Loading…
GCC 2017 has ended
The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.

The full printed program is also available.
View analytic
Wednesday, June 28 • 12:30 - 15:00
Galaxy for Proteomics

Sign up or log in to save this to your schedule and see who's attending!

Tutorial

The Galaxy bioinformatics platform has emerged as a valuable resource for mass spectrometry (MS) based proteomic informatics. An active community of researchers and users, including the Galaxy for proteomics (Galaxy-P) team, continues to extend Galaxy for these applications.

This hands-on workshop will guide participants through the essential steps for using Galaxy for the analysis of MS-based proteomics data, focusing on protein identification and more advanced multi-omic applications. Workflows from emerging applications integrating genomic and proteomic data (such as proteogenomics and metaproteomics) will also be demonstrated.

In order to extend the reach of these workflows to the greater community, the Galaxy-P team has partnered with both the JetStream cyberinfrastructure resource (http://jetstream-cloud.org/) and Amazon Web Services (https://aws.amazon.com).

The workshop will be constructed to follow the steps based on the structure below:

  1. Instructions on how to access the resource (30 minutes)
    • This workshop will provide participants background on Galaxy-P software and workflows that have been made available on the resource. Attendees will take away knowledge on how to access this resource and possibly make use of it for their own MS-based proteomics informatics needs.
  2. Introduction to Proteomics (1 hour)
    • Attendees will learn about inputs for proteomics search and also available software in Galaxy for sequence database searching, which identifies proteins via matching of MS data to sequence databases. Use of these tools and optimization of parameters will be demonstrated and discussed.
  3. Multi-omics Workflows ( 1 hour) Attendees will be exposed to a variety of tools and workflows for filtering results in Galaxy. Emphasis will be on these two workflows
    1. Proteogenomics Workflow: Used for filtering identified peptides from proteogenomic analyses.
    2. Metaproteomics Workflow: Used for identifying genera from identified peptides from metaproteomics analysis.

At the end of the workshop, attendees will have working knowledge of MS-based proteomics tools; experience in setting up basic workflows for protein identification, as well as more advanced workflows in proteogenomics and metaproteomics. 

Participants will be given temporary accounts to a cloud-based Galaxy instance to participate in hands-on workshop activities.

Prerequisites
  • Galaxy 101 or equivalent experience.
  • A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best. 

Instructors
CB

Clemens Blank

University of Freiburg
avatar for JJ Johnson

JJ Johnson

Senior Software Developer, Minnesota Supercomputing Institute, University of Minnesota
Galaxy for genomics and proteomics
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota
avatar for Tim Griffin

Tim Griffin

Center for Mass Spectrometry and Proteomics, University of Minnesota
University of Minnesota


Wednesday June 28, 2017 12:30 - 15:00
Sully 3 Level 1, Le Corum

Attendees (4)