(SW2) The Galaxy Platform as an Accessible, Core Laboratory Solution for Proteogenomic Analysis and Informatics

Workshop Sponsors:

 

The two proteomics workshops - SW1 Proteomic DIA Workflow and SW2 Galaxy Platform - can be paired. Attend both for the same cost as a Full Day Workshop.

Lunch will be provided for all attendees.

Sunday, April 22

8:00 pm – 12:00 pm

Organizer:
Pratik Jagtap
University of Minnesota
 
Instructors:
Tim Griffin, Pratik Jagtap and Praveen Kumar
University of Minnesota
 

An increasing number of researchers are generating large-scale ‘omics’ data via core research facilities. This is being driven by technologies for high throughput genome and transcriptome sequencing, and proteome characterization using mass spectrometry becoming more mature and cost-effective. As a result, many researchers are turning to generating integrative analysis of these ‘multi-omics’ datasets given the great potential to provide novel biological insights. These multi-omics applications are particularly challenging for data analysis, as they require the use of multiple, domain-specific software programs on scalable infrastructure capable of handling the computing and storage needs of this large-scale data.

Fortunately, a solution does exist in the form of the open, freely available Galaxy framework for workflow management. Galaxy has been shown to solve the problems of software integration and scalability for multi-omics analysis, and additionally offer benefits for sharing complete workflows in a user-friendly environment accessible by wet-bench scientists. In this workshop, we will introduce the use of Galaxy platform for multi-omics data analysis applications. As a representative example, we will focus on the maturing field of proteogenomic applications. Proteogenomics most commonly integrates RNA-Seq data, for generating customized protein sequence databases, with mass spectrometry-based proteomics data, which are matched to these databases to identify novel protein sequence variants. (Cancer Res. (2017); 77(21):e43-e46. doi: 10.1158/0008-5472.CAN-17-0331.) Focusing on the perspective of a core facility or biological user, we will demonstrate the benefits of Galaxy for these analyses via hands-on demonstrations.

Workshop Content:
The course will include a basic introduction to Galaxy framework and its use for ‘omics’ data analysis. The morning session will include a hands-on session on the use of Galaxy followed by a tutorial for users to understand the basic use of Galaxy platform in proteomics. Use of open-source software tools will be discussed in this session. Sharing of datasets, workflows and histories will also be discussed, giving the attendees a familiarity with Galaxy web-based user interface and the basics of its operation. In the later part, the workshop will cover use of analytical workflows to generate proteogenomics workflows. The use and understanding of modules for analytical workflows for proteogenomics analysis will also be discussed.

Testimonials from past workshops on Galaxy for multi-omics:

“This is the best workshop I have ever attended. The GalaxyP folks gave great background to proteomics and just did a great job of going through their excellent suite of tools and workflows.” – Biological Researcher, John Hopkins University, Baltimore, Maryland.

“Hit of the day! Really nice intro to MS proteomics for non-proteomics people.” – Post-doctoral computational researcher, University of Rennes, France.

Workshop Schedule:
8:00 am – 8:15 am Introduction to Galaxy Platform and multi-omic studies
8:15 am – 9:15am - RNASeq Data Processing: Data Analysis using Galaxy platform
9:15 am – 10:00 am - Hands-on session for proteomics data analysis using Galaxy
10:00 am – 10:30 am - Morning Refreshment Break
10:30 am – 12:00 pm - Identification of novel proteoforms and visualization
12:00 pm – 1:00 pm - Lunch
   
Workshop Goals:
Introduce the Galaxy framework as a solution for data analysis across ‘omics’ domains
Provide hands-on experience to attendees in using Galaxy
Demonstrate use of Galaxy for a proteogenomic analysis (RNA-seq and proteomic integrative analysis)
Lay the foundation for attendees to implement Galaxy at their own facility or institution to meet ‘omics’ data
 
Target Audience

The target audience will be core facility managers and personnel, as well as biological researchers attending the conference interested in finding solutions to their ‘omic data analysis challenges. We would also anticipate the workshop drawing some interest from bioinformatics software developers interested in learning more about Galaxy as a resource to deploy and publish their domain-specific software.

Our workshop would be targeted to an audience of mixed expertise. We would expect that attendees would have a working knowledge of some ‘omics domain. No prior knowledge or experience with Galaxy would be necessary.

Attendees should have access to a personal laptop.

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