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Collaboration on gene expression integration and comparison PDF Print E-mail
Written by Virginia Gonzalez   
Monday, 02 November 2009 13:33

We are developing Bgee (http://bgee.unil.ch/), a database which allows the comparison of gene expression patterns between different species.
At present, Bgee only contains animal data (indeed, mostly vertebrate data). We would be interested in collaborating with the Gramene team to develop a plant version. Bgee integrates in situ, microarray and EST based expression data (RNA-seq in the pipeline), and links it to homologous genes and to homologous organs. I believe that a plant version would be very timely, given the large increase in plant related data which is occuring beyond Arabidopsis.

BioPortal 2.2 Release PDF Print E-mail
Written by Virginia Gonzalez   
Thursday, 29 October 2009 12:34
The BioPortal team is pleased to announce the release of BioPortal 2.2 (http://bioportal.bioontology.org/). Release notes and known issues are listed below.

New Features

Ontology Views

Views in BioPortal are subsets or other derivatives of ontologies in the repository that you can share with the community. You can upload views for any ontology, and review them, add notes, create mappings, and use REST Web services to access them programmatically.
A view can also serve as a mechanism to define value sets, which are quite useful in combination with the BioPortal ontology-term selection widget.
BLAST 2.2.22 now available PDF Print E-mail
Written by Virginia Gonzalez   
Tuesday, 20 October 2009 13:22

This release includes new BLAST+ command-line applications.

The BLAST+ applications have a number of advantages over the older applications and users are encouraged to migrate to the new applications.  The new applications can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST  These applications have been built with the NCBI C++ toolkit. Changes from the last release are listed below.

The older C toolkit applications (e.g., blastall) are still available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.22/

Changes from the last release are listed below.

IPMB Gramene and Plant Ontology workshop PDF Print E-mail
Written by Virginia Gonzalez   
Thursday, 22 October 2009 23:10
The 9th International Plant Molecular Biology (IPMB) Congress (http://www.ipmb2009.org/) to be held from October 25-30, 2009 in St. Louis, MO, USA to the Gramene Database and Plant Ontology Workshop.

The workshop is free and open to everyone.

Time: Monday October 26, 6-9pm

Location: Room # 104/105 @ the meeting venue

Workshop Title: Comparative Plant Genomics with the Gramene database and Plant Ontology project
Gramene's 30th release PDF Print E-mail
Written by Virginia Gonzalez   
Friday, 09 October 2009 13:03
The Gramene team is happy to announce the 30th release of our website. This release includes the latest version 55 of the Ensembl genome browser displaying a total of thirteen distinct genomes; two new comparative maps; updates to proteins, genes, alleles, and pathways; new large-scale SNP-chip based genotype datasets for rice and Arabidopsis plus the addition of a basic coordinate-based search tool that allows you to retreive allele calls; and, lastly, and entirely new module focusing on our germplasm resources targeted at the breeding community.

For more details, please see our detailed release notes:


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