Thursday, June 8, 2023 6/8/2023

A Cloud-based Dockerized Metagenomics Analysis of Biofilm Microbiome

Award Number: P20GM103443
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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Project Summary Biofilms are complex formations of microbial communities composed of different types of microorganisms such as bacteria, viruses and fungi. They are responsible for the majority of human microbial infections. Understanding how biofilm impacts human health and how it can be controlled is becoming increasingly important for preventive medicine. Here, we propose the development of a Biofilm Metagenomics Workflow Self-Learning Module to aid in the understanding of biofilm’s role in human health. Metagenomics has emerged as a powerful tool for the genomic analysis of biofilm through function-based gene sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing provides the ability to comprehensively sample all genes in all organisms present in each biofilm sample using Quorum Sensing signatures. Our Biofilm Metagenomics Workflow Self-Learning Module will provide students with an analysis resource beneficial for the aggregation of knowledge about speci¿c genes, microbial communities and its metabolic pathways. Because this learning module will be available through cloud computing, students can focus on biofilm metagenomics analysis rather than first having to install software and verifying software versioning. Our cost-effective optimization Docker Image will include the packaging of the workflow along with sample datasets related to the three focus use cases. These “small” datasets will ensure that the cloud computing resources will not be over allocated. Users will also be able to upload other sample data and our module will include a data controller that will verify that before the workflow is executed, the input and parameters are checked to ensure that they fall into the “acceptable” range. Impact: We will use our combined expertise to develop a Biofilm Metagenomics Workflow Self-Learning Module. This learning module will include instructional videos, a Dockerized, interactive workflow implemented using Jupyter Notebook, and practicum exercise that will enable self-learning on toy datasets. This will provide the educational community with a Biofilm Metagenomics resource that will aid in their understanding of how biofilm impacts human health. The Biofilm Metagenomics Workflow is a generalized solution, allowing researchers to deploy it to alternate platforms and apply it to a wide range of use cases.


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: 2023 ( Subtotal = $0 )
2023	2022	UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	20	5/4/2023	SUPPLEMENT FOR EXPANSION	$0
2023	2022	UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	001	20	5/29/2023	SUPPLEMENT FOR EXPANSION	$0


Issue Date FY: 2022 ( Subtotal = $4,544,671 )
2022	2022	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	001	20	5/16/2022	SUPPLEMENT FOR EXPANSION	$26,228
2022	2022	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	008	21	9/10/2022	SUPPLEMENT FOR EXPANSION	$527,317
2022	2022	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	005	21	9/7/2022	NON-COMPETING CONTINUATION	$3,319,582
2022	2022	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	009	21	9/12/2022	SUPPLEMENT FOR EXPANSION	$78,684
2022	2022	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	007	21	9/9/2022	SUPPLEMENT FOR EXPANSION	$369,177
2022	2022	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	003	20	7/5/2022	SUPPLEMENT FOR EXPANSION	$117,839
2022	2022	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	002	20	6/28/2022	SUPPLEMENT FOR EXPANSION	$0
2022	2022	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	006	21	9/8/2022	SUPPLEMENT FOR EXPANSION	$105,844
2022	2021	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	004	20	7/11/2022	NON-COMPETING CONTINUATION	$0
2022	2021	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	20	12/13/2021	NON-COMPETING CONTINUATION	$0


Issue Date FY: 2021 ( Subtotal = $4,487,760 )
2021	2021	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	003	20	9/15/2021	NON-COMPETING CONTINUATION	$3,772,381
2021	2021	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	006	20	9/27/2021	NON-COMPETING CONTINUATION	$0
2021	2021	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	005	20	9/17/2021	SUPPLEMENT FOR EXPANSION	$250,000
2021	2021	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	004	20	9/16/2021	SUPPLEMENT FOR EXPANSION	$309,810
2021	2021	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	002	19	6/7/2021	SUPPLEMENT FOR EXPANSION	$155,569
2021	2020	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	001	19	5/16/2021	COMPETING CONTINUATION	$294,863
2021	2019	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	18	5/16/2021	NON-COMPETING CONTINUATION	-$294,863


Issue Date FY: 2020 ( Subtotal = $3,824,325 )
2020	2020	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	003	19	9/16/2020	SUPPLEMENT FOR EXPANSION	$121,272
2020	2020	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	002	19	9/7/2020	COMPETING CONTINUATION	$3,703,053
2020	2019	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	001	18	9/6/2020	NON-COMPETING CONTINUATION	$0
2020	2019	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	18	5/18/2020	NON-COMPETING CONTINUATION	$0


Issue Date FY: 2019 ( Subtotal = $3,064,038 )
2019	2019	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	18	5/1/2019	NON-COMPETING CONTINUATION	$3,064,038


Issue Date FY: 2018 ( Subtotal = $3,106,217 )
2018	2018	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	002	17	9/7/2018	NON-COMPETING CONTINUATION	$0
2018	2018	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	001	17	8/8/2018	NON-COMPETING CONTINUATION	$3,106,217
2018	2017	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	16	7/18/2018	NON-COMPETING CONTINUATION	$0


Issue Date FY: 2017 ( Subtotal = $3,164,568 )
2017	2017	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	001	16	7/31/2017	NON-COMPETING CONTINUATION	$316,458
2017	2017	THE UNIVERSITY OF SOUTH DAKOTA	414 E CLARK ST	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	16	5/24/2017	NON-COMPETING CONTINUATION	$2,848,110


Issue Date FY: 2016 ( Subtotal = $3,241,731 )
2016	2016	UNIVERSITY OF SOUTH DAKOTA	414 EAST CLARK STREET	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	15	7/18/2016	NON-COMPETING CONTINUATION	$3,241,731


Issue Date FY: 2015 ( Subtotal = $3,509,779 )
2015	2015	UNIVERSITY OF SOUTH DAKOTA	414 EAST CLARK STREET	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	003	14	8/20/2015	COMPETING CONTINUATION	$17,962
2015	2015	UNIVERSITY OF SOUTH DAKOTA	414 EAST CLARK STREET	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	004	14	8/31/2015	COMPETING CONTINUATION	$225,000
2015	2015	UNIVERSITY OF SOUTH DAKOTA	414 EAST CLARK STREET	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	002	14	7/15/2015	COMPETING CONTINUATION	$3,266,817
2015	2014	UNIVERSITY OF SOUTH DAKOTA	414 EAST CLARK STREET	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	001	13	7/14/2015	SUPPLEMENT FOR EXPANSION	$0
2015	2013	UNIVERSITY OF SOUTH DAKOTA	414 EAST CLARK STREET	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	13	7/13/2015	NON-COMPETING CONTINUATION	$0


Issue Date FY: 2014 ( Subtotal = $2,327,669 )
2014	2014	UNIVERSITY OF SOUTH DAKOTA	414 EAST CLARK STREET	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	13	9/24/2014	SUPPLEMENT FOR EXPANSION	$2,327,669
2014	2013	UNIVERSITY OF SOUTH DAKOTA	414 EAST CLARK STREET	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	001	13	9/24/2014	NON-COMPETING CONTINUATION	$0


Issue Date FY: 2013 ( Subtotal = $3,044,801 )
2013	2013	UNIVERSITY OF SOUTH DAKOTA	414 EAST CLARK STREET	VERMILLION	SD	57069	CLAY	USA	Biomedical Research and Research Training	000	13	5/23/2013	NON-COMPETING CONTINUATION	$3,044,801


Issue Date FY: 2012 ( Subtotal = $3,140,484 ) (Continued on the next page)
Grand Total All Awards = $37,456,043

Sum of Action Amount is $37,456,043;

Grand Total = $37,456,043

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A Cloud-based Dockerized Metagenomics Analysis of Biofilm Microbiome

Award Number: P20GM103443

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

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