Oral Presentation 23rd Annual Lorne Proteomics Symposium 2018

Galaxy-P: an accessible resource for multi-omics analysis   (#17)

Maria A Doyle 1 , Pratik D Jagtap 2 , Björn A Grüning 3 , Jim E Johnson 4 , Ira R Cooke 5 , Tim J Griffin 2
  1. Research Computing Facility, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
  2. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
  3. Department of Computer Science, University of Freiburg, Freiburg, Germany
  4. Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
  5. Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, Australia

Galaxy is a hugely popular bioinformatics workbench that provides bench scientists with access to thousands of open-source tools through a user-friendly interface. The Galaxy-P project and community (http://galaxyp.org/) is an extension of Galaxy that focuses on multi-omic integration, including integrative analysis of mass spectrometry (MS)-based proteomics, genomic and transcriptomic data (1).

Proteogenomics lies at the intersection of proteomics and genomics and is an emerging field of biological research in cancer and other areas. Proteogenomics integrates genomic and transcriptomic data with MS-based proteomics data to directly identify expressed, variant protein sequences. Metaproteomics research on the other hand integrates metagenomic / metatranscriptomic data with MS-based proteomics data to perform taxonomic and functional analysis of expressed proteins. Both these analyses are computationally intensive, requiring many software tools to be integrated into sophisticated workflows which challenges its adoption by non-expert, bench scientists. The Galaxy-P project have recently developed Galaxy-based resources for proteogenomic informatics (2, 3) and metaproteomics informatics (4) with the aim of providing more researchers access to, and training in these multi-omics research fields.

This talk will highlight some of the proteomics tools available in Galaxy and it's new multi-omics capability. It will also discuss how R/Bioconductor tools can be easily integrated into Galaxy, enabling sophisticated statistical analyses to be performed, as well as highlighting other features that make Galaxy an incredibly valuable, accessible resource for bench scientists.

  1. https://z.umn.edu/galaxypreferences
  2. Chambers, M.C. et al. Cancer Res 77(21), e43-e46 (2017).
  3. https://z.umn.edu/proteogenomicsgateway
  4. https://z.umn.edu/metaproteomicsgateway