This page includes a complete list of our published modules.

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Training Course	Description	Estimated Time	Collection	Coding Language	Task	Domain
Bash: Combining Commands	This module will teach you how to combine two or more commands in Bash to create more complicated pipelines in Bash.	30 min	Learn to code	Bash
Bash / Command Line 101	This course teaches learners to navigate their computer, as well as view and edit files, from the command line using Bash.	40 min	Learn to code	Bash
Bash: Searching and Organizing Files	This module will teach you how to use the bash shell to search and organize your files.	30 min	Learn to code	Bash	Data management
Bash: Conditionals and Loops	This module teaches you how to iterate through "for" loops and write conditional statements in Bash.	60 min	Learn to code	Bash
Bash: Reusable Scripts	This module will teach you how to create and use simple Bash scripts to make repetitive tasks as simple as possible.	60 min	Learn to code	Bash
Understanding the Bias-Variance Tradeoff	The bias-variance tradeoff is a central issue in nearly all machine learning analyses. This module explains what the tradeoff is, why it matters for machine learning, and what you can do to manage it in your own analyses.	20 min	Machine Learning, Statistics
Citizen Science	This is an overview of citizen science for biomedical researchers.	45 min	Intro to data science
Research Data Management Basics	Learn the basics about research data management.	40 min	Intro to data science		Data management
Types of Data Storage Models	This course will focus on different data storage solutions available to an end user and the unique characteristics of each type. This course will also cover how each storage type impacts one’s access to data and computing capabilities.	30 min	Infrastructure and technology		Data management
Data Visualization in ggplot2	This module includes code and explanations for several popular data visualizations, using R’s ggplot2 package. It also includes examples of how to modify ggplot2 plots to customize them for different uses (e.g. adhering to journal requirements for visualizations).	60 min	Learn to code	R	Data visualization
Data Visualization in Open Source Software	Introduction to principles of data vizualization and typical data vizualization workflows using two common open source libraries: ggplot2 and seaborn.	20 min			Data visualization
Data Visualization in seaborn	This module includes code and explanations for several popular data visualizations using python’s seaborn library. It also includes examples of how to modify seaborn plots to customize them for different uses.	60 min	Learn to code	Python	Data visualization
Database Normalization	Learn about the concept of normalization and why it’s important for organizing complicated data in relational databases.	40 min			Data management	EHR data
Demystifying Application Programming Interfaces (APIs)	Understand what an application programming interface (API) is and why APIs are useful!	30 min	Demystifying, Infrastructure and technology
Demystifying the Command Line Interface	Understand what the command line interface is and why it’s useful!	15 min	Demystifying, Infrastructure and technology
Demystifying Containers	Containers can be a useful tool for reproducible workflows and collaboration. This module describes what containers are, why a researcher might want to use them, and what your options are for implementation.	20 min	Demystifying
Demystifying Geospatial Data	This module is a brief introduction to geospatial (location) data.	15 min	Demystifying			Geospatial data
Demystifying Large Language Models	Learn about large language models (LLM) like ChatGPT.	60 min	Demystifying, Machine Learning			Text data
Demystifying Machine Learning	An approachable and practical introduction to machine learning for biomedical researchers.	60 min	Demystifying, Machine Learning
Demystifying Python	This module introduces the Python programming language, explores why Python is useful in research, and describes how to download Python and Jupyter.	20 min	Demystifying	Python
Demystifying Regular Expressions	Learn about pattern matching using regular expressions, or regex.	30 min	Demystifying			Text data
Demystifying SQL	SQL is a relational database solution that has been around for decades. Learn more about this technology at a high level, without having to write code.	40 min	Demystifying			EHR data
Directories and File Paths	In this module, learners will explore what a directory is and how to describe the location of a file using its file path.	15 min	Infrastructure and technology
Getting Started with Docker for Research	This tutorial combines a hands-on interactive Docker tutorial published by Docker Inc with an academic article outlining best practices for using Docker for research.	60 min	Infrastructure and technology	Bash
The Elements of Maps	This is a general overview of ways that geospatial data can be communicated visually using maps.	45 min			Data visualization	Geospatial data
Generalized Linear Regression	What is generalized linear regression (including logistic regression) and when might you need it?	60 min	Statistics		Data analysis
Genomics Tools and Methods: Quality Control	Get started with genomics! This module walks you through how to analyze FASTQ files to assess read quality, the first step in a common genomics workflow - identifying variants among sequencing samples taken from multiple individuals within a population (variant calling).	40 min		Bash		Omics data
Genomics Tools and Methods: Computing Setup	This module walks you through setting up your own copy of a genomics analysis AMI (Amazon Machine Image) to run genomics analyses in the cloud.	30 min	Infrastructure and technology	Bash		Omics data
Encoding Geospatial Data: Latitude and Longitude	This is an introduction to latitude and longitude and the importance of geocoding - encoding geospatial data in the coordinate system.	15 min			Data visualization	Geospatial data
Git Command Line Interface versus Graphical User Interface	Compare the two ways of interacting with Git to decide which is best for you.	30 min	Infrastructure and technology		Data management
Creating a Git Repository	Create a new Git repository and get started with version control.	60 min	Learn to code	Git, Bash
Exploring the History of your Git Repository	This module will teach you how to look at past versions of your work on Git and compare your project with previous versions.	30 min		Git, Bash
Intro to Version Control	An introduction to what version control systems do and why you might want to use one.	15 min	Infrastructure and technology		Data management
Setting Up Git on Mac and Linux	This module provides recommendations and examples to help new users configure git on their computer for the first time on a Mac or Linux computer.	15 min	Infrastructure and technology	Git	Data management
Setting Up Git on Windows	This module provides recommendations and examples to help new users configure Git on their Windows computer for the first time.	25 min	Infrastructure and technology	Git, Bash	Data management
How to Troubleshoot	Learning to use technical methods like coding and version control in your research inevitably means running into problems. Learn practical methods for troubleshooting and moving past error codes and other difficulties.	30 min	Intro to data science
Introduction to Null Hypothesis Significance Testing	This is an introduction to NHST for biomedical researchers.	40 min	Statistics		Data analysis
Learning to Learn Data Science	Discover how learning data science is different than learning other subjects.	20 min	Intro to data science
Omics Orientation	This module provides a brief introduction to omics and its associated fields.	15 min	Demystifying			Omics data
Transform Data with pandas	This is an introduction to transforming data using a Python library named pandas.	60 min		Python	Data wrangling
Python Basics: Exercise	Practice the skills acquired in the Python Basics sequence by working through an exercise.	30 min	Learn to code	Python
Python Basics: Lists and Dictionaries	Learn about collection objects, specifically lists and dictionaries, in Python.	15 min	Learn to code	Python
Python Basics: Loops and Conditionals	Learn how to use loops and conditional statements in Python.	20 min	Learn to code	Python
Python Basics: Functions, Methods, and Variables	Learn the foundations of writing Python code, including the use of functions, methods, and variables.	20 min	Learn to code	Python
Python Practice	Use the basics of Python coding, data transformation, and data visualization to work with real data.	60 min	Learn to code	Python
R Basics: Introduction	Introduction to R and hands-on first steps for brand new beginners.	60 min	Infrastructure and technology, Learn to code, Intro to data science	R
R Basics Practice	Use the basics of R coding, data transformation, and data visualization to work with real data.	60 min		R	Data visualization, Data wrangling
R Basics: Transforming Data With dplyr	Learn how to transform (or wrangle) data using R’s dplyr package.	60 min	Learn to code	R	Data wrangling
R Basics: Visualizing Data With ggplot2	Learn how to visualize data using R’s ggplot2 package.	60 min	Learn to code	R	Data visualization
Missing Values in R	A practical demonstration of how missing values show up in R and how to deal with them. Note that this module does not cover statistical approaches for handling missing data, but instead focuses on the code you need to find, work with, and assign missing values in R.	45 min	Learn to code	R	Data wrangling
R Practice	Use the basics of R coding, data transformation, and data visualization to work with real data.	60 min	Learn to code	R
Reshaping Data in R: Long and Wide Data	A module that teaches how to reshape tabular data in R, concentrating on some typical shapes known as "long" and "wide" data.	60 min	Learn to code	R	Data wrangling
Summary Statistics in R	Learn to calculate summary statistics in R, and how to present them in a table for publication.	30 min	Learn to code, Statistics	R	Data analysis
Regular Expressions Basics	Begin to use regular expressions, or regex, for simple pattern matching.	60 min	Learn to code			Text data
Regular Expressions: Flags, Anchors, and Boundaries	Use flags, anchors, and boundaries in regular expressions, or regex, for complex pattern matching.	45 min	Learn to code			Text data
Regular Expressions: Groups	Use regular expressions, or regex, for complex pattern matching involving capturing and non-capturing groups.	30 min	Learn to code			Text data
Regular Expressions: Lookaheads	Use regular expressions, or regex, for complex pattern matching involving lookaheads.	30 min	Learn to code			Text data
Reproducibility, Generalizability, and Reuse	This module provides learners with an approachable introduction to the concepts and impact of research reproducibility, generalizability, and data reuse, and how technical approaches can help make these goals more attainable.	60 min	Intro to data science
SQL Basics	Structured Query Language, or SQL, is a relational database solution that has been around for decades. Learn how to do basic SQL queries on single tables, by using code, hands-on.	60 min	Learn to code	SQL	Data wrangling	EHR data
SQL, Intermediate Level	Learn how to do intermediate SQL queries on single tables, by using code, hands-on.	60 min	Learn to code	SQL	Data wrangling	EHR data
SQL Joins	Learn about SQL joins: what they accomplish, and how to write them.	60 min	Learn to code	SQL	Data wrangling	EHR data
Statistical Tests in Open Source Software	This module provides an overview of the most commonly used kinds of statistical tests and links to code for running many of them in both R and python.	20 min	Statistics	R, Python	Data analysis
Tidy Data	Tidy is a technical term in data analysis and describes an optimal way for organizing data that will be analyzed computationally.	45 min	Intro to data science, Demystifying
Using the REDCap API	REDCap is a research data capture tool used by many researchers in basic, translational, and clinical research efforts. Learn how to use the REDCap API in this module.	60 min	Infrastructure and technology	R, Python