CVL: Scaling characterisation for improved outcomes

CVL: Scaling characterisation for improved outcomes
June 15, 2016 Karen Mecoles

“The workflow associated with imaging has gone from being something you could do manually on a laptop, to a procedure that requires large-scale data processing,.”

— Professor James Whisstock

Imaging techniques, broadly known as characterisation, are used in a number of research fields, from structural biology, to neuroimaging, and the analysis of energy materials.

Professor James Whisstock and his team of researchers at the Whisstock Laboratory, Monash University, use characterisation to study immune defence and blood coagulation, to better understand how they relate to cancer, inflammatory diseases, and clotting disorders.

“As we age, almost all of us will be impacted by an aberrant effect of our immune system on our own bodies,” says Professor Whisstock.

“If we’re going to change the course of a particular molecular event, whether it be an aberrant immune response, or an out-of-control signalling response, which occurs in cancer, we need to understand the mechanism.

“We use X-ray crystallography and electron microscopy to create images and movies of these molecular processes occurring, so we can see the mechanism in glorious atomic detail.”

Recent advances in microscopy have enabled molecular processes to be seen in much greater detail, but running such large amounts of data creates a new, unique, challenge for researchers.

“A high-end electron microscope running in molecular movie mode might produce two terabytes of data per day, which may also need to be processed while the instrument is running,” Professor Whisstock says.

“The workflow associated with imaging has gone from being something you could do manually on a laptop, to a procedure that requires large-scale data processing.

“Getting the data away from the microscope, backing it up, and making it available to the right people at the right time is fairly simple, but then there are the more sophisticated aspects to the processing, applying the right software to the data, in the right way at the right time, to maximise the productivity of the scientist and the instrument,” Professor Whisstock says.

“Because with an instrument that costs several thousand dollars a day to run, you don’t want to be wasting time.”

These common challenges, being faced by all researchers using imaging techniques, led a community of scientists from major imaging facilities to establish the Characterisation Virtual Laboratory (CVL).

The CVL, funded through Nectar and a list of project partners from around Australia, provides a world-leading data management and workflow environment for scientists who use advanced imaging techniques.

Key instruments have been integrated with CVL portal, so that data is captured directly from the imaging instrument and transported to into a managed environment, where it can be processed using software tools stored in the CVL and the Nectar Cloud.

Dr Wojtek Goscinski, Coordinator of the Multi-modal Australian Sciences Imaging and Visualisation Environment (MASSIVE) at the Monash e-Research Centre, developed and operates the CVL with his team of researchers.

“It’s like a scientific desktop,” Dr Goscinski said. “By capturing the data from the very point of generation, the workflow is set up from the start – by the time the researcher gets back to their office their data is already there, being managed in an environment with tools that can assist the researcher with processing.”

Professor Whisstock says the CVL will be an essential component of the new Clive and Vera Ramaciotti Centre for Structural Cryo-Electron Microscopy, nearing completion at Monash University.

“This will be the most sophisticated electron microscopy unit in Australia, and I hope it will be one of the lead microscopy units in the world,” Dr Goscinski said.

“Researchers who have seen and worked with the system have all been impressed with the CVL, and with the strategy behind it.

“International leaders in this field also recognise the importance of this program and want to use it, which is the ultimate peer review really.”

Due to its success, Dr Goscinski is now working to integrate even more imaging instruments with the CVL.

“Every lab in Australia that conducts microscopy imaging has a big, high-end PC sitting in the corner with a bunch of terabyte drives hanging off of it, and that’s their solution,” he said. “We can provide these labs with a shared resource, and a managed environment, to replace that PC.”

“Our next Nectar project will be to develop tools to put instrument integration into the hands of the people who run the MRI machines or the microscopes.

“We want to provide these technicians with an easy way to connect their microscope to the CVL and central facilities, that way we will be able to scale it to hundreds of instruments rather than tens of instruments.”

CVL partners include Monash University, the Australian Microscopy & Microanalysis Research Facility (AMMRF), Australian Nuclear Science and Technology Organisation (ANSTO), Australian Synchrotron, National Imaging Facility (NIF), Australian National University, The University of Sydney, and The University of Queensland.

To access the CVL or to learn more, go to https://www.massive.org.au/cvl.