News highlights

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

Bioinformatics of Plants and Plant Pathogens

An EMBL-EBI training course on the Bioinformatics of Plants and Plant Pathogens, will be held in Hinxton, UK, 23rd-25th June, 2016.

Mining Plant Variation Data

Registration now closed!

Workshop on plant variation data, re-sequencing projects and GWAS analyses within transPLANT, hosted at The European Bioinformatics Institute, Cambridge, UK from 1st July to 3rd July. Click here to apply.

BSC releases COMPSs version 1.2

The Grid Computing and Clusters group of Barcelona Supercomputing Center is proud to announce the release of COMPSs version 1.2. A framework for easily implement distributed applications.

Filling the gap between sequence and function; a bioinformatics approach

This thesis focuses on deriving function from sequence information, with the emphasis on plant sequence data.

The genome assembly decision support system

A decisions support system to evaluate and recommend the most suitable strategy for genome sequencing and assembly.

The transPLANT integrated search

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

Training videos

Video tutorials

A library of video tutorials.

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.

Exploiting and understanding Solanaceous genomes

Registration now closed!

The 3rd transPLANT user training workshop will be held in Wageningen, the Netherlands on October 13-14, 2014, focused on the latest developments in the key plant data resources in Europe and how to use them with a special reference to Solanaceae genomes, especially tomato and potato.

User survey

The results of a new survey of bioinformatics stakeholders' needs in the field of agronomic research are now available.

The transPLANT resource registry

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

Variation archive

Genome-scale resequencing is now widespread in plants, to identify variation in natural populations and crop stocks. The transPLANT variation archive has been developed to provide a system for the persistent storage and analysis of variation data from plant species.

Phenotype standardisation activities

MIAPPE - Minimum Information about Plant Phenotyping Experiment

We have created a portal to disseminate our activities in the area of phenotypic data standardisation to serve as a source of information to the phenotyping community: http://cropnet.pl/phenotypes

Agricultural-Omics

Registration now closed!

An overview of data, resources, tools and pipelines for 'omics datasets within the agricultural sciences.

Take the transPLANT survey

Survey now closed! View the results.

We are collecting information about the needs of bioinformaticians in the field of agronomic research. Our goal is to chart the current resource landscape to both coordinate its development and to identify gaps that can be filled by transPLANT.

The survey contains 41 questions. Thanks in advance for your involvement.

Ensembl Plants, Release 18

The Ensembl Genomes Project, including Ensembl Plants, is pleased to announce release 18 of Ensembl Genomes.

transPLANT workshop on resources for Triticeae genomics and phenotyping standards

Registration now closed!

We are pleased to announce the 2nd transPLANT user training workshop to be held in Poznań, Poland, 27-28 June 2013. The workshop focuses on plant genomics resources with special reference to Triticeae and topics related to standardisation and annotation of plant phenotypic data. We target experimental biologists and plant breeders; no prior informatics training is assumed.

Genomes to Germplasm

Registration now closed!

A Meeting on "Genomes to Germplasm" will be held in INRA, Versailles, France from 28th February - 2nd March 2013.

Press release: Polish Potential and Contribution to EU Success in ICT

A press release presenting the research potential and contribution of Polish organizations to R&D and deployment projects financed by DG-INFSO by means of the 7th Framework Programme and the Competitiveness and Innovation Programme.

Ensembl Plants, Release 16

The Ensembl Genomes Project, including Ensembl Plants, is pleased to announce release 16 of Ensembl Genomes. In this release, new species in Ensembl Plants include Hordeum vulgare (barley), Solanum tuberosum (potato) and Musa acuminata (banana). Improvements on the wheat assembly and the ability to highlight annotations in gene trees have also been released.

Report on the Crop Plant Trait Ontology Workshop

Plant breeders, biologists, and bioinformaticians from ten countries, seven US states, and two plant agribusinesses gathered in Corvallis, Oregon, September 13th-15th, 2012 for a Crop Plant Trait Ontology Workshop.

Crop Plant Trait Ontology Workshop, Oregon State University

Registration now closed!

The goals of the workshop are to develop ontology terms and definitions for the Plant Ontology (http://www.plantontology.org/) and the Reference Plant Trait Ontology (under development) and applications that utilize those resources.

The ultimate goal is to establish a semantic framework for meaningful cross-species queries across gene expression and phenotype data sets from plant genomics and genetics experiments.

transPLANT user training workshop

Registration now closed!

A workshop focused on triticeae (wheat and barley mainly) data resources and tools, and include tutorials on data access and use from INRA, EBI-EMBL, IPK and MIPS.

This workshop is targeted at (experimental) biologists, breeders, bio-informaticians and all other data users as no prior (informatics) knowledge or skills are required.

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.

Ensembl Plants, Release 14

This release of Ensembl Plants includes the newly sequenced Solanum lycopersicum (tomato) genome.

Ensembl Plants, Release 13

This release of Ensembl Plants includes the genome of Brassica rapa [1].

Crop Ontologies for Agronomic Traits

Registration now closed!

A meeting to discuss the potential application of trait and phenotype ontologies to describe agronomic traits in crop plants.

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