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:

February 2016 Gramene Webinar: Updates on Plant Reactome

Register to join us online on Tuesday, February 16, 2016, at 2:00 pm EST/11:00 am PST.

Plant Reactome is a freely available resource of curated metabolic, signaling, and regulatory pathways from the reference species rice, and gene homology-based pathway projections for 58 other plants including Arabidopsis, maize, grape, strawberry, tomato, etc. Plant Reactome uses a eukaryotic cell model for pathway visualization, and allows uploading and analysis of omics data.

Gramene updates published in Jan, 2016 issue of Nucleic Acids Research

The recent updates in Gramene database have been summarized in the article “Gramene 2016: comparative plant genomics and pathway resources” published in the January 2016 issue of Nucleic Acids Research focused on biological databases.

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 ( 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.

Follow up on Nov 2015 Webinar: Variant Effect Prediction using the standalone perl scripts

In  November 2015 Gramene Webinar, Matt Geniza, (a graduate student, Jaiswal Lab at Oregon State University) presented how to use standalone Perl script and command line protocols for Variant Effect Predictor (VEP) analysis. This option is for advanced users who are familiar with the Unix/Linux command line. Also, users are expected to have a SNP DATA file before proceeding for this exercise.

Announcing Gramene database build 48b highlighting Plant Reactome

The Gramene project ( team is pleased to announce its release #48b highlighting the new version of Plant Reactome database ( In this release the Plant Reactome database has expanded gene homology-based pathway projections to 58 plant species.

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 with details as to why this meeting would be beneficial for your research.


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