News highlights

News from the transPLANT project and partners. See also the transPLANT newsletter.

Ensembl Plants, Release 15

We have added a set of homoeologous SNPs between wheat A, B and D genomes using wheat contigs aligned to Brachypodium distachyon as a reference framework, a structural variation dataset for

Training workshop in plant pathogenic genomics

Registration now closed!

A hands-on training workshop in plant pathogenic genomics, focused on the new resource PhytoPath and including coverage of Ensembl Fungi, Ensembl Protists and PHI-base will be held at the EBI in September, aimed at PhD students and post-doctoral researchers who are working on fungal and oomycete-induced disease in plants. Find out more details and register.

Genome-wide patterns of genetic variation in Arabidopsis published

Published today in Nature Genetics, Magnus Nordborg and colleagues have produced a high-resolution description of the global pattern of genetic variation in Arabidopsis.

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Relevant publications

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden.

Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from Sweden to obtain as complete a picture as possible of variation in a single region.

GnpIS: an information system to integrate genetic and genomic data from plants and fungi

Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can generate lots of heterogeneous and unrelated data.

Extraction and prediction of biomedical database identifier using neural networks towards data network construction

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The transPLANT integrated search

Get results from ten different plant genomics databases in a single click.
Try a sample search...

The transPLANT variation archive

variation archive

Store, accession and update plant variation data. Now accepting submissions.

transPLANT training resources

Training resources

A collection of training resources from transPLANT related events. Browse the materials.

The transPLANT resource registry

Search for genomic resources for plant species of agricultural and scientific importance. Try a sample search...

transPLANT

is a European-Union funded e-infrstructure to support computational analysis of genomic data from crop and model plants. The project funds coordination and research activities; and provides free access to tools, training and data standards.

You can use this site to:

For more information contact us or join to the mailing list.

Training

transPLANT is running a series of training courses across Europe. The next one will be held at EMBL-EBI, Hinton, UK, 1st-3rd July, 2015. When registration is opened, details will be posted here.

  • You can access material from the previous transPLANT training courses here.
  • We are developing a series of videos, guiding users through some of the most interesting and complex data sets available for plants. View the first video, focused on resources for the barley genome, here.

Standards

The development and adoption of data standards is vital to the interoperability of data. transPLANT is currently pursuing the development of standards for plant phenotyping data, in collaboration with other interested groups. Visit our Phenotype standardisation portal to see the latest proposals and get involved.