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57 discussions

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, 4 months

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, 5 months

Learn how to search cotton markers using MegaSearch

by Yu, Jing

How to Search Markers in CottonGen using MegaSearch https://www.youtube.com/watch?v=NrwYZB_ywsg [cid:69fe6229-1c3d-4467-b2b4-f2132322e0c2]

2 years, 7 months

Today: CottonGen Workshop at PAG

by Main, Doreen

Good Morning Cotton Folks, We hope you can join us for today's NRSP10 Database workshop which will cover how to use CottonGen for genetics, genomics, and breeding research (description below). Cheers Dorrie Title: Database Resources for Crop Genomics, Genetics and Breeding: NRSP10 Location: Pacific F-G (2nd Floor)<https://plan.core-apps.com/pag_2023/place/2199b42248257468d9d9489c6a85af04?…> Date: Sunday, Jan 15 1:30 PM Duration: 2 hours 10 minutes Talks: * Updates on Genetics Data and Tools in Rosaceae, Cotton, Citrus, Vaccinium and Pulse Crop Databases (Sook Jung) * Updates on Genomics Data and Tools in Rosaceae, Cotton, Citrus, Vaccinium and Pulse Crop Databases (Jodi Humann) * Updates on Germplasm and Diversity Data and Tools in Rosaceae, Cotton, Citrus, Vaccinium and Pulse Crop Databases (Nahla Bassil) * A Peach Breeders Perspective on Using the Breeding Information Management System for Crop Breeding (Ksenija Gasic) Dorrie Main, Ph.D. Professor Mainlab Bioinformatics Department of Horticulture Washington State University 303c Plant Sciences Building Pullman, WA 99164-6414 Tel: 509-335-2774 (office) Email: dorrie(a)wsu.edu<mailto:dorrie@wsu.edu> URL: www.bioinfo.wsu.edu<http://www.bioinfo.wsu.edu/> Publications: Google Scholar<https://scholar.google.com/citations?user=MvVbhu4AAAAJ&hl=en> I will listen and believe you if someone is threatening you - Lauren's Promise (see https://www.laurenmccluskey.org/) WSU Pullman is located in the homelands of the Nimíipuu (Nez Perce) Tribe and Palus people.

2 years, 9 months

Recruiting a postdoc working on cotton CRISPR genome editing and seed oil improvement

by Yu, Jing

A postdoc position is immediately available at the Dr. Baohong Zhang's cotton research lab at East Carolina University. The coming postdoc will be majorly responsible for performing scientific research in the field of cotton oilseed improvement using advanced molecular tools, including CRISPR/Cas-based genome editing. The initiation appointment will be with $57600 annual salary plus health insurance and other benefit. The person with cotton genetic transformation and bioinformatics background is preferred. If you are interested, please directly contact Dr. Baohong Zhang at zhangb(a)ecu.edu<mailto:zhangb@ecu.edu>. You may also find more details about this position in the following website: https://ecu.peopleadmin.com/postings/39884<https://urldefense.com/v3/__https:/ecu.peopleadmin.com/postings/39884__;!!J…>.

3 years, 10 months

FW: Death of Dr. Sukumar Saha

by Yu, Jing

From: Jones, Don <DJones(a)cottoninc.com<mailto:DJones@cottoninc.com>> Sent: Sunday, September 05, 2021 6:25 PM To: Jones, Don <DJones(a)cottoninc.com<mailto:DJones@cottoninc.com>> Subject: Death of Dr. Sukumar Saha Friday Dr. Sukumar Saha passed away from a heart attack. His obituary is shown in the link below. Please remember his family at this difficult time. https://www.lowndesfuneralhome.net/obituary/sukumar-saha<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.lownd…> [cid:image001.jpg@01D7A28B.3BCB1DC0] DON C. JONES Ph.D. DIRECTOR, AGRICULTURAL AND ENVIRONMENTAL RESEARCH COTTON INCORPORATED 6399 WESTON PARKWAY CARY, NC 27513 P: 919.678.2367<tel:919.678.2367> C:919.389-3349<tel:919.389-3349> F: 919.678.2233<tel:919.678.2233> E: DJONES(a)COTTONINC.COM<mailto:DJONES@COTTONINC.COM> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

4 years, 1 month

Help us chart the future of agricultural data!

by Jung, Sook

Dear Researchers, Breeders, Database Providers, Funders, Editors, Students, Software Engineers, and other Scientists, Do you want easy access to better quality data? We are THRILLED to announce that AgBioData (https://www.agbiodata.org/) has received a three-year NSF RCN award to expand our community committed to improving quality and access to agricultural data. New activities will include organizing workshops, establishing new working groups, and developing FAIR curriculum for scientists. We are expanding the consortium and welcome new members, especially students, post-docs, big-data scientists, funding agency scientists, and members of the scientific publishing community interested in solving common FAIR data issues. We invite all of you to an important kickoff All-Hands Meeting on Sept 1st at 10 am PDT (find your local time - https://bit.ly/389VeJA). At this meeting, you will hear about our RCN objectives, the benefits of joining AgBioData, and how YOU can make a difference in the biological data environment for years to come. Please pre-register for this meeting at: https://iastate.zoom.us/meeting/register/tJcld-iqqD4vE9awJKcFGnmHwxtCNc_a7U… We are also hiring a scientist to coordinate AgBioData activities, outreach and curriculum development. Please help us publicize this opportunity! Applications should be submitted by August 31 to https://phoenix-bioinformatics.hirehive.com/job/83452/scientific-program-co…. Thank you! The AgBioData Steering Committee: Jacqueline Campbell, Darwin Campbell (coordinator), Ethy Cannon, Laurel Cooper, Lisa Harper, Eva Huala, Sook Jung, Monica Poelchau,L eonore Reiser, Meg Staton, Marcela Tello-Ruiz Sook Jung, Ph.D. Assistant Research Professor of Bioinformatics Department of Horticulture Washington State University

4 years, 1 month

Scientific Program Coordinator position for AgBioData Consortium

by Jung, Sook

Hello, A full time 3-year term Scientific Program Coordinator position for AgBioData Consortium is available. Scientific Program Coordinator Phoenix Bioinformatics and The AgBioData Consortium are seeking a Program Coordinator to support the activities of a recently funded three year NSF Research Coordination Network award (https://www.nsf.gov/awardsearch/showAward?AWD_ID=2126334&HistoricalAwards=f…<https://urldefense.com/v3/__https:/www.nsf.gov/awardsearch/showAward?AWD_ID…>). The AgBioData RCN aims to accelerate research in agricultural science by increasing the accessibility and reuse of large- scale biological data. We will do this by creating a network of Genomic, Genetic and Breeding Databases, researchers, scholarly publishers, and funders to advance data capture, findability, access, interoperability, reusability, and sustainability. This is a unique opportunity for an individual seeking to advance into a variety of careers away from the bench such as teaching at primarily undergraduate institutions, biocuration, database project management or scholarly publishing. The Program Coordinator will support the activities of the RCN and work collaboratively with the Steering Committee to ensure the timely completion of the RCN objectives. The position reports to the AgBioData Steering Committee and the coordinator will be part of a diverse and skilled professional team at Phoenix Bioinformatics. This position is a full time, remote working position with collaborators across multiple US time zones so hours can be flexible. View the job posting for further details : https://phoenix-bioinformatics.hirehive.com/job/83452/scientific-program-co…<https://urldefense.com/v3/__https:/phoenix-bioinformatics.hirehive.com/job/…> Best, Sook Sook Jung, Ph.D. Assistant Research Professor of Bioinformatics Department of Horticulture Washington State University

4 years, 2 months

FW: [ICGI] Nominations for ICGI co-chairs are now open

by Yu, Jing

From: cotton(a)zju.edu.cn <cotton(a)zju.edu.cn> Sent: Wednesday, January 13, 2021 5:31 PM To: icgi-list(a)cottongen.org Subject: [ICGI] Nominations for ICGI co-chairs are now open Dear ICGI members, Per our bylaws, nominations for ICGI co-chairs are now open, closing 1 February. We will elect co-chairs of each workgroup (Structural Genomics, Functional Genomics, Comparative Genomics and Bioinformatics, Germplasm and genetic stocks, and Breeding and applied Genomics) and the co-chair of ICGI overall, with the current co-chairs ascending to the Chair positions. Please send your nominations to me (cotton(a)zju.edu.cn<mailto:cotton@zju.edu.cn>), including the email address of the person(s) you wish to nominate and the office (s) that you wish to nominate them for. It would be appreciated if you would check with the prospective nominee first to make sure that s/he is willing to serve, although I will check with them as well. Pending any unexpected delays, nominations will CLOSE on 1 February, the election will open shortly thereafter (I will provide a link to it then), and the election will CLOSE on 1 March. Thank you in advance. Tianzhen Zhang, Chair, ICGI ________________________________ Dr.Tianzhen Zhang Distinguished Professor College of Agriculture and Biotechnology, Zhejiang University Hanzhou 310058, Zhejiang Province, China Tel./Fax: +86 571 88982971 E.mail: cotton(a)zju.edu.cn<mailto:cotton@zju.edu.cn>

4 years, 9 months

Invitation: CottonGen in the NRSP10 training workshop at PAG

by Main, Doreen

Hi Folks, Please join us for the NRSP10 workshop at PAG which covers many aspects of using the database resources we develop that are implemented in CottonGen. The NRSP10 project is up for renewal and significantly funds work on CottonGen. Workshop: Database Resources for Crop Genomics, Genetics and Breeding: NRSP10 When: Sunday January 13, 1.30 – 3.40 PM Where: Meeting Room Presentations 1.30: Overview of NRSP10 - Achievements and Future Plan (Dorrie Main) 1.45: Using the Online GenSAS Platform for Community Genome Annotation (Jodi Humman) 2.00: Tripal v3, the Collaborative Online Database Platform for Genomic, Genetic and Breeding Databases 2.15: Using NRSP10 Data and Tools for Basic Research (Sook Jung) 2.30: Using NRSP10 Data and Tools for Translational Research (Cameron Peace) 2.45: Using NRSP10 Data and Tools for Breeding (Ksenija Gasic) 3.00: Global Performance Prediction Tool in Tripal BIMS (Craig Hardiner) 3.15: Open Discussion of NRSP10 Overview NRSP10 is a USDA NIFA, industry and US Land Grant Universities funded project which provides standardized database and informatic resources for undeserved or specialty crops such as tree fruit, nuts, cotton and berries. It builds on existing database resources developed for Rosaceae (Genome Database for Rosaceae, www.rosaceae.org), Citrus (Citrus Genome Database, www.citrusgenomedb.org), Vaccinium (Genome Database for Vaccinium, www.vaccinium.org), Cool Season Food Legumes (Cool Season Food Legume Genome Database, www.csfl.org) and Cotton (CottonGen, www.cottongen.org). Developed using Tripal, an open-source, resource-efficient, modular, well supported software platform, these community databases provide centralized access to integrated genomic, genetic and breeding data and analysis tools for 24 crops representing a combined annual production value of over $25B. In this training workshop, we present progress in NRSP10 through a series of presentations by users and discuss the next 5 year plan for this project. Cheers Dorrie Dorrie Main, PhD Professor of Bioinformatics Department of Horticulture Washington State University 45 Johnson Hall Pullman, WA 99164-6414 Tel: 509-335-2774 (office) Email: dorrie(a)wsu.edu<mailto:dorrie@wsu.edu> URL: www.bioinfo.wsu.edu<http://www.bioinfo.wsu.edu/>

6 years, 9 months

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