Trans-national Infrastructure for Plant Genomic Science

Call: FP7-INFRASTRUCTURES-2011-2

Outputs

Publication:

transPLANT Resources for Triticeae Genomic Data, Spannagl et al., The Plant Genome doi:10.3835/plantgenome2015.06.0038

https://www.animalsciencepublications.org/publications/tpg/articles/9/1/plantgenome2015.06.0038

Tools:

All the tools are available on the transPLANT website (search, resource registry, variation archive, assembly and annotations, phenotypes, virtual plant breeding).

Project description

Food and energy security are major challenges facing humanity in the coming decades. The falling costs of nucleotide sequencing are opening up significant opportunities for crop improvement through plant breeding and increased understanding of plant biology; in particular through interpreting the growing volume of plant genomics data in the context of phenotype. However, at present, there is no adequare infrastructre for plant genomic data. transPLANT will develop a new infrastructure for this data, leveraging the experience of medical informatics while addressing the particular challenges and opportunities of plant genomics.

Compared with vertebrate genomes, plant genomes may be large and have complex evolutinary histories, which makes their analysis a hard problem (both in terms of theory, and in terms of the compute resources required for data storage and analysis). Issues include genome size, polyploidy, and the quantity, diversity and dispersed nature of data in need of integration.

To address these problems, transPLANT will develop distributed solutions, exploiting the expertise of the project partners in particular species and problems to provide a seamless set of computational and interactive services to the plant research community. These services will be developed on top of the outputs of RTD activities designed to build new repositories and develop new algorithms, and with the input from the plant science and other related communities garnered through extensive networking activities. A series of training workshops will educate the community in the use of transPLANT tools and data.

transPLANT will be built on standard technologies for data exchange and representation, service provision, virtual compute infrastructure, and interface development; where such standards are currently lacking (as in phenotype description), they will be developed in the context of the project.

Web site: http://www.transplantdb.eu/