Table 2. Overview of course Days 1–3.

Topic	Exercise/ Examples	Biological problem
Day 1
Getting Started
Variables	Creating variables; basic operations on variables
Arrays	Indexing, storing, retrieving, and elementary operations	Image visualization
Built-in Functions	Summary statistics
Data visualization	Histograms, color maps, and plots
INTEGRATION	Summary statistics and plotting to characterize an unknown dataset	Mystery ‘microarray’ dataset
Arrays II	Cropping and subsampling	Image manipulation
Conditional statements	Logical operations on arrays (<, >, = =)
INTEGRATION	Normalize and modify an image with built-in functions and logical operators	Image manipulation and visualization
INTEGRATION	Compare single cell reporter expression from images of co-cultured wild-type and mutant cells
Day 2
Review of Day 1
Functions	Inputs, outputs, scope, and naming
Functions	Convert script from Day 1 into a function	Image normalization and visualization
Loops	for
Conditional statements	if, elseif, else, while
INTEGRATION	96-well plate growth curve data
Strings	Data type conversion and basic pattern matching	Basic bioinformatics (find a ‘motif’)
Cell arrays	Dealing with mixed data types	Data plus metadata
INTEGRATION	Yeast cells: Protein expression changes and cell growth over time—image series
Day 3
Binomial distribution, null hypothesis, p-value	Binomial rat—simulation	Choice behavior in animals
Bootstrapping methods	2-sample neuron comparison—resampling	Morphological characterization of neurons
False positive statistics	“researcher degrees of freedom” and multiple hypothesis testing	Neuronal data—simulation

Summary of the topics covered in Days 1–3 of the course, the examples and exercises, and the biological motivation.