Wednesday, February 5, 2025 2/5/2025

Enhancements to the GMOD Suite of Genome Annotation and Visualization Tools

Award Number: R01HG004483
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

Group Awards By:

View Award Abstract

Usability remains a significant barrier to broader adoption of cutting-edge bioinformatics tools, due to a lack of user-friendly web interfaces. The Generic Model Organism Database (GMOD) provides standards-based software components from which web-facing genome databases can be quickly assembled. JBrowse, the genome browser of GMOD, aims to "democratize" genome informatics by making genome annotations and sequence analysis tools more accessible to the broader community of biologists, using JavaScript and the dynamic web. JBrowse is now in active use by thousands of websites and over a hundred thousand users, with over a million hits per month. Its annotation editing plugin, Apollo, is used by many NIH-funded projects to coordinate contributions from professional biocurators and motivated experts in the community. In this phase of the JBrowse project, we plan to build machine learning capabilities into JBrowse: to make automated recommendations to users that help them more rapidly review evidence and form hypotheses, to help developers of AI tools assemble and curate genomic datasets, and to present the results of machine learning analyses of genomic data dynamically to the user on demand. We also propose to enhance JBrowse's capabilities for using genomic synteny as a navigation tool to move between related genomes, view evolutionarily conserved gene structures and their associated alignments, and visualize genome annotations in their phylogenetic context. We will also significantly improve JBrowse's speed and design via series of systematic performance and usability benchmarks, and by user testing at design sprints. Finally, we will continue GMOD's outreach/helpdesk efforts with focused workshops, training materials, and documentation to maximize the utility of GMOD/JBrowse to the broader community.


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: 2025 ( Subtotal = $584,929 )
2025	2025	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 201	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	000	16	12/31/2024	NON-COMPETING CONTINUATION	$584,929
														Subtotal = $584,929

Issue Date FY: 2024 ( Subtotal = $663,262 )
2024	2024	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 201	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	002	15	8/2/2024	COMPETING CONTINUATION	$54,144
2024	2024	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 201	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	001	15	2/26/2024	COMPETING CONTINUATION	$609,118
2024	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 201	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	000	14	11/21/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $663,262

Issue Date FY: 2022 ( Subtotal = $650,645 )
2022	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 201	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	000	14	5/3/2022	NON-COMPETING CONTINUATION	$650,645
														Subtotal = $650,645

Issue Date FY: 2021 ( Subtotal = $663,205 )
2021	2021	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	000	13	4/20/2021	NON-COMPETING CONTINUATION	$663,205
														Subtotal = $663,205

Issue Date FY: 2020 ( Subtotal = $1,035,242 )
2020	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	000	12	4/17/2020	NON-COMPETING CONTINUATION	$680,475
2020	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	001	12	9/4/2020	SUPPLEMENT FOR EXPANSION	$354,767
														Subtotal = $1,035,242

Issue Date FY: 2019 ( Subtotal = $693,035 )
2019	2019	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	004	11	4/24/2019	NON-COMPETING CONTINUATION	$693,035
2019	2018	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	001	10	10/29/2018	COMPETING CONTINUATION	$958
2019	2018	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	003	10	3/26/2019	COMPETING CONTINUATION	$2,777
2019	2016	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	000	9	10/29/2018	NON-COMPETING CONTINUATION	-$958
2019	2016	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Human Genome Research	002	9	3/26/2019	NON-COMPETING CONTINUATION	-$2,777
														Subtotal = $693,035

Issue Date FY: 2018 ( Subtotal = $702,575 )
2018	2018	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	2150 SHATTUCK AVE RM 313	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	10	5/18/2018	COMPETING CONTINUATION	$702,575
2018	2018	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	2150 SHATTUCK AVE RM 313	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	002	10	9/25/2018	COMPETING CONTINUATION	$75,114
2018	2016	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	2150 SHATTUCK AVE RM 313	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	001	9	9/25/2018	NON-COMPETING CONTINUATION	-$75,114
														Subtotal = $702,575

Issue Date FY: 2017 ( Subtotal = $0 )
2017	2014	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	2150 SHATTUCK AVE RM 313	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	001	7	5/16/2017	COMPETING CONTINUATION	$98,313
2017	2013	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	2150 SHATTUCK AVE RM 313	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	6	5/16/2017	NON-COMPETING CONTINUATION	-$98,313
														Subtotal = $0

Issue Date FY: 2016 ( Subtotal = $377,625 )
2016	2016	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	9	4/18/2016	NON-COMPETING CONTINUATION	$377,625
														Subtotal = $377,625

Issue Date FY: 2015 ( Subtotal = $376,934 )
2015	2015	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	8	4/25/2015	NON-COMPETING CONTINUATION	$376,934
														Subtotal = $376,934

Issue Date FY: 2014 ( Subtotal = $399,999 )
2014	2014	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	001	7	6/30/2014	COMPETING CONTINUATION	$399,999
2014	2013	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	6	6/25/2014	NON-COMPETING CONTINUATION	$0
														Subtotal = $399,999

Issue Date FY: 2013 ( Subtotal = $376,156 )
2013	2013	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	6	7/16/2013	NON-COMPETING CONTINUATION	$376,156
														Subtotal = $376,156

Issue Date FY: 2012 ( Subtotal = $427,095 )
2012	2012	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	5	9/7/2012	NON-COMPETING CONTINUATION	$427,095
														Subtotal = $427,095

Issue Date FY: 2011 ( Subtotal = $472,751 )
2011	2011	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	4	9/6/2011	COMPETING CONTINUATION	$472,751
														Subtotal = $472,751

Issue Date FY: 2010 ( Subtotal = $288,719 )
2010	2010	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	3	9/28/2010	SUPPLEMENT FOR EXPANSION	$288,719
2010	2009	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	001	3	9/28/2010	NON-COMPETING CONTINUATION	$0
														Subtotal = $288,719

Issue Date FY: 2009 ( Subtotal = $288,719 )
2009	2009	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	001	3	8/10/2009	NON-COMPETING CONTINUATION	$288,719
2009	2008	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	2	3/16/2009	NON-COMPETING CONTINUATION	$0
														Subtotal = $288,719

Issue Date FY: 2008 ( Subtotal = $288,719 )
2008	2008	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	2	8/28/2008	NON-COMPETING CONTINUATION	$288,719
														Subtotal = $288,719

Issue Date FY: 2007 ( Subtotal = $318,924 )
2007	2007	UNIVERSITY OF CALIFORNIA, REGENTS	481 UNIVERSITY HALL	BERKELEY	CA	94704	ALAMEDA	USA	Human Genome Research	000	1	8/22/2007	NEW	$318,924
														Subtotal = $318,924

Grand Total All Awards = $8,608,534

Top

All Categories

About

Search

Reports

Data Submission

Award Information

Enhancements to the GMOD Suite of Genome Annotation and Visualization Tools

Award Number: R01HG004483

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

Federal Websites

Department of Health & Human Services

HHS Operating Divisions

HHS Staff Divisions

Download A Document Viewer