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Shortening the development cycle time of Trans Proteomic Pipeline tools with high performance computing

Award Number: R01GM087221
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2010
PERIOD OF PERFORMANCE END DATE: 04/30/2023

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Shortening the development cycle time of Trans Proteomic Pipeline tools with high performance computing - Project Summary Mass spectrometry (MS) based proteomics is currently the most widely used technology for the analysis of complex protein mixtures. It has the ability to detect and quantify the abundance of thousands of proteins and their variants, post-translational modifications, protein:protein and protein:drug interactions per experiment. The Trans-Proteomic Pipeline (TPP) is a free and open-source suite of software tools for the analysis of mass spectrometry (MS) proteomics data that has been widely used by the community for over 15 years. Our ongoing award for the maintenance and development of the TPP has four aims in which we 1) enhance the TPP to process datasets from emerging workflows, 2) add statistical analysis and visualization capabilities for large datasets, 3) respond to the needs of the community with functional and usability enhancements, and 4) expand our user base with improved training and on-line learning. Great progress has been made on these aims during the project period. However, current development for one of the main tools that we are currently focusing on has been severely hindered by aging computational servers purchased in 2012 and inadequate development of computing resources. We propose to address this problem via the purchase and deployment of a pair of high- memory, high-core count, fast-disk compute servers, substantially accelerating our development cycle so that the algorithm development can be completed more rapidly, and the completed algorithm can be further rapidly optimized to run with more modest hardware requirements routinely. Deployment of these machines will streamline our software development by providing rapid feedback on software changes and further developments and their impact on search speed and enable us to provide tools to our users more rapidly, accelerating the progress of many other research programs that use the TPP for data processing.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2024 ( Subtotal = -$749 )
2024	2021	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	001	11	2/13/2024	SUPPLEMENT FOR EXPANSION	-$120
2024	2021	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	11	2/13/2024	NON-COMPETING CONTINUATION	-$629
														Subtotal = -$749

Issue Date FY: 2021 ( Subtotal = $624,789 )
2021	2021	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	001	11	8/20/2021	SUPPLEMENT FOR EXPANSION	$100,000
2021	2021	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	11	4/21/2021	NON-COMPETING CONTINUATION	$524,789
														Subtotal = $624,789

Issue Date FY: 2020 ( Subtotal = $524,789 )
2020	2020	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	10	5/1/2020	NON-COMPETING CONTINUATION	$524,789
														Subtotal = $524,789

Issue Date FY: 2019 ( Subtotal = $524,789 )
2019	2019	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	002	9	5/28/2019	NON-COMPETING CONTINUATION	$524,789
2019	2018	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	001	8	12/13/2018	COMPETING CONTINUATION	$1,183
2019	2017	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	7	12/13/2018	NON-COMPETING CONTINUATION	-$1,183
														Subtotal = $524,789

Issue Date FY: 2018 ( Subtotal = $524,789 )
2018	2018	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	8	7/20/2018	COMPETING CONTINUATION	$524,789
														Subtotal = $524,789

Issue Date FY: 2017 ( Subtotal = $509,505 )
2017	2017	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	001	7	6/2/2017	NON-COMPETING CONTINUATION	$50,951
2017	2017	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	7	3/30/2017	NON-COMPETING CONTINUATION	$458,554
														Subtotal = $509,505

Issue Date FY: 2016 ( Subtotal = $509,505 )
2016	2016	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Biomedical Research and Research Training	000	6	6/10/2016	NON-COMPETING CONTINUATION	$509,505
														Subtotal = $509,505

Issue Date FY: 2015 ( Subtotal = $509,505 )
2015	2015	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Biomedical Research and Research Training	000	5	4/15/2015	NON-COMPETING CONTINUATION	$509,505
														Subtotal = $509,505

Issue Date FY: 2014 ( Subtotal = $521,297 )
2014	2014	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Biomedical Research and Research Training	000	4	3/31/2014	COMPETING CONTINUATION	$521,297
														Subtotal = $521,297

Issue Date FY: 2012 ( Subtotal = $565,009 )
2012	2012	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Biomedical Research and Research Training	000	3	8/20/2012	NON-COMPETING CONTINUATION	$565,009
														Subtotal = $565,009

Issue Date FY: 2011 ( Subtotal = $566,534 )
2011	2011	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Biomedical Research and Research Training	000	2	8/26/2011	NON-COMPETING CONTINUATION	$566,534
														Subtotal = $566,534

Issue Date FY: 2010 ( Subtotal = $589,424 )
2010	2010	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Biomedical Research and Research Training	000	1	8/31/2010	NEW	$589,424
														Subtotal = $589,424

Grand Total All Awards = $5,969,186

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Shortening the development cycle time of Trans Proteomic Pipeline tools with high performance computing

Award Number: R01GM087221

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/01/2010

PERIOD OF PERFORMANCE END DATE: 04/30/2023

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