An International Symposium of the Association of Biomolecular Resource Facilities

(SW1) The Galaxy Platform for Metaproteomic Characterization of Microbiomes

Workshop Sponsors



Not just for genomics anymore: Galaxy for proteomics and multi-omics

Pratik Jagtap and Tim Griffin, University of Minnesota
Tim Griffin, Pratik Jagtap and James Johnson

Did you think that Galaxy is just for genomic data analysis? Not anymore. Come to this workshop to learn how Galaxy can be used for proteomic data analysis, and also applications that cross the ‘omic domains.

With a focus on metaproteomics for characterizing microbiomes, we will help participants learn how to utilize tools for mass spectrometry-based proteomics in Galaxy. Metaproteomics is a multi-omic approach, which characterizes proteins expressed by microorganism communities (microbiomes). Participants will also learn how to leverage metagenomics data to generate protein sequence databases used for proteomic analysis, and utilize the protein information to gain better functional understanding of microbiomes. In addition to receiving hands-on instruction on the use of the Galaxy platform and its implementation, participants will gain experience with the latest software tools and workflows for proteomic and metaproteomic data analysis developed via worldwide collaborative efforts.

Workshop Content:
Metaproteomics analysis is emerging as an effective approach for identifying microorganisms and functional role of the microbiome in response to environment or host-physiology. Metaproteomics characterizes proteins expressed by microorganism communities (microbiome) present in environmental samples or a host organism. Mass spectrometry (MS)-based metaproteomics has catalyzed new discoveries into the functional dynamics of microbiomes (Wilmes et al 2015, doi: 10.1002/pmic.201500183). Metaproteomic informatics is distinctly challenging due to the large databases and complex processing steps involved. This challenge limits widespread use of metaproteomics. Through modular workflows, we demonstrate the use of the Galaxy bioinformatics framework as a metaproteomic informatics solution. Our results demonstrate the power of discovery metaproteomics to add functional understanding to microbiomes, beyond what is possible using traditional metagenomic approaches.
Recent Galaxy-P Publications:
Workshop Schedule:
Saturday, March 25, 2017 (8:00 am - 12 noon; lunch is included from 12 noon - 1:00 pm)
Introduction to Microbiomes and metaproteomic analysis (Pratik Jagtap)
Basics of Data Analysis and Database Search using Galaxy platform. (Tim Griffin)
Metaproteomic analysis – Exploring taxonomy of the microbiome (James Johnson)
Metaproteomic analysis - Exploring function of the microbiome (Pratik Jagtap)
Summary and Conclusion. (Tim Griffin, Pratik Jagtap and James Johnson)
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
Who can attend?

Core facility managers and personnel, as well as biological researchers attending the conference interested in finding solutions to the ‘omic data analysis challenges. Also bioinformatics software developers interested in learning more about Galaxy as a resource to deploy and publish their domain-specific software. (Published references:

The workshop will be targeted to an audience of mixed expertise. Attendees should have a working knowledge of some ‘omics domain.  We will provide a brief background on the data types covered in the workshop (e.g. mass spectrometry-based proteomics data). No prior knowledge or experience with Galaxy is necessary.

Attendees should have access to a personal laptop.


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.

Platinum Sponsors of the ABRF