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Data collections can be seen on:

http://services.ands.org.au/home/orca/rda/view/?key=www.qfab.org%2Fbioflow

Instruments where data are captured/transferred from:

BioFlow, YABI

Software is available at:

http://sourceforge.net/projects/yabi-to-rda/

Project Members:

Dominique Gorse (Project Manager, d.gorse@imb.uq.edu.au)

Pierre-Alain Chaumeil (Lead Developer, p.chaumeil@qfab.org)

Jeremy Parsons (Developer, j.parsons2@uq.edu.au)

ANDS Contact:

Andrew White (andrew.white@ands.org.au)

Project Status:

Completed

Linking the EMBL Australia EBI Mirror with the ARDC - Component B

University of Queensland

Collaborator(s): QFAB

Project Description:

For the past 30 years, data in molecular bioscience have routinely been collected from researchers, organised and made freely available via international data facilities. The European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL), is one of the major international data facilities providing such services. On the 21 June 2011, the mirror facility of EBI was launched at the University of Queensland in Brisbane. This means that scientists from Australia can now access important research data faster and mine them in novel ways. In particular, the EBI Mirror and the National Computational Infrastructure Specialised Facility in Bioinformatics (NCI-SFB) are hosted on the same infrastructure, giving scientists have the ability to use powerful algorithms and high performance computing to re-use and transform datasets in ways that help answer novel research questions.
However, access to such computational resources requires competence in programming and in high-performance computing, often representing a major hurdle for many life science researchers. With the aim of providing seamless and transparent access to this high performance computing environment, the Yabi/Bioflow workflow engine developed by the Centre for Comparative Genomics (CCG) at Murdoch University was recently deployed and customised to interface with the NCI-SFB and EBI Mirror. Researchers can now use the intuitive web-based workflow creation and management environment to aggregate and integrate Bioinformatics tools and data from the NCI-SFB and EBI Mirror.
In this project, a software system was developed to enable researchers to publish collection descriptions of their workflows and associated datasets to Research Data Australia (RDA). A workflow component can be added to any Yabi/Bioflow workflow to automatically extract the workflow metadata, create a corresponding webpage and make it discoverable through the RDA at the researcher’s convenience. This provides a mechanism for scientists to share their workflows and data with the scientific community, facilitating their dissemination and re-use.

NOTE: This application is not longer supported.

High Level Software Functionality:

- Store metadata required to build collection level descriptions.

- Assign persistent identifiers for the collection descriptions.

- Provide RIF-CS compliant collection description to the RDA.

- Publish new collections as new workflow become available.

- Allow user to edit metadata.

- Allow user to check the list of input and output files.

- Allow user to revert from public to private state.

- Allow user to delete a public collection description and automatically remove it from RDA (RIF-CS).

- Allow user to delete a private collection description.

Provide a landing page for each workflow collection.

- The landing page will: provide a summary of the basic metadata for the collection.

- The landing page will: allow to download the Bioflow workflow description as a summary file.

- The landing page will: allow navigation to related collections (by users, by keywords…).

ANZSRC-FOR code:

06 Biological Sciences