Proteomatic

a platform for high-throughput MS/MS data evaluation and deployment of processing scripts

by Michael Specht

Abstract

     Proteomatic provides an operating system-independent and user-friendly data evaluation platform that enables the construction and execution of MS/MS data evaluation pipelines using free software. Required external programs, such as for peptide identification and quantitation, are downloaded automatically. Due to a design which implements a strict separation of functionality and presentation, new processing steps can be added easily.

     From the perspective of an experimentalist, Proteomatic provides a way to establish and run flexible data evaluation pipelines. From the bioinformatic researcher's point of view, Proteomatic provides a simple way to deploy novel processing scripts – and therefore new functionality – to the lab. Proteomatic scripts are highly accessible because a graphical user interface (GUI) is created automatically, with no GUI programming knowledge required. Proteomatic runs on Windows, Mac OS X, and Linux, and provides the same functionality on all three operating systems. Although originally designed for the field of mass spectrometry, Proteomatic can be used in any high-throughput file-based data processing scenario and it is the aim of the workshop to teach the necessary steps to add new functionality (proteomics-related or other) to the system.
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Target audience and aims of the workshop..

     This workshop is intended for scientists who spend a substantial amount of their time writing software and feel that it may desirable to provide this functionality to other scientists or use the functionality in a greater context such as in a processing pipeline. After an introduction to Proteomatic and its usage, the workshop shifts gears and presents Proteomatic from the software developer's perspective. In a hands-on programming session, the development of a Proteomatic script will be demonstrated. Therefore, participants are required to be familiar with one of the scripting languages Ruby, Python, or PHP.


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