Canary Foundation CPAS Development Awards

The Broad Institute of Harvard and MIT: The Carr and Mani Laboratories (Broad Institute) will work in collaboration with the McIntosh Laboratory (Fred Hutchinson Cancer Research Center) to integrate multiple tools into the CPAS workflow of the Labkey.org platform in order to allow label-free analysis of high resolution mass spectrometry. The work will integrate Broad tools PePPER with the FHCRC platform msInspect and CPAS, and foster applications for finding serum biomarkers for cancer.

British Columbia Cancer Research Center, Terry Fox Laboratory: Ryan Brinkman (UBC) will work in collaboration with Adam Triestar (Treestar Software) to improve the analysis workflow for flow cytometry and its application to cancer in the Labkey platform with FlowJo, a leading analysis platform for flow cytometry developed by Adam Triestar.

The Institute for Systems Biology (ISB): John Boyle will lead a collaboration between the ISB and Harvard Partners (Kutherlepati lab) to improve a general workflow for the CPAS algorithms, allowing simpler integration of novel tools into the system, and making it easier to install and manage large proteomics installations.

University of Washington: The Jay Heinecke laboratory, in collaboration with the David Goodlett laboratory, will make several extensions to the platform to support more intensive mining and interrogation of data, including interrogating the relationships of genes to proteins, improving the ability to compare proteins across runs, and support more general purpose exporting of data for further analysis.

Indiana University, Purdue University and IUIPI : A team of researchers, led by PI Jake Chen, will develop tools and procedures for annotating experimental protocols and data and loading these annotations into CPAS using the Experimental Archive (XAR) standardized format. The purpose of the annotation framework is to allow proteomics researchers to manage multiple experimental designs, experimental protocols, data storage parameters, and experimental results in a way that fosters consistency across different labs.  This consistency is a key goal of the National Cancer Institute (NCI) and the Human Proteome Organization (HUPO).