marcela.karey's blog

Gramene book chapter in the Plant Bioinformatics volume of the Methods in Molecular Biology protocols series

In recent months, the Plant Bioinformatics volume of the Methods in Molecular Biology protocols series edited by Professor David Edwards of the University of Queensland, Australia, was published.  This volume included 18 chapters covering various topics of interest to the plant research community and featured bioinformatic resources available for plant researchers.  The Gramene Database was featured in one of those chapters.

Gramene build #50: Planned updates and new data sets

Release 50 of Gramene is scheduled for March 22, 2016. Our intentions for this release are:

Gramene is attending the PAG Conference 2016 — See you in San Diego!

Come meet the Gramene team and get the latest updates to Gramene’s comparative genomics and pathways visualization/mining tools to aid your research of plant models and crops!

The Gramene workshop will give a broad overview of Gramene’s database resources and use cases demonstrating many specific topics like how to:

Gramene database build 49 released

The Gramene Team is pleased to announce its release #49. In collaboration with Ensembl Plants we are providing in this release:

  • New EMS-derived mutation data for Sorghum bicolor (see example)

  • New variation data for Oryza glumaepatula

Gramene Mart Webinar on Tues, Dec 15, 2015 @ 2:00 pm EDT

Data Mining with Gramene!

The Gramene database (http://www.gramene.org) invites you to a FREE 30-min webinar on How to Extract Plant Genomic Data Using BioMart.

The webinar will demonstrate how to explore data for 39 plant reference genomes in the Gramene and Ensembl Plants databases, including sequence, gene structure and annotations such as protein domains and ontology associations, homologs, genetic and structural variations.

GARNet/Egenis Workshop on Big Data: April 2016

Click on the link below to view the full schedule for the GARNet/Egenis workshop on 'Integrating Large Data into Plant Science: From Big Data to Discovery'.

Detailed schedule as PDF

This will take place in Dartington Hall, Totnes, Devon UK. There are a limited number of places available for delegates so anyone interested in attending should contact geraint@garnetcommunity.org.uk with details as to why this meeting would be beneficial for your research.

Gramene database build 48 released

The Gramene Team is pleased to announce its release #48. In collaboration with Ensembl Plants we are providing in this release:

  • New ATLAS gene expression annotations

  • New pairwise alignment between Solanum tuberosum and S. lycopersicum (build 2.50)

  • New pairwise alignments between Theobroma cacao and: 1) Arabidopsis thaliana, 2) Oryza sativa, and 3) Vitis vinifera

Gramene BLAST Webinar on Tues, Oct 20, 2015 @ 2:00 pm EDT

Have a BLAST with Gramene!

The Gramene database invites you to a FREE 30-min webinar on Gramene BLAST.

This webinar will highlight important features of the sequence BLAST tool and demonstrate how to maximize your chances of getting the best BLAST hits. The tool allows aligning query sequences against genomic DNA, cDNAs and translated peptides of 39 plant genomes in Gramene.

New Plant Ontology Release available

A new Plant Ontology (PO) data release is available on the PO browser.

See the highlights in the PO's News blog and complete details in PO's release notes.

Gramene database build 47 released

The Gramene Team is pleased to announce its release #47 featuring the new Plant Reactome, we are providing version 3 of the Reactome software platform. Notable new features include:

  • Data analysis tools

    • Diagram overlay visualization of gene lists, Uniprot IDs, compound identifiers, and/or -omics expression data

    • Inter-species pathway comparison

  • Advanced search features built on the Apache Solr platform

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