The Proteios Software Environment - An extensible multi-user platform for management and analysis of proteomics data Export

@article{citeulike:4321838, abstract = {Proteome analysis involves many steps that generate large quantities of data in different formats. This creates a need for automatic data merging and extraction of important features from data. Furthermore, meta-data need to be collected and reported to enable critical evaluation of results. Many data analysis tools are developed locally in research labs and are non-trivial to adapt for other labs, preventing optimal exploitation of generated data. The proteomics field would benefit from user-friendly analysis and data management platforms in which method developers can make their analysis tools available for the community. Here we describe the Proteios Software Environment (ProSE) that is built around a web-based local data repository for proteomics experiments. The application features sample tracking, project sharing between multiple users, and automated data merging and analysis. ProSE has built-in support for several quantitative proteomics workflows, and integrates searching in several search engines, automated combination of the search results with pre-determined false discovery rates, annotation of proteins and submission of results to public repositories. ProSE also provides a programming interface to enable local extensions, as well as database access using web services. ProSE provides an analysis platform for proteomics research and is targeted for multi-user projects with needs to share data, sample tracking, and analysis result. ProSE is open source software available at http://www.proteios.org}, author = {Levander, Fredrik and Hakkinen, Jari and Vincic, Gregory and Mansson, Olle and Warell, Kristofer}, citeulike-article-id = {4321838}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/pr900189c}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/pr900189c}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19354269}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19354269}, doi = {10.1021/pr900189c}, journal = {Journal of Proteome Research}, keywords = {analysis, opensource, proteomics, software, webserver}, number = {ja}, posted-at = {2009-05-07 00:55:34}, priority = {2}, title = {The Proteios Software Environment - An extensible multi-user platform for management and analysis of proteomics data}, url = {http://dx.doi.org/10.1021/pr900189c}, volume = {0}, year = {0000} }

TY - JOUR ID - citeulike:4321838 L3 - citeulike-article-id:4321838 N2 - Proteome analysis involves many steps that generate large quantities of data in different formats. This creates a need for automatic data merging and extraction of important features from data. Furthermore, meta-data need to be collected and reported to enable critical evaluation of results. Many data analysis tools are developed locally in research labs and are non-trivial to adapt for other labs, preventing optimal exploitation of generated data. The proteomics field would benefit from user-friendly analysis and data management platforms in which method developers can make their analysis tools available for the community. Here we describe the Proteios Software Environment (ProSE) that is built around a web-based local data repository for proteomics experiments. The application features sample tracking, project sharing between multiple users, and automated data merging and analysis. ProSE has built-in support for several quantitative proteomics workflows, and integrates searching in several search engines, automated combination of the search results with pre-determined false discovery rates, annotation of proteins and submission of results to public repositories. ProSE also provides a programming interface to enable local extensions, as well as database access using web services. ProSE provides an analysis platform for proteomics research and is targeted for multi-user projects with needs to share data, sample tracking, and analysis result. ProSE is open source software available at http://www.proteios.org IS - ja JF - Journal of Proteome Research TI - The Proteios Software Environment - An extensible multi-user platform for management and analysis of proteomics data VL - 0 KW - analysis KW - opensource KW - proteomics KW - software KW - webserver AU - Levander, Fredrik AU - Hakkinen, Jari AU - Vincic, Gregory AU - Mansson, Olle AU - Warell, Kristofer PY - 2000/// UR - http://dx.doi.org/10.1021/pr900189c ER -