pythonforbio.
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Curriculum

Learning paths

Four paths, each a group of modules. Open any module directly; nothing is locked.

paths
4
lessons
118
graded
32
path 01 · 18 lessons · 2 modules

Foundations

Covers Python itself — types, collections, loops, functions, files, errors and classes — then the data layout and coordinate conventions used throughout bioinformatics. Skip to the next path if you already write Python.

Open
Modules
  1. 01Python Basics12
  2. 02Core Concepts6
By the end you can
  • Write Python functions that read files and handle errors
  • Choose between a list, a dictionary and a tuple
  • Read and reason about tidy and wide data layouts
Progress
0/18
path 02 · 59 lessons · 4 modules

Python Data Stack

The three libraries most analysis is built on. Arrays and broadcasting first, then dataframes, then the plotting APIs used to inspect results.

Open
Modules
  1. 01NumPy18
  2. 02pandas21
  3. 03Plotting14
  4. 04Library Overview6
By the end you can
  • Replace loops over rows with array operations
  • Load, filter, join and reshape tables with pandas
  • Build figures with matplotlib and seaborn
Progress
0/59
path 03 · 17 lessons · 2 modules

Bioinformatics Core

Biopython's sequence and record model, plus the genomic file formats and coordinate conventions that cause most of the errors in practice.

Open
Modules
  1. 01Genomics Basics2
  2. 02Biopython15
By the end you can
  • Parse FASTA, FASTQ, GenBank and GFF files
  • Work with Seq, SeqRecord and SeqFeature objects
  • Run and interpret sequence alignments
Progress
0/17
path 04 · 24 lessons · 2 modules

Clinical Variants

HGVS notation and the biocommons toolchain, then applied pipelines: reading VCFs, normalising variants and building annotated tables.

Open
Modules
  1. 01HGVS Nomenclature11
  2. 02Applied Workflows13
By the end you can
  • Parse and validate HGVS variant descriptions
  • Normalise variants and convert between c., g. and p. coordinates
  • Build an annotated variant table from a VCF
Progress
0/24