From telloruiz at cshl.edu  Wed Sep  1 11:42:42 2021
From: telloruiz at cshl.edu (Tello-Ruiz, Marcela)
Date: Wed, 1 Sep 2021 15:42:42 +0000
Subject: [Gramene-announce] Help us chart the future of agricultural data! -
 AgBioData RCN kick off meeting TODAY Sept 1st @ 1 pm ET
Message-ID: <87ff313861654108b81d3a6b135c5b08@cshl.edu>

Dear Gramene users, friends and colleagues,

I would like to share the below message with you from AgBioData, which we fully support.

Dear Researchers, Breeders, Database Providers, Funders, Editors, Students, Software Engineers, and other Scientist,


Do you want easy access to better quality data?  We are THRILLED to announce that AgBioData<https://www.agbiodata.org/> (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<https://iastate.zoom.us/meeting/register/tJcld-iqqD4vE9awJKcFGnmHwxtCNc_a7UJM>.


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<https://phoenix-bioinformatics.hirehive.com/job/83452/scientific-program-coordinator-newark?source=TAIR>.


Thank you!


The AgBioData Steering Committee:

Monica Poelchau, Sook Jung, Ethy Cannon, Jacqueline Campbell, Lisa Harper, Leonore Reiser, Marcela K. Tello-Ruiz, Laurel Cooper, Eva Hula, Meg Staton, and Darwin Campbell


* About AgBioData<https://www.agbiodata.org>
* AgBioData RCN<http://https://www.nsf.gov/awardsearch/showAward?AWD_ID=2126334>



From telloruiz at cshl.edu  Fri Sep 10 12:08:00 2021
From: telloruiz at cshl.edu (Tello-Ruiz, Marcela)
Date: Fri, 10 Sep 2021 16:08:00 +0000
Subject: [Gramene-announce] Gramene release 64 is out with 21 new reference
 genomes and the latest maize B73
Message-ID: <63a0816740b143d4bc524adafb800778@cshl.edu>

Dear Plant Researchers,


The Gramene Knowledgebase Team is pleased to announce its Release #64 (see release notes*) with the Genome browser providing access to information on 114 reference genomes and 123,064 gene family trees. This release features the new sequence assembly and gene annotation (version 5) of the B73 maize reference genome from Hufford et al (2021)**. We have also added 21 new reference genomes, including quinoa, asparagus, spelt, opium poppy, sesame, Persian walnut, a relative of wasabi, eucalyptus and white oak (roble) trees, nine varieties of bread wheat, and a variety of each, barley and potato. In addition, updates were applied to the assembly and annotation of the banana, white Guinea yam, and Peruvian cotton genomes. With these new and updated genomes, our comparative genomics collection totals 340 pairwise DNA alignments and 80 synteny maps. New SNP variation datasets are now provided for black and soy beans

The Plant Reactome is the pathway knowledgebase of Gramene. We utilize the Reactome pathway data model to represent plant metabolic, transport and signaling pathways, developmental processes, organ differentiation, and transcriptional regulatory networks. Manual biocuration is conducted in Japonica rice, the reference species, and pathways are then projected via gene orthology to other species including crops and model plants, lower plants and single-cell photoautotrophs. In this release, homology-based pathway projections were added for version 5 of the B73 maize genome but version 4 pathway projections will continue to be available for comparison. Plant Reactome continues to host 320 rice curated pathways and their gene-orthology based projection for 106 species.

The Gramene Knowledgebase is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. The genome databases were built in direct collaboration with Ensembl Plants, and the Plant Reactome database was produced in collaboration with the Reactome project. Core funding for the project is provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 1907-21000-030-00D), and the National Science Foundation (NSF IOS-1127112).

The FTP site is being updated and will soon be made available. Please let us know if you have any questions or suggestions.

The Gramene Team

Gramene website: https://www.gramene.org
Contact us: https://www.gramene.org/feedback

* Release notes build 64: https://www.gramene.org/release-notes-64

** To access the assembly and annotation of the 26 maize inbred lines that serve as the founders for the maize nested association mapping (NAM) population described in Hufford et al (2021), please see Gramene's Maize PanGenome site at https://maize-pangenome.gramene.org<https://maize-pangenome.gramene.org/>. DOI: <https://doi.org/10.1126/science.abg5289> 10.1126/science.abg5289<https://doi.org/10.1126/science.abg5289>.



<https://maize-pangenome.gramene.org/>



