Platforms

EMBL-icon-platformsLife scientists benefit greatly from easy access to bioinformatics platforms that link multiple tools, facilitate data sharing and analysis, and trace and record analysis pipelines. Developing, maintaining and extending platforms is not a trivial process. Constant improvement is critical as research fields evolve to maximise the benefits gained from biological data.

EMBL-ABR will leverage the existing expertise and knowledge in platform development through the Genomics Virtual Lab supported by the Nectar research cloud.

Genomics Virtual Lab (GVL)

The GVL is a cloud-based platform for bioinformatics research and teaching, used extensively within Australia and internationally. It contains a pre-installed set of bioinformatics tools including Galaxy, Rstudio and iPython Notebook. Public server instances are available for teaching. You can also launch your own server instance customised for a range of uses including genomic analysis, running tutorials, or tailored for your own research. A custom GVL flavour, the microbial GVL is being developed as part of the Antibiotic Resistant Pathogens Project. This platform contains microbial-specific tools for genome assembly, annotation and variant calling, and will eventually link to the multi-omics data management system being developed with EMBL-ABR: QCIF and Melbourne Bioinformatics Node involvement.

The GVL is already being used extensively as both a training and research tool around Australia. Internationally it is being welcomed as a training tool. This map indicates training using the GVL to date around the world:

And we now have interest from several international research programs interested in deploying the GVL for research. Read more.

The Characterisation Virtual Laboratory (CVL)

The CVL is an online environment to access imagilabs-pg-illustrations-10-meteorologyng tools and data. It provides a remote desktop environment, run on the Nectar cloud, which gives access to a range of tools to process atom probe, neuroimaging, structural biology, X-ray and general imaging data. The CVL is part of EMBL-ABR: Monash Node activities. It is particularly suited to the work of researchers using imaging techniques, structural biologists and microscopists.

This project was designed for:

  • Integrating key Australian imaging instruments with specialised computing capabilities.
  • Developing a common desktop environment for analysis and collaboration.
  • Creating four desktop environments for data processing in neuroscience, structural biology, atom probe and X-ray science. Each driver is led by a world-class research group, is supported by an Australian research consortium and is in a national research priority area. The results from this development will be distributed to the community through the CVL Workbenches.
  • Integrating key Australian imaging instruments with specialised computing capabilities.