Python for Bioinformatics
summary
Describes concrete workflows: uses IPython notebook plus requests to query Ensembl's REST API, turns a plain list of gene symbols into chromosome coordinates, then uses pybedtools (a bedtools wrapper) to sort and merge intervals so variant callers can run fast. Shows an embeddable Dalliance genome browser prototype in the notebook to visualize large remote BAMs without downloading. Claims this pipeline is practical, reproducible, and demonstrably works on real cancer sequencing examples.
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chapters (25)
- 0:00Intro
- 1:43Welcome
- 2:37Overview
- 3:04How life works
- 4:56Human genome
- 6:31Proteins
- 8:00Genetic Code
- 10:05Next Generation Sequencing
- 13:56IPython Notebook
- 18:03Project Euler
- 19:12Notebook
- 23:32Table of contents
- 24:34Dalliance
- 27:40Example
- 29:38Band Files
- 31:39REST API
- 32:17Ensemble REST API
- 32:51HTTP Header
- 33:35Secret Name
- 35:55Merge
- 40:03Writing a paper
- 40:40Authorial
- 41:15Research Infrastructure
- 42:33Researcher Cloud
- 45:17Collaboratory
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