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NSF Funds Planteome Project

The National Science Foundation (NSF) has funded the Planteome Project to develop common reference ontologies and applications for plant biology.

Gramene database build 45 released

The Gramene Team is pleased to announce its release #45. In collaboration with Ensembl Plants we are providing in this release:

  • Updated genome assembly and gene set for medicago and the wild rice Oryza meridionalis.

  • Whole genome alignments between Triticeae genomes using Assembly to Assembly Comparison, ATAC.

Webinar: Maize Data & Resources in Gramene on Tues, April 7, 2015 @ 2:00 pm EDT

Gramene Webinar on Maize data & resources in the Gramene database

Tuesday, April 7, 2015 @ 2:00 PM EDT

Learn the benefits of using Gramene to accelerate your research goals. During this webinar, we will demo the use of Gramene's comparative genomics visualization and analysis resources through practical examples of general interest to maize researchers.

This webinar will highlight the most recent maize data additions to the Gramene website including:

Webinar: Gene Family Trees on Tues, Mar 17, 2015 @ 2:00 pm EST

Gramene Webinar on Visualization and Analysis of Gene Family Trees

Tuesday, March 17, 2015 @ 2:00 PM EST

Learn the benefits of using Gramene to accelerate your research goals. Our comparative genomics platform of 39 plant species enables you to:

  • List orthologs and paralogs, and view these relationships within phylogenetic trees, whole genome alignments, and synteny maps.

  • Explore and visualize functional annotations, expression, and variation in your favorite genes.

Planteome project is looking for a software and database developer

There is an immediate opening for a software and database developer to work on the NSF funded Planteome project (www.planteome.org). This open-source computational biology, comparative genomics, and bioinformatics project involves the development and maintenance of databases, software and automated data analysis pipelines. The incumbent will have a proven track record of database development in MySQL (with exposure to Solr, noSQL, and/or MongoDB) and experience developing software in Python, Perl, PHP, and Java.

Gramene Webinar: The Gramene Ensembl Genome Browser. Tues, Feb 24, 2015 @ 2:00 - 2:30 pm EST

Gramene Webinar February 2015 Tuesday, February 24, 2015 @ 2:00 - 2:30 PM EST

Learn the benefits of using Gramene to accelerate your research goals. Our comparative genomics platform of 40 plant species enables you to:

  • Explore and visualize functional annotations, expression, and variation in your favorite genes.

  • List orthologs and paralogs, and view these relationships within phylogenetic trees, whole genome alignments, and synteny maps.

Recent Advances in Plant Reactome - PAG 2015

Plant Reactome is a resource for plant metabolic and regulatory pathways built using the Reactome model. At present, Plant Reactome has curated metabolic and regulatory pathways from rice and Arabidopsis, and the orthology-based projections of pathways for additional 33 plant species including several Oryza species, and maize. We are developing tools that can support analysis and visualization of user-defined expression data.

PAG 2015: Some Highlights

Contributions from Sushma Naithani, Kapeel Chougule and Yinping Jiao.

During the Gramene workshop at PAG 2015, participants were introduced to various resources and tools available at the Gramene database. Powerpoint slides used during these presentations are available in Gramene's Outreach FTP.

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Gramene Webinar: The Plant Reactome. Tues, Feb 3, 2015 @ 2:00 - 2:30 pm EST

The Plant Reactome webinar has been rescheduled for next Tuesday, February 3rd, 2015 @ 2:00 - 2:30 pm EST

Gramene database build 44 released

The Gramene Team is pleased to announce its release #44. In collaboration with Ensembl Plants we are providing in this release:

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