What is Galaxy?

Galaxy is web-based portal to many applications for data intensive biological research, such as next-gen sequencing, genomics, and much more. Galaxy is an open platform enabling researchers to retrieve data from local and remote sources, create workflows, and share analyses with other researchers.

Accessing Galaxy

The Tufts Galaxy is located at galaxy.tufts.edu and is restricted to the Tufts domain ( *.tufts.edu) so accessing Galaxy remotely requires a VPN connection to the Tufts domain to gain access.

New users must register to use Galaxy. On the top in the tab bar under Users there is a Register selection. Use this to enter your email address, a password ( not your Tufts password), and a short username. Once registered, you can use the Login selection to sign in.

What Can I Do With Galaxy?

Upload Data
Data can be uploaded into Galaxy from several sources. Local data can be directly uploaded through the web interface or using FTP if the data is too large (>2 Gb) to load through the browser. To FTP data to Galaxy, use your FTP client to connect to galaxy.tufts.edu using the username (email) and password that you signed up with. Once uploaded you can retrieve the data files from the Get Data/Upload file left navigation window.
Data can be uploaded from a remote site using an URL (http:// or ftp:// ). In addition Galaxy has portals to
several genomic repositories,e.g. UCSC, Ensembl, which allow searching and retrieving datasets directly into Galaxy
Perform Basic Data Manipulations
Galaxy comes with a large set of applications for manipulating sequences and biological data ( Filtering, Sorting,Text Manipulation , Genomic Interval Data). Following mapping of NGS data to a reference genome, much of the resulting data is columnar ( BED, GFF, intervals) and Galaxy has a robust set of tools for manipulating and formatting this type of data.
Bioinformatics and NGS applications
Galaxy has an extensive toolshed of bioinformatics tools available for processing NGS datasets ( Mapping, QC, Variant Detection) as well as Motif tools, Metagenomic analysis, and others.
Create Workflows
Doing an analysis using Galaxy creates a series of steps and intermediates which result from each step. These are called histories and can be saved and shared with others. Multiple histories are possible within an account. A workflow can be generated from a history track and used to analyze new data sets in a consistent manner. Galaxy has a GUI tool for creating new workflows or uploading existing workflows that have been shared.

Where To Go For Help?

The Galaxy team has assembled an array of videos and other tutorials under Learn Galaxy. The help tab on the main Galaxy window has links to this resource as well as to mailing lists ( very helpful! ), and other support venues. Watch the most current Galaxy videos at Vimeo: http://vimeo.com/galaxyproject. Galaxy acts a portal to many other sites. To learn about these sites visit sites.tufts.edu/biotools and view the links under Learning Bioinformatics Resources, particularly the UCSC, NCBI, and Ensembl channels.

If you encounter issues or need help using the Tufts Galaxy, please send email to tts-research@tufts.edu for assistance.

What Else Is There To Know?

The Tufts Galaxy is not designed for storing files. There is a quota for each user (20 GB). If you reach this quota, you will be unable to use Galaxy for analysis. If this point is reached, you must delete one or more of your histories from the system. This might take awhile so it is good practice to download final data, plus any intermediate data of interest when an analysis has finished, and clean up that history by removing files

As mentioned above histories can be converted into workflows, so you can save the process of a history for later use.

 

Questions? Need help?

Send email to tts-research@tufts.edu or call 617-627-3376 for general help.

This page maintained by Research Technology/TTS
Last updated: September 16, 2016 by D. Lapointe