The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

Enis Afgan ,Vahid Jalili ,Anton Nekrutenko ,Helena Rasche ,Martin Čech ,Björn Grüning ,Aysam Guerler ,Dannon Baker ,Saskia Hiltemann ,D L Clements ,Jeremy Goecks ,James Taylor ,Bérénice Batut ,Dave Bouvier ,Nicola Soranzo ,Jennifer Hillman-Jackson ,Marius Van Den Beek ,Nate Coraor ,John Chilton ,Daniel Blankenberg

doi:10.1093/nar/gky379

Abstract

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

Highlights

Started in 2005, Galaxy enables biologists without programming and systems administration expertise to perform computational analysis through the Web [1]
Histories, workflows and visualizations can all be shared with individuals, or they can be shared via the Web using links such as https://usegalaxy.org/u/jeremy/h/ hpac-exome-analysis Galaxy objects can be published; published items are listed together and available to all users
We have recently extended this interface to include citations so that scientists can reference the methods used in their analysis

Summary

Introduction

Started in 2005, Galaxy (https://galaxyproject.org) enables biologists without programming and systems administration expertise to perform computational analysis through the Web [1]. Using the Galaxy GUI, users can upload their own data or retrieve data from public databases, choose analysis tools, set tool inputs and parameters and run tools. The Galaxy GUI includes a workflow editor where users can create automated, multistep analyses using drag and drop.

Results

Conclusion