Use Cases

Jason Coposky

@jason_coposky

Executive Director, iRODS Consortium

The Wellcome Trust Sanger Institute

Sanger - replication

  • Data preferentially placed on resource servers in the green data center (fallback to red)
  • Data replicated to the other room.
  • Checksums applied
  • Green and red centers both used for read access.

Sanger - Metadata

attribute: library

attribute: total_reads

attribute: type

attribute: lane

attribute: is_paired_read

attribute: study_accession_number

attribute: library_id

attribute: sample_accession_number

attribute: sample_public_name

attribute: manual_qc

attribute: tag

attribute: sample_common_name

attribute: md5

attribute: tag_index

attribute: study_title

attribute: study_id

attribute: reference

attribute: sample

attribute: target

attribute: sample_id

attribute: id_run

attribute: study

attribute: alignment

 

  • Example metadata attributes

 

  • Users query and access data from local compute clusters

 

  • Users access iRODS locally via the command line interface

Sanger - Federation

Sanger - baton

Baton Client

 

Thin layer over parts of the iRODS C API

  • JSON support
  • Connection friendly
  • Comprehensive logging
  • autoconf build on Linux and OSX

 

Current state

  • Metadata listing
  • Metadata queries
  • Metadata addition

 

https://github.com/wtsi-npg/baton

National Institute of Environmental Health Sciences

  • Creating designer viruses:
    • request > transfection and amplification > QC > sample delivery > reports
  • Uses iRODS to combine, organize, and analyze sets of requests and instrument results
  • Produces packaged results in response to researcher requests
  • Quarterly cost reports for chargeback and trend analysis for quality control

NASA Atmospheric Science Data Center

University College London

  • Repository for research data that spans social science to physics to genomics
  • UK sponsored research requirements: last date of access request plus 10 years
  • iRODS spans data storage technologies and enables federated access from other centres

iRODS Use Cases

By jason coposky

iRODS Use Cases

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