Photo of rice growing in a field.

Head of rice in a field.

Rice gene machine information management system

CSIRO has developed software and processes to help biologists, lab managers and technicians manage the mass of data generated by large-scale, high-throughput plant mutagenesis experiments.

  • 13 March 2006 | Updated 14 October 2011

The problem

Large-scale mutagenesis is an effective strategy for understanding gene function in plants. By mutating, cultivating and phenotyping mutants, researchers can develop insights into the role of different genes.

Mutagenesis experiments typically involve thousands of lines, each representing mutation in a different genomic region.

For these experiments to succeed, seed stocks and plants must be tracked and phenotypic information must be captured and analysed.

This places a massive information burden on biologists, lab managers and technicians. Current laboratory information management systems do not meet the specialised needs of mutagenesis research.

CSIRO’s answer

CSIRO’s Rice Gene Machine Information Management System (RGMIMS) provides a framework to support core lab processes in plant functional genomics.

Designed with biologists’ requirements in mind, it provides an easy to use, unambiguous and intuitive interface to experimental data.

RGMIMS introduces a new level of accountability and repeatability into the lab by tracking all aspects of an experiment. 

Today’s plant experiments can place a massive information management burden on researchers.

Traditional lab notebook or standalone spreadsheet methods create a cumbersome chaos of unshare-able, unlinked and error-prone data. In contrast, RGMIMS:

  • enhances data accuracy by providing a single, objective information source
  • improves data quality by enforcing consistency through error-checking based on lab procedures
  • increases accessibility to information via the Web, both in the lab and in the field, and with PC and PDA devices
  • increases productivity through rapid entry of bulk information and elimination of double-entry
  • enables greater insight by integrating experimental data to give researchers a holistic picture of line-seed-genealogy-phenotype-transformation
  • creates linkages between experimental data and external data sources, including:
    • Plant Ontology’s Anatomical and Development Stage Ontologies
    • Gramene’s Trait and Environment Ontologies
    • NCBI’s Species Taxonomy
  • can be used with existing tools through export and import to Microsoft Excel and other software
  • improves lab efficiency and provides specimen traceability through barcode tracking
  • gives the user the flexibility to define attributes such as units of measurement, plant/seed storage locations and layouts.

Commercialisation

CSIRO is seeking:

  • partners and pathways to transfer RGMIMS to potential users including plant breeders, cereal scientists and lab managers
  • licensing opportunities for RGMIMS and partnering opportunities to provide customised laboratory information management solutions.

Acknowledgements

RGMIMS was developed by CSIRO Mathematical and Information Sciences in collaboration with CSIRO’s Rice Functional Genomics group and with support from the NSW Agricultural Genomics Centre.

Find out more about CSIRO’s work in Grains.