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Developing the Apollo software for high-throughput annotation of multiple genomes

Award Number: R01GM080203
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: 08/01/2007
PERIOD OF PERFORMANCE END DATE: 08/31/2027

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Developing the Apollo software for high-throughput annotation of multiple genomes - Genome sequencing is becoming cheaper and more powerful. However, a bottleneck to scientific progress using these data is the generation of high-quality genome annotations, describing the location and function of the genes in genomic DNA. In the past, these annotations were generated exclusively by professional biocurators, and these biocurators continue to be a critical source of expertise. However, the number of such biocurators is small compared to the amount of genomic DNA that is available. In recent years, professional biocuration has been supplemented by a growing volunteer force of interested biologists, each generally interested in one or two genes of interest. Although genome annotation is often done in bulk using computational tools, there is currently no substitute for a final pass of manual annotation. This is most commonly done using our Apollo software, which allows for live simultaneous collaborative annotation over the web. Our proposal here is to improve Apollo so as to empower both professional biocurators and crowdsourcing volunteers. We will empower professional biocurators by giving them the power tools they need to simultaneously annotate multiple genomes (by exploiting synteny), annotate variants, and annotate the function of genes. We will empower the crowdsourcing volunteers by lowering barriers to entry, making Apollo more usable. For all users we will train machine learning systems to automatically detect common annotation errors and suggest improvements. We will support Apollo users with maintenance, bugfixing, and various feature requests, as well as extensive outreach including outreach to developers.


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 = $413,581 )
2024	2024	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 201	BERKELEY	CA	94710	ALAMEDA	USA	Biomedical Research and Research Training	000	16	8/26/2024	NON-COMPETING CONTINUATION	$413,581
														Subtotal = $413,581

Issue Date FY: 2023 ( Subtotal = $461,731 )
2023	2023	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 201	BERKELEY	CA	94710	ALAMEDA	USA	Biomedical Research and Research Training	001	15	8/24/2023	COMPETING CONTINUATION	$461,731
2023	2021	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 201	BERKELEY	CA	94710	ALAMEDA	USA	Biomedical Research and Research Training	000	14	8/8/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $461,731

Issue Date FY: 2022 ( Subtotal = $0 )
2022	2021	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 201	BERKELEY	CA	94710	ALAMEDA	USA	Biomedical Research and Research Training	000	14	8/2/2022	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2021 ( Subtotal = $351,173 )
2021	2021	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Biomedical Research and Research Training	000	14	6/4/2021	NON-COMPETING CONTINUATION	$351,173
														Subtotal = $351,173

Issue Date FY: 2020 ( Subtotal = $352,427 )
2020	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Biomedical Research and Research Training	000	13	6/1/2020	NON-COMPETING CONTINUATION	$352,427
														Subtotal = $352,427

Issue Date FY: 2019 ( Subtotal = $320,941 )
2019	2019	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Biomedical Research and Research Training	002	12	5/24/2019	NON-COMPETING CONTINUATION	$320,941
2019	2018	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1608 4TH ST STE 220	BERKELEY	CA	94710	ALAMEDA	USA	Biomedical Research and Research Training	001	11	4/23/2019	COMPETING CONTINUATION	$234,008
2019	2017	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1 CYCLOTRON RD	BERKELEY	CA	94720	ALAMEDA	USA	Biomedical Research and Research Training	000	10	4/23/2019	NON-COMPETING CONTINUATION	-$234,008
														Subtotal = $320,941

Issue Date FY: 2018 ( Subtotal = $288,645 )
2018	2018	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	2150 SHATTUCK AVE RM 313	BERKELEY	CA	94704	ALAMEDA	USA	Biomedical Research and Research Training	001	11	9/10/2018	COMPETING CONTINUATION	$288,645
2018	2017	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1 CYCLOTRON RD	BERKELEY	CA	94720	ALAMEDA	USA	Biomedical Research and Research Training	000	10	9/5/2018	NON-COMPETING CONTINUATION	$0
														Subtotal = $288,645

Issue Date FY: 2017 ( Subtotal = $575,700 )
2017	2017	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1 CYCLOTRON RD	BERKELEY	CA	94720	ALAMEDA	USA	Biomedical Research and Research Training	001	10	6/2/2017	NON-COMPETING CONTINUATION	$57,570
2017	2017	REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE	1 CYCLOTRON RD	BERKELEY	CA	94720	ALAMEDA	USA	Biomedical Research and Research Training	000	10	4/18/2017	NON-COMPETING CONTINUATION	$518,130
														Subtotal = $575,700

Issue Date FY: 2016 ( Subtotal = $575,700 )
2016	2016	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	000	9	4/29/2016	NON-COMPETING CONTINUATION	$575,700
														Subtotal = $575,700

Issue Date FY: 2015 ( Subtotal = $575,700 )
2015	2015	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	000	8	4/17/2015	NON-COMPETING CONTINUATION	$575,700
														Subtotal = $575,700

Issue Date FY: 2014 ( Subtotal = $575,634 )
2014	2014	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	001	7	4/29/2014	COMPETING CONTINUATION	$575,634
2014	2013	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	000	6	4/28/2014	NON-COMPETING CONTINUATION	$0
														Subtotal = $575,634

Issue Date FY: 2013 ( Subtotal = $604,264 )
2013	2013	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	001	6	4/28/2014	NON-COMPETING CONTINUATION	$0
2013	2013	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	000	6	5/20/2013	NON-COMPETING CONTINUATION	$604,264
														Subtotal = $604,264

Issue Date FY: 2012 ( Subtotal = $623,221 )
2012	2012	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	000	5	5/1/2012	NON-COMPETING CONTINUATION	$623,221
														Subtotal = $623,221

Issue Date FY: 2011 ( Subtotal = $621,048 )
2011	2011	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	001	4	8/1/2011	NON-COMPETING CONTINUATION	$56,459
2011	2011	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	000	4	4/28/2011	NON-COMPETING CONTINUATION	$564,589
														Subtotal = $621,048

Issue Date FY: 2010 ( Subtotal = $616,989 )
2010	2010	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	001	3	4/14/2010	COMPETING CONTINUATION	$616,989
2010	2008	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	000	2	4/12/2010	NON-COMPETING CONTINUATION	$0
														Subtotal = $616,989

Issue Date FY: 2008 ( Subtotal = $380,802 )
2008	2008	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	000	2	8/1/2008	NON-COMPETING CONTINUATION	$380,802
														Subtotal = $380,802

Issue Date FY: 2007 ( Subtotal = $383,483 )
2007	2007	LAWRENCE BERKELEY LABORATORY	POST OFFICE BOX 528	BERKELEY	CA	94701	ALAMEDA	USA	Biomedical Research and Research Training	000	1	7/17/2007	NEW	$383,483
														Subtotal = $383,483

Grand Total All Awards = $7,721,039

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Developing the Apollo software for high-throughput annotation of multiple genomes

Award Number: R01GM080203

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: 08/01/2007

PERIOD OF PERFORMANCE END DATE: 08/31/2027

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