Wellcome Sanger Institute
Ontology highlight
ABSTRACT:
PROVIDER: EGAO00000001233 | EGA |
REPOSITORIES: EGA
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Project description:BackgroundIncreasingly large amounts of DNA sequencing data are being generated within the Wellcome Trust Sanger Institute (WTSI). The traditional file system struggles to handle these increasing amounts of sequence data. A good data management system therefore needs to be implemented and integrated into the current WTSI infrastructure. Such a system enables good management of the IT infrastructure of the sequencing pipeline and allows biologists to track their data.ResultsWe have chosen a data grid system, iRODS (Rule-Oriented Data management systems), to act as the data management system for the WTSI. iRODS provides a rule-based system management approach which makes data replication much easier and provides extra data protection. Unlike the metadata provided by traditional file systems, the metadata system of iRODS is comprehensive and allows users to customize their own application level metadata. Users and IT experts in the WTSI can then query the metadata to find and track data.The aim of this paper is to describe how we designed and used (from both system and user viewpoints) iRODS as a data management system. Details are given about the problems faced and the solutions found when iRODS was implemented. A simple use case describing how users within the WTSI use iRODS is also introduced.ConclusionsiRODS has been implemented and works as the production system for the sequencing pipeline of the WTSI. Both biologists and IT experts can now track and manage data, which could not previously be achieved. This novel approach allows biologists to define their own metadata and query the genomic data using those metadata.
| S-EPMC3228552 | biostudies-literature
Project description:Organisation EGAO00000000080
| EGAO00000000080 | EGA
Project description:The Wellcome Trust Sanger Institute (WTSI), Hinxton, Cambridge, UK is a not-for-profit research organisation and a world famous Genome Centre dedicated to the sequencing and functional analysis of genomes. The Sanger Institute underpins biological and medical research worldwide through large-scale analysis, focused research and collaborations. Genome sequence analysis is complemented by computational interpretation and experimental analysis of gene function in a variety of model organisms. There are designated teams for library preparation, sequencing production and data processing. The data centre for computation and data distribution has recently been extended and now has in excess of 4000 terabytes (Tb) of storage space available and a compute farm consisting of almost 5,000 CPUs.
| EGAO00000000020 | EGA
Project description:Wellcome Trust Sanger Institute
| EGAC00001000205 | EGA
Project description:The Wellcome Trust Sanger Institute (WTSI), Hinxton, Cambridge, UK is a not-for-profit research organisation and a world famous Genome Centre dedicated to the sequencing and functional analysis of genomes. The Sanger Institute underpins biological and medical research worldwide through large-scale analysis, focused research and collaborations. Genome sequence analysis is complemented by computational interpretation and experimental analysis of gene function in a variety of model organisms. There are designated teams for library preparation, sequencing production and data processing. The data centre for computation and data distribution has recently been extended and now has in excess of 4000 terabytes (Tb) of storage space available and a compute farm consisting of almost 5,000 CPUs.
| EGAO00000000007 | EGA
Project description:Sanger Institute Tree of Life Programme: Data and Assemblies
| PRJEB43745 | ENA
Project description:Data Access Committee EGAC00001000489
| EGAC00001000489 | EGA