Galaxy-P Case Study (Proteomics)

Research objectives
Professor Tim Griffin collaborated with MSI to develop and deploy tools to automate proteomics analysis tasks. The result was a set of tools incorporated into the Galaxy framework, and additional funding to expand his group’s work into related fields.
The first objective was to provide an integrated, community-based MS-proteomics workflow framework through development of Galaxy-P. The second objective was to incorporate tools into Galaxy-P that executed Windows-based software. The final objective was to  catalyze Galaxy-P usage in the larger proteomics researcher community through educational and promotional activities.
How we worked with the researchers
MSI staff collaborated with the Griffin group from the proposal writing through the completion of the project. There was 1.5 FTE of effort dedicated to MSI throughout the 3-year project as well as funds for dedicated hardware. MSI staff had weekly meetings to update the progress, requirements, and research outcomes.


  • MSI collaborated with the Griffin group to develop and deploy tools for MS-based proteomics analysis. After deploying tools, MSI consultants worked with researchers in the Griffin lab to test the tools while answering real research questions. Over the course of the project, MSI staff contributed to many presentations and publications to promote Galaxy-P.
  • This first year of the project focused on creating and deploying new features required to analyze MS-based proteomics data. This included analysis tools, visualizers, and file conversion tools. A public instance of Galaxy-P was deployed for any researcher to view and test the basic functionality of Galaxy-P at A second instance was deployed and is tied to MSI hardware for use by anyone within the University of Minnesota at
  • The second year of the project focused on bug fixes, improving performance, and working with the core Galaxy developers at Penn State to incorporate changes into the main Galaxy distribution. MSI staff made changes to the hardware and the deployment process to streamline future changes and upgrades.
  • The final year of the project has focused on research applications, additional hardware/software tuning to handle real research applications, and promotion of the tools. Over the course of the project, at least 11 presentations were given at conferences to describe the capabilities and architecture of the solution. During the final year, a workshop was held to give additional users hands-on experience with Galaxy-P. A proposal from the Griffin group and MSI for a related extension to Galaxy was recommended for funding and began on Sept 1, 2015.