From cer17 at cornell.edu Mon Dec 4 15:10:50 2006 From: cer17 at cornell.edu (Claire Hebbard) Date: Mon, 4 Dec 2006 15:10:50 -0500 Subject: Fwd: Re: Message-ID: Dear Cereal Researchers, Attached in PDF format is the December Gramene Newlsetter. You will find information on upcoming Gramene presentations, Gramene news, community news and employment opportunities, and a community calendar. This newsletter should be available online next week. Look for a reformatted newsletter in 2007! -- Sincerely, The Gramene Database Team ***************************************************************** Gramene(www.gramene.org) is a curated, open-source, web-accessible data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations. ***************************************************************** This work is funded by the National Science Foundation (NSF) and the USDA-Agricultural Research Service, and was previously funded by the USDA Initiative for Future Agriculture and Food Systems (IFAFS). We are thankful to numerous collaborators and contributors for help in curation and for sharing their datasets and tools. ***************************************************************** The Gramene-announce listserve is used to notify registered users of timely information concerning Gramene (www.gramene.org) or the rice community. If you want to unsubscribe from this mailing list, you can send mail to with the following command in the body of your email message: unsubscribe gramene-announce This mailing list is only for announcements by Gramene developers. To correspond with Gramene developers and users, subscribe to the gramene list by sending an email to majordomo at gramene.org and in the body of the e-mail (not the subject line) write: subscribe gramene . You may also contact the Gramene team through the "Feedback" button at the top of the Gramene website. -------------- next part -------------- A non-text attachment was scrubbed... Name: dec2006newsletter 1.pdf Type: application/pdf Size: 75279 bytes Desc: not available URL: From cer17 at cornell.edu Tue Dec 19 11:05:15 2006 From: cer17 at cornell.edu (Claire Hebbard) Date: Tue, 19 Dec 2006 11:05:15 -0500 Subject: New Gramene Release! Message-ID: Dear Colleagues: Gramene (http://www.gramene.org) is proud to announce the release #23 of Gramene. For detailed information on the newest updates, please see the release notes at http://www.gramene.org/documentation/release_notes/releasenotes.html Gramene web site features: Species pages (http://www.gramene.org/species/) link to the species pages has been placed on the navigation bar at the top of page. These pages have been broken down into more but smaller pages, and the consistency of format between the species has been improved. Now you can navigate between species from any species page, not just from the introduction pages. Gramene Data Summary for select species: The species pages now have a summary overview of all the genomic data for that specie in Gramene. For an example see the Rice Data http://www.gramene.org/oryza/rice_stat.html Gramene DB statistics for the last year is now linked to the Gramene site map (http://www.gramene.org/sitemap.html). See the bottom left of this page and click on "DB Stats over Time" (http://www.gramene.org/dbstat/dbstat.html) Gramene Database: Genomes: Much new and updated data. Also, tree-based visualization of orthologs/paralogs for rice/maize/arabidopsis. Maps: With this release, in addition to an update to CMap 0.16, all data (map sets, maps, features, and correspondences) in the Maps Module are built from the Markers Module that have correlations, and the Gramene Annotated Nipponbare Sequence no longer includes all features on the Ensembl Rice Genome Assembly, but has only features that have correspondences to other maps. This was done to reduce visual clutter as well as improve server response time. All mappings are still present in the Markers Module and can be visualized in the Rice Genome Browser. The map set still includes all rice gene models. In addition, we have for the first added QTL to the map set. The Maps Module should be considered to be primarily a visualization tool and for comparative mapping. Users are encouraged to consult the Markers Module for primary information about markers, their mappings, and map set information. Markers: This release of Gramene marks the first time that the Markers Module contains all map sets, maps, and mappings. All visualizations in the Maps Module are now generated from the Markers Module. Proteins: The Gramene protein database provides curated information on SP-Trembl entries from family Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochondrial and secretory pathway targeting) and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to provide functional characteristics. Ontologies: We are making progress on integrating ontologies with other databases, as shown in their associations. Genes: We're making progress in ontology associations to TO, PO or GO; new microRNA genes, and map position links. QTL: New - when available you will find multiple links to QTL mapping positions and the inferred positions on the Gramene Annotated Nipponbare Sequence. Pathways: Version 1.2 of RiceCyc Diversity: The Diversity database has 626 germplasm accessions (587 unique) and 524 SSR markers (247 unique) for rice; 48 germplasm accessions and 3802 SNP markers for wheat; and 302 germplasm accessions with SNP data, 1,543 germplasm accessions with SSR data, 897 SNP and 520 SSR markers for maize. -- Sincerely, The Gramene Database Team ***************************************************************** Gramene(www.gramene.org) is a curated, open-source, web-accessible data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations. ***************************************************************** This work is funded by the National Science Foundation (NSF) and the USDA-Agricultural Research Service, and was previously funded by the USDA Initiative for Future Agriculture and Food Systems (IFAFS). We are thankful to numerous collaborators and contributors for help in curation and for sharing their datasets and tools. ***************************************************************** The Gramene-announce list-serve is used to notify registered users of timely information concerning Gramene (www.gramene.org) or the rice community. If you want to unsubscribe from this mailing list, you can send mail to with the following command in the body of your email message: unsubscribe gramene-announce This mailing list is only for announcements by Gramene developers. To correspond with Gramene developers and users, subscribe to the Gramene list by sending an email to majordomo at gramene.org and in the body of the e-mail (not the subject line) write: subscribe gramene . You may also contact the Gramene team through the "Feedback" button at the top of the Gramene web site. -------------- next part -------------- An HTML attachment was scrubbed... URL: