transPLANT: Trans-national Infrastructure for Plant Genomic Science

Food and energy security are major challenges facing humanity in the coming decades. The falling costs ofnucleotide sequencing are opening up significant opportunities for crop improvement through plant breeding andincreased understanding of plant biology; in particular through interpreting the growing volume of plant genomicsdata 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 whileaddressing the particular challenges and opportunities of plant genomics.Compared with vertebrate genomes, plant genomes may be large and have complex evolutinary histories, whichmakes their analysis a hard problem (both in terms of theory, and in terms of the compute resources requiredfor data storage and analysis). Issues include genome size, polyploidy, and the quantity, diversity and dispersednature of data in need of integration.To address these problems, transPLANT will develop distributed solutions, exploiting the expertise of the projectpartners in particular species and problems to provide a seamless set of computational and interactive servicesto the plant research community. These services will be developed on top of the outputs of RTD activitiesdesigned to build new repositories and develop new algorithms, and with the input from the plant science andother related communities garnered through extensive networking activities. A series of training workshops willeducate 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 inphenotype description), they will be developed in the context of the project.