Community-Driven Data Analysis Training for Biology

Abstract

The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.

Keywords: data analysis; genomics; next-generation sequencing; proteomics; training.

Figure 1.. Key elements of an interactive tutorial.

A. A list of tutorials dedicated to Metagenomics. There is a set of introductory slides and two hands-on tutorials. B. A fragment of introductory material within a tutorial. C. A “hands-on” element with upper box contains instructions for running a tool inside Galaxy and shown example output of Krona tool. The question box at the bottom contains togglable answer field. D. Summary of key points for this tutorial displayed on the bottom of the tutorial. E. Fragment of Galaxy interface showing interactive tour balloon.

Figure 2.. Structure and development of content in GitHub

(http://github.com/galaxyproject/training-material). The material is organized in different topics, each topic in a dedicated directory. Inside each topic’s directory, the structure is the same: a metadata file, a directory with the topic introduction slide decks, a directory with the tutorials and a directory with the Dockerfile describing the details to build a container for the topic that would contain a dedicated Galaxy instance with all tools relevant for the tutorials. Inside the topic directory, each tutorial related to the topic has its own subdirectory with several files: a tutorial file written in Markdown with hands-on, an optional slides file to support the tutorial, a directory with Galaxy Interactive Tours to reproduce the tutorial, a directory with workflows extracted from the tutorial, a file with the links to the input data needed for the tutorial and a file with the description of needed tools to run the tutorial. The process of development of new content is shown at the bottom of the figure.

Figure 3.. History of training activities.

Number (A) and location (B) of registered training events organized by the Galaxy Training Network since 2015. C. Number of tutorial contributors per month.