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64th ASMS Conference on Mass Spectrometry and Allied Topics San Antonio, Texas, United States June 5-9, 2016 |
Galaxy had a strong presence at the 2016 ASMS meeting.
| Day | Time | Location | Presentation | Speaker | Links |
|---|---|---|---|---|---|
| June 6 | 8:50 | Hemisfair 3 | Embracing Complexity and Diversity: Discovery Metaproteomics of Multiple Microbiomes using the Galaxy Framework | Pratik Jagtap | Slides, Video* |
| 10:30 | Poster Session, Odd Numbered | Poster MP 265: A Multi-omics Visualization Platform (MVP) Plug-in for Galaxy-based Applications | Thomas McGowan | Poster | |
| 12:30 | Poster Session, Even Numbered | Poster MP 266 From Start to Finish: a complete proteogenomic informatics environment implemented in the Galaxy | Getiria Onsongo | Poster | |
| Poster MP 436 Complementary ERLIC and RPLC online separations significantly expand sequence coverage in MS-based proteomic and proteogenomic studies | Candace Guerrero | Poster | |||
| June 7 | 10:30 | Poster Session, Odd Numbered | Poster TP 775: Quantitative Top Down Proteomics in Translational Research: Markers for Rejection in Peripheral Blood Following Kidney Transplantation | Philip Compton | |
| 12:30 | Poster Session, Even Numbered | Poster TP 388: Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy to Reveal Human Proteomic Variation | Anthony Cesnik | ||
| June 8 | 12:30 | Poster Session, Even Numbered | Poster WP 390 Galaxy-P: recent developments and emerging applications | Timothy Griffin | Poster |
| Poster WP 392: APOSTL: An interactive Galaxy Pipeline For Reproducible Analysis of Affinity Proteomics Data | Brent Kuenzi | ||||
| Poster WP 396: High Performance Computing at the National Resource for Translational and Developmental Proteomics | Ryan Fellers | ||||
| 5:45 | Room 305 | Workshop 14: Galaxy for Proteomics Data Analysis: An Interactive Demonstration | Timothy Griffin | Tutorial | |
Workshop 14: Galaxy for Proteomics Data Analysis: An Interactive Demonstration
Wednesday, 5:45-7:00 PM, Room 305
Organizer: Tim Griffin, University of Minnesota
The Galaxy framework has emerged as a useful and powerful tool for MS-based proteomics data analysis and also multi-omic application (for example see recent publications such as Nat Biotechnol. 2015, 33:137-9; Mol Cell Proteomics. 2015, 14:3087-93; Mol Cell Proteomics. 2012, 11:M111.015974). The Galaxy operating environment offers an informatics workbench where disparate software can be deployed and integrated into complex workflows. Galaxy also offers the ability to share complete workflows and data with other users, promoting reproducibility and dissemination of even complex data analysis schemes.
This workshop will provide attendees the opportunity to take Galaxy for a 'test drive' in analyzing MS-based protoemics data. Attendees will have the opportunity to access a Galaxy instance and walk through the basic steps of setting up an analysis of representative MS data from a proteomics experiment. The hands-on tutorial will include steps such as pre-processing of mass spectral data, sequence database searching, and filtering and visualizing outputs.
Attendees will also be introduced to basic operations and concepts of the Galaxy operating environment, such as the creation of histories and workflows, and functionalities for sharing tools and workflows with others. An overview of the current state of software available in Galaxy for proteomics and multi-omics applications will also be provided.
The workshop will be led by both developers and users well-versed in the use of Galaxy for multi-omics data analysis.
Attendees are encouraged to bring a laptop computer to participate.
Accessible Galaxy-P Docker container
We have built a Docker container containing a Galaxy instance with the tools used in our ASMS workshop. This container can be downloaded to your local computer, installed, and used for gaining more experience with Galaxy and its use in proteomics data analysis.
See the instructions on accessing and installing the Docker container. When prompted, select “View the file” and hit “OK”. This documentation also provides instructions on how to use the Galaxy interface, build Histories and Workflows with some of the available tools, as well as other Galaxy functions. This mirrors the content presented in the ASMS workshop, with additional details on the use of Galaxy.
See the Galaxy-P entry in the public Galaxy servers directory for additional Galaxy-P resources.