Welcome to the MSI Cargill Computer Lab. Center for Mass Spectrometry and Proteomics Phone (612) (612)
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1 Welcome to the MSI Cargill Computer Lab
2 CMSP and MSI collaboration. TINT ( Proteomics Software. Data storage. Galaxy-P (
3 GALAXY PLATFORM Benefits of Galaxy Goecks J et al Genome Biol. 2010;11(8):R86. A web-based bioinformatics data analysis platform. Software accessibility and usability. Share-ability of tools, workflows and histories. Reproducibility and ability to test and compare results after using multiple parameters. Software tools can be used in a sequential manner to generate analytical workflows that can be reused, shared and creatively modified for multiple studies.
4 TOOLS & WORKFLOWS Software tools can be used in a sequential manner to generate analytical workflows that can be reused, shared and creatively modified for multiple studies. For example, Protein Database Downloader downloads UniProt protein FASTA databases of various organisms.
5 Galaxy-P:
6 HOW TO DOWNLOAD A DATABASE? Galaxy-P:
7 HOW TO DOWNLOAD A DATABASE? Log in using your MSI login and password. Click on Import history and click on start using this history 4 Go to tools and search for Protein Database Downloader
8 Protein Database Downloader
9 HOW TO GENERATE A DATABASE? Download human database. Download contaminants database. Merge databases by using the Merge FASTA database
10 8 Generate a workflow and rename it.
11 GENERATING A WORKFLOW
12 GENERATING A WORKFLOW Workflow generated by Alan Blakely, GalaxyP Summer Student
13 Examples of some of the pages and workflows Merged database construction for proteogenomic/ metaproteomic analysis Workflow for proteogenomic studies Workflow for metaproteomic studies And many more.
14 Proteogenomics Workflow Galaxy-P provides an integrated platform for every step of proteogenomic analysis. Build target database download and translate EST databases or perform gene prediction with Augustus. Numerous tools for identification and text manipulation. Workflow utilizing BLAST to identify novel peptides. Tool to assess peptide-spectrum matches and visualize spectra. Visualize identified peptides on the genome. 140 steps: Seamless, integrated proteogenomic workflow. Flexible and accessible workflows for improved proteogenomic analysis using Galaxy framework. J. Proteome Res., Just Accepted Manuscript DOI: /pr500812t Link: z.umn.edu/pgfirstlook
15 INTERESTED IN GALAXYP? Visit or to enlist your name for interest development. Follow us on twi3er.com/usegalaxyp
16 GALAXY-P EXERCISE FOR USING EXISTING WORKFLOWS
17 GALAXYP Using ProteinPilot within Galaxy-P: z.umn.edu/ppingp
18 9 Go to data library USING A WORKFLOW 10 Search for itraq Import to current history
19 12 Click on Analyze Data Click on Click on import workflow and start using this workflow
20 15 Click on Run option in the workflow 16 Click on Run workflow
21 GALAXYP Using ProteinPilot within Galaxy-P: z.umn.edu/ppingp
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