numpy · pandas · scipy · matplotlib · networkx · IPython
Read a protein interaction network
Map 12 DNA-damage response proteins to STRING, retain isolates, compare confidence thresholds, and inspect evidence channels.
numpy · pandas · matplotlib · networkx · IPython
Inspect hemoglobin in three dimensions
Rotate real 1A3N coordinates, inspect heme and its neighbors, and connect chain numbering to a RefSeq protein sequence.
numpy · pandas · scipy · matplotlib · py3Dmol · IPython
How does a small drug fit into a protein pocket?
Turn a real 3D model, find the drug and its neighbors, and learn what a distance measurement can tell us.
numpy · pandas · scipy · matplotlib · py3Dmol · IPython
How does an antibody meet a protein surface?
Follow three colors in a real 3D model and discover where an antibody piece meets its target protein.
numpy · pandas · scipy · matplotlib · py3Dmol · IPython
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