Title: "Design and development of open source software for discovery and validation of biomarkers"
Speaker: Mi-Youn Brusniak, Institute for Systems Biology, Seattle, WA
Place: PHYS 223;
Date: April 10, 2012, Tuesday
Time: 4:30pm


Mi-Youn Brusniak, Ph.D. is a Computational Biologist/Senior Software Engineer in the proteomics department at the Institute for Systems Biology in Seattle, WA. She will discuss Liquid Chromatography Mass Spectrum (LC-MS) based approaches for discovery and validation of biomarkers and general proteomics research that uses shotgun or targeted methodologies. Rapidly adapting robust open source software enables researchers to gain biological insights using high throughput and data rich experiments in a timely manner. Dr. Brusniak will introduce several open source software packages developed by ISB, including Corra-ATAQS, which is an integrated software platform that supports all stages of discovery and validation of biomarkers by utilizing high mass accuracy LC-MS data and by querying and selecting appropriate LC-MS parameters to seamlessly create Selected Reaction Monitoring (SRM) targeted methods in an open source software environment. She will introduce several case studies and briefly discuss the challenges of developing open source software.

Associated Reading:
Mi-Youn Brusniak et al. 2008. Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics 9:542.

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