Bioinformatics Software Development Projects

DIMSA Project

Principal Investigator: Michael Frietas
Funding Agency: TBD
Duration: October 2005 - December 2005

The DIMSA (Data Intensive Mass Spect Analysis) project aims to automate the process of Mass Spect data analysis pipeline, which is an integral part of the proteomics research. The DIMSA project includes all steps of the MS/MS analysis pipeline: input file conversion, database searching, output file conversion and integrative analysis of the result. XML-based, the DIMSA project is easily extensible to additional search engines and analysis modules.

A prototype of the pipeline is currently under implementation. This will have all the primitive components of the pipeline. It will include:

  • Input user interface – for input parameter selection, data file upload, and submission of the searching jobs.
  • Output user interface – for displaying the results from several search engines. The first page should present a comprehensive look of the results, which could be a table that lists all the protein hits in the first column, and then check marks for those that are hit by an individual search engine in the following columns. Clicking on each program name will give the result returned by that program. moving the mouse over a check mark will pop up a window that shows the matching score of the protein hit by a specific program. Clicking on a protein hit will give the results of that protein by all the programs.
  • Database searching – in the first stage, only the command line programs X!Tandem and Omssa will be implemented in the pipeline. Mascot will be incorporated later.

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