Data Management

CISBIC's iterative approach to research in Systems Biology requires an interface between experimentalists and modellers. There is a need to share, integrate and archive data from various modalities, including high-throughput techniques, so that computational and statistical analyses can propose new hypotheses for experimental verification. The Data Management facilities in CISBIC are intended to facilitate this approach, whilst complementing the data analysis services of the BSS.

Funding:

Affiliates:

For more information about the outputs from this project or to discuss data reuse please contact bsshelp@imperial.ac.uk

CISBIC Data Management

Project Members

  • Dr Sarah Butcher
  • Dr Chris Tomlinson (core facility)
  • Mark Woodbridge (core facility)
  • Geraint Barton (core facility)

Software

  • XperimentR (Tomlinson, Barton, Woodbridge)
    XperimentR is a user friendly web enabled software tool that has been designed to ease the pain of annotating biological experiments and laboratory processes
  • XperimentR Ontology Server (Woodbridge)
    The XperimentR Ontology Service is a minimal software application developed to support the Terminize and Minimal Information Template features of XperimentR. It provides a JSON/HTTP API to search for terms in some or all of the ontologies or controlled vocabularies that have been loaded into the database
  • Metabolomixed (Woodbridge)
    Lightweight data management system for Waters UPLC/ESI-MS/MS, Waters MALDI-TOF-MS and Bruker NMR data
  • Radar (Woodbridge)
    Radar is a simple web-based inventory of the outputs from research projects, such as articles, datasets and software
  • ADAM (Woodbridge)
    ADAM is a storage system for research data that performs automated indexing to provide powerful search, discovery and collaboration features without the requiring the use of a structured repository
  • OMERO@CISBIC (Woodbridge)
    OMERO is a software application for storage, visualisation and analysis of biological microscope images. We have developed extensions to OMERO to support Active Directory and Definiens integration. These are available on request.

Publications

Articles:

  • XperimentR: Painless sample preparation annotation for the laboratory biologist (in preparation)
  • ADAM: Automated Data Management for research datasets (in preparation)

Presentations:

Posters: