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Multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis

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dc.contributor.author Parikh, Jignesh R en_US
dc.contributor.author Askenazi, Manor en_US
dc.contributor.author Ficarro, Scott B en_US
dc.contributor.author Cashorali, Tanya en_US
dc.contributor.author Webber, James T en_US
dc.contributor.author Blank, Nathaniel C en_US
dc.contributor.author Zhang, Yi en_US
dc.contributor.author Marto, Jarrod A en_US
dc.date.accessioned 2012-01-11T21:09:33Z
dc.date.available 2012-01-11T21:09:33Z
dc.date.copyright 2009 en_US
dc.date.issued 2009-10-29 en_US
dc.identifier.citation Parikh, Jignesh R, Manor Askenazi, Scott B Ficarro, Tanya Cashorali, James T Webber, Nathaniel C Blank, Yi Zhang, Jarrod A Marto. "multiplierz: an extensible API based desktop environment for proteomics data analysis" BMC Bioinformatics 10:364. (2009) en_US
dc.identifier.issn 1471-2105 en_US
dc.identifier.uri http://hdl.handle.net/2144/3191
dc.description.abstract BACKGROUND. Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge. RESULTS. We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. CONCLUSION. Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research. en_US
dc.description.sponsorship Dana-Farber Cancer Institute; National Human Genome Research Institute (P50HG004233); National Science Foundation Integrative Graduate Education and Research Traineeship grant (DGE-0654108) en_US
dc.language.iso en en_US
dc.publisher BioMed Central en_US
dc.rights Copyright 2009 Parikh et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. en_US
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en_US
dc.title Multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis en_US
dc.type article en_US
dc.identifier.doi 10.1186/1471-2105-10-364 en_US
dc.identifier.pubmedid 19874609 en_US
dc.identifier.pmcid 2774704 en_US


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Copyright 2009 Parikh et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Except where otherwise noted, this item's license is described as Copyright 2009 Parikh et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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