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GCC BOSC 2018
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The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are joining together for a unified event to be held in Portland, Oregon, United States, June 25-30, 2018.  The event features two days of training, a two day meeting, and finish with two or four days of intense collaboration at the GCC OBF CollaborationFest Core and Encore events.  The meeting will feature joint and parallel sessions, and shared keynotes, poster and demo sessions, and social events.  Colocating GCC and BOSC will bring together the widest possible community of bioinformatics developers and practitioners into a single place.  At this event the whole will be greater than the sum of the parts.

The event is organized by Oregon Health & Science University and will be held at Reed College, a small liberal arts college in Portland. Conference housing is available in two Reed College residence hall complexesPortland is a vibrant city in the American Northwest, close to the Cascade Mountains, the Oregon Coast, and the Columbia River. 

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Monday, June 25 • 3:30pm - 6:00pm
Galaxy For Proteogenomics !

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Large-scale ‘omics’ data generation is driven by high throughput genome and transcriptome sequencing, and proteome characterization using mass spectrometry. 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.

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.)

Workshop Content:

The course will include a basic introduction to proteomics and will include a hands-on session that will cover use of analytical workflows to generate proteomic databases from RNASeq data. The use and understanding of modules for analytical workflows for proteogenomics analysis will be discussed.

Workshop Schedule:

  • Introduction to multi-omic studies
  • RNASeq Data Processing: Generating protein sequence search databases using Galaxy platform
  • Hands-on session for proteomics data analysis using Galaxy
  • Identification of novel proteoforms and visualization

Workshop Goals:

  • Introduce the Galaxy framework as a solution for data analysis across ‘omics’ domains
  • 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 analysis and informatics needs

Third of 3 sessions in the Introduction to Using Galaxy series.

Prerequisites:

  • a general knowledge of Galaxy (for example, you should be familiar with the material in Galaxy 101 or have attended Introduction to Galaxy).
  • a wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best.

Speakers
avatar for Tim Griffin

Tim Griffin

Center for Mass Spectrometry and Proteomics, University of Minnesota
University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota
avatar for JJ Johnson

JJ Johnson

Minnesota Supercomputing Institute, University of Minnesota
University of Minnesota


Monday June 25, 2018 3:30pm - 6:00pm
PAB 320 Performing Arts Building, Reed Campus