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GCC BOSC 2018 has ended
The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are meeting together in Portland, Oregon, United States, June 25-30, 2018.  There will be two days of training, a two+ day meeting, and four days of intense collaboration.  The meeting features joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.


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

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Workshop Tutorial
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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.

Computational infrastructure for this workshop is generously provided by Jetstream, NSF's user-friendly cloud computing environment  for researchers.

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

Senior Software Developer, Minnesota Supercomputing Institute, University of Minnesota
Galaxy for genomics and proteomics
avatar for Praveen Kumar

Praveen Kumar

Graduate Student, University of Minnesota
avatar for Subina Mehta

Subina Mehta

Researcher, University of Minnesota




Monday June 25, 2018 3:30pm - 6:00pm
PAB 104 Performing Arts Building, Reed Campus

Attendees (15)