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CottonGen Year of 2023 in Review

by Yu, Jing

[A close up of a sign Description automatically generated]<http://www.cottongen.org/> More Data. We added more data in 2023 including 18 new whole genome assembly<https://www.cottongen.org/tools/jbrowse>, QTL<https://www.cottongen.org/tripal_megasearch?datatype=tripal_megasearch_qtl>, markers, genetic map<https://www.cottongen.org/tripal_megasearch?datatype=tripal_megasearch_feat…>, genotype<https://www.cottongen.org/find/snp/genotype>, and phenotype<https://www.cottongen.org/find/qualitative_traits> data. We also started adding GWAS data and added more expression data! Check the 'Data Overview<https://www.cottongen.org/data_overview/1>' page for currently available data. New and Updated Tools. MegaSearch<https://www.cottongen.org/tripal_megasearch?datatype=tripal_megasearch_qtl> and MapViewer<https://www.cottongen.org/MapViewer> are updated to display GWAS data, and the Expression Heatmap <https://www.cottongen.org/heatmap> allows researchers to quickly and easily identify patterns of gene expression that are associated with specific conditions or treatments. New Short Video Tutorials. This year we made six new video tutorials How to search cotton markers using <https://www.youtube.com/watch?v=NrwYZB_ywsg> MegaSearch<https://www.youtube.com/watch?v=NrwYZB_ywsg> How to view genomes linked to genetic maps<https://www.youtube.com/watch?v=ZHn-tIHKhfw> How to use <https://youtu.be/Ia3v650TZAg> MegaSearch<https://youtu.be/Ia3v650TZAg> for Gene and Transcripts<https://youtu.be/Ia3v650TZAg> How to search traits and see all the linked data<https://youtu.be/nKo8c7s5pHc> How to use the Expression Heatmap Tool<https://youtu.be/QU6trudNegg?si=PtobLDQSwNkiHzwQ> How to view correspondences between genomes and genetic maps<https://www.youtube.com/watch?v=dFMn9g5NsTw> NewsLetters. We sent out four quarterly NewsLetters<https://www.cottongen.org/CottonGen_newsletter> Join us at 2024 January Conferences: Beltwide Cotton Conference - Cotton Improvement Conference: Thur. Jan. 4 at 4-4:15 PM "Using CottonGen for Cotton Improvement"<https://www.cotton.org/beltwide/bw24-final-printed-program.pdf> PAG - Tripal Database Network and Initiatives Sat, Jan. 13 at 5:14-5:32 PM "TripalMap Mapviewer 2.1"<https://plan.core-apps.com/pag_2024/event/b44b10371958e4ecc7a77988eb6d8903> PAG - National Research Support Project (NRSP10) Sun, Jan. 14 at 1:30-3:40 PM Database Resources for Crop Genomics, Genetics and Breeding<https://plan.core-apps.com/pag_2024/event/2b5bdde4-f492-45ee-a07b-7d570fdd9…> PAG - Digital Tools and Resources Tue, Jan.16 at 12-12:30 PM "CottonGen<https://plan.core-apps.com/pag_2024/event/b44b10371958e4ecc7a77988eb6ad6db> 2023: New Data and New Functionality to enable cotton research discovery and crop improvement"<https://plan.core-apps.com/pag_2024/event/b44b10371958e4ecc7a77988eb6ad6db> Subscribe to the Mailing List<https://www.cottongen.org/mailing_list>

1 year, 6 months

Training video: Learn how to view correspondences between genomes and genetic maps

by Yu, Jing

[A screenshot of a video Description automatically generated]<https://www.youtube.com/watch?v=dFMn9g5NsTw>

1 year, 7 months

BIMS Webinar on November 28, 8.30 PST/11.30 EST AM

by Jung, Sook

Zoom Info Join from PC, Mac, Linux, iOS, or Android: https://wsu.zoom.us/j/93646942616 Meeting ID: 936 4694 2616 www.breedwithbims.org<http://www.breedwithbims.org/> [cid:a968c967-c87c-4b6d-b755-d4adcf9b9d4b] Sook Jung, Ph.D. (she/her) Associate Professor of Bioinformatics Department of Horticulture Washington State University Email: sook_jung(a)wsu.edu<mailto:sook_jung@wsu.edu> ORCID: 0000-0003-3968-2769 Publications: Google Scholar<https://scholar.google.com/citations?user=Z4C1MoEAAAAJ&hl=en>

1 year, 7 months

FW: BIMS Webinar on November 28, 8.30 PST/11.30 EST AM

by Yu, Jing

________________________________ From: Jung, Sook via COTTONGEN-LIST <cottongen-list(a)cottongen.org<mailto:cottongen-list@cottongen.org>> Sent: Tuesday, November 14, 2023 5:28 PM To: bims(a)bioinfo.wsu.edu<mailto:bims@bioinfo.wsu.edu> <bims(a)bioinfo.wsu.edu<mailto:bims@bioinfo.wsu.edu>> Cc: gdr-list(a)bioinfo.wsu.edu<mailto:gdr-list@bioinfo.wsu.edu> <gdr-list(a)bioinfo.wsu.edu<mailto:gdr-list@bioinfo.wsu.edu>>; cottongen-list(a)cottongen.org<mailto:cottongen-list@cottongen.org> <cottongen-list(a)cottongen.org<mailto:cottongen-list@cottongen.org>> Subject: [CottonGen]BIMS Webinar on November 28, 8.30 PST/11.30 EST AM [EXTERNAL EMAIL] Zoom Info Join from PC, Mac, Linux, iOS, or Android: https://wsu.zoom.us/j/93646942616<https://urldefense.com/v3/__https://wsu.zoom.us/j/93646942616__;!!JmPEgBY0H…> Meeting ID: 936 4694 2616 www.breedwithbims.org<https://urldefense.com/v3/__http://www.breedwithbims.org/__;!!JmPEgBY0HMszN…> [cid:a968c967-c87c-4b6d-b755-d4adcf9b9d4b] Sook Jung, Ph.D. (she/her) Associate Professor of Bioinformatics Department of Horticulture Washington State University Email: sook_jung(a)wsu.edu<mailto:sook_jung@wsu.edu> ORCID: 0000-0003-3968-2769 Publications: Google Scholar<https://urldefense.com/v3/__https://scholar.google.com/citations?user=Z4C1M…>

1 year, 7 months

CottonGen Newsletter October 2023

by Yu, Jing

[Read the CottonGen Newsletter,Subscribe to the Mailing List] [A screenshot of a web page Description automatically generated]<https://www.cottongen.org/sites/default/files/cottongen_newsletters/CottonG…>

1 year, 8 months

Training video: Learn How to use the Expression Heatmap Tool

by Yu, Jing

How to use the Expression Heatmap Tool https://youtu.be/QU6trudNegg<%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20https:/youtu.be/QU6trudNegg> [A screenshot of a computer Description automatically generated]<https://youtu.be/QU6trudNegg>

1 year, 9 months

CottonGen Newsletter July 2023

by Yu, Jing

[A screenshot of a web page Description automatically generated]<https://www.cottongen.org/sites/default/files/cottongen_newsletters/CottonG…>

1 year, 11 months

Training video: How to search traits and see all the linked data

by Yu, Jing

Learn how to search traits and see all the linked data. https://youtu.be/nKo8c7s5pHc [A screenshot of a computer Description automatically generated with medium confidence]<https://youtu.be/nKo8c7s5pHc>

2 years

Training video: Learn How to Use MegaSearch for Genes and Transcripts

by Yu, Jing

How to Use MegaSearch for Genes and Transcripts https://youtu.be/Ia3v650TZAg [A screenshot of a cotton database Description automatically generated with low confidence] <https://youtu.be/Ia3v650TZAg>

2 years, 1 month

CottonGen Newsletter April 2023

by Yu, Jing

[A close-up of a web page Description automatically generated with low confidence]<https://www.cottongen.org/CottonGen_newsletter>

2 years, 2 months

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