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.

Improve your Galaxy text life: The Query Tabular Tool

“…Via an example in metabolomics, we also demonstrate how Query Tabular can enable new manipulations and analyses of textual data within a single, simplified workflow, that would otherwise require separate workflow development if attempted using existing Galaxy tools. The Query Tabular tool has also proven useful and versatile for developing workflows used for multi-omic informatic training workshops ( http://galaxyp.org/workshops/) and online training via the Galaxy Training Network ( http://galaxyproject.github.io/training-material 13 ). The free and open tool is available to any Galaxy user, and should provide a valuable addition to the Galaxy tool box for developing analysis workflows.…”

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

“…For a swift introduction into the analysis of MSI data in Galaxy, we have developed training material for metabolomics and proteomic use cases and deposited it to the central repository of the Galaxy Training Network [51,52]. The training materials consist of a comprehensive collection of small example datasets, step-by-step explanations and workflows that enable any interested researcher in following the training and understanding it through active participation.…”

A Galaxy-based training resource for single-cell RNA-seq quality control and analyses

“…Over 30 scientific groups involved in Galaxy-related training contribute to the Galaxy Training Network (GTN) (https://galaxyproject.org/teach/gtn/). The GTN provides online training materials as well as coordinating Galaxy training events worldwide [16].…”