Submitted by marcela.karey on Mon, 01/06/2014 - 13:16
Please join the Gramene Team for their upcoming workshop at the Plant and Animal Genomes (PAG) 2014 Conference!
Learn the latest updates to Gramene’s comparative genomics and pathways visualization/mining tools to aid your research of plant models and crops.
Workshops will give a broad overview of Gramene’s database resources and demonstrate many specific topics like how to:
Submitted by marcela.karey on Thu, 12/19/2013 - 13:12
This 1/2-day FREE workshop will take place on Wednesday, December 5 of 2013 from 12 – 5 pm at the Hershey Bldg. (West Conference Rm) of the Cold Spring Harbor Laboratory. It will also be broadcasted online, see details below.
It will cover hands-on examples to get you started doing Genome Assembly, Annotation, and RNA-Seq using tools developed by the iPlant Collaborative, a cyberinfrastructure project funded by the National Science Foundation.
Participants will get hands-on experience with the following iPlant cyberinfrastructure:
Submitted by marcela.karey on Mon, 12/02/2013 - 17:25
The Gramene Team is pleased to announce its release #39. In collaboration with Ensembl Plants we are providing in this release:
Submitted by marcela.karey on Mon, 12/02/2013 - 17:24
“Did you know that there are millions of DNA building blocks encoded in the genome of a plant? How can scientists possibly study this vast amount of data? With computers! Come and explore the tools of modern biology used to examine the complexities of DNA. This camp will involve hands-on activities where you will extract genetic material from a plant, assemble DNA sequences, identify genes using computers, examine your plant’s genome with visualization software, and test and look at your results in the laboratory. No programming skills required!”
Submitted by olson on Mon, 12/02/2013 - 17:23
Since publishing the initial assembly of the reference strain (B73) in 2008, the maize sequencing project has released two updates. The initial assembly and RefGen_v2 are based on a BAC (bacterial artificial chromosome) sequencing strategy. RefGen_v2 included ~2000 updated BAC sequences and improved upon the initial assembly by resolving overlaps between BACs in the minimum tiling path to define the 10 chromosome pseudomolecules.
Image:
Improved GRMZM5G891969 gene model. A denovo contig provided two missing exons needed to merge two apparently distinct gene models (GRMZM5G823855 and GRMZM5G891969) into a single model that is conserved in sorghum (Sb01g050450).
Submitted by olson on Mon, 12/02/2013 - 16:37
The maize sequencing project had been running an EnsEMBL based genome browser, comparative analysis tools, and biomart at maizesequence.org, but this responsibility been transferred to gramene.org. Gramene hosts the current maize B73 reference genome sequence (RefGen_v3) and annotations along with regularly updated database cross references and comparative analyses provided by Gramene and collaborators at plants.ensembl.org.
Submitted by admin on Wed, 09/18/2013 - 14:32
Immediate opening is available for a recent PhD graduate (0-3 years after PhD award) to apply for a full-time postdoctoral scholar position. The biocuration would involve to annotating plant metabolic, signaling and regulatory pathways for developing an online Plant Pathway database. The curator will be responsible for
Submitted by admin on Thu, 09/05/2013 - 14:09
The Grape Research Coordination Network (GRCN)-2013 meeting was held in UC Davis, from July9-12, 2013. About 70 participants including scientists, postdocs, graduate and undergraduate students attended this meeting. Several groups in the grape community are generating high-throughput genomic data sets and need a bioinformatics infrastructure. Several grape researchers use Gramene's genome portal, especially the grape genome browser and are very positive about the functionality of this portal. They view Gramene as a model database for organizing various genomic and genetic resources.
Submitted by admin on Wed, 08/14/2013 - 12:01
The Gramene Team is pleased to announce its release #38. In collaboration with Ensembl Plants we are providing in this release:
Submitted by admin on Wed, 08/07/2013 - 20:04
Gramene currently hosts ten species-specific Pathways Databases; RiceCyc (Oryza sativa japonica), SorghumCyc (Sorghum bicolor), MaizeCyc (Zea mays), BrachyCyc (Brachypodium distachyon), AraCyc(Arabidopsis thaliana), MedicCyc(Medicago truncatula), PoplarCyc(Populus trichocarpa), CoffeaCyc(Coffea canephora), LycoCyc(Solanum lycopersicum
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