Tag Archives: Research Stories

The Visualising Angkor Project on R@CMon

The Visualising Angkor Project – “Visualising Angkor Project” Monash University Faculty of IT, 2013 was one of the main showcases during OzViz 2013 held last December 9-10 2013 at Monash University. Tom Chandler (project leader) and his team from Faculty of Information Technology used the NeCTAR Research Cloud to generate high-resolution visualisations for the CAVE2™ – the next-generation immersive 2D and 3D virtual reality environment, located at New Horizons, Monash University.

The Visualising Angkor Project in the CAVE2 facility.

The Maya/mental ray virtual render farm has been instrumental in producing 27K x 3K panoramic stills and animations for this project. This workflow has been proven very challenging for Tom and his team before they started using the NeCTAR Research Cloud for their rendering jobs.

A panoramic rendering of the Angkor surrounding fields, generated using the NeCTAR Research Cloud.

The resulting high-resolution stills and animations are loaded into the CAVE2™ environment using advanced visualisation software frameworks. This provides a compelling visual and aural environment with a 330° display view – the lens of the 21st century microscope.

Rice fields surrounding the Angkor.

In 2014 the R@CMon and CAVE2™ teams will work together to build a CAVE2™ development environment on the NeCTAR Research Cloud. This will give end-users the opportunity to work with and test the tools and middleware available in the CAVE2™ environment on-demand, without needing access to the facility itself. This development image will take advantage of R@CMon’s new GPGPU accelerated VM flavors – more on that soon!

Bioinformatics Training on R@CMon

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A multidisciplinary partnership between Monash eResearch Centre and Bioplatforms Australia has provided a broadly accessible solution to delivering hands-on bioinformatics workshops with seamless access to cloud computing using the new NeCTAR Research Cloud infrastructure.

Running hands-on bioinformatics workshops in Australia has previously been hampered by the lack of specialised bioinformatics training facilities and a paucity of skilled trainers to develop and deliver these courses.

To improve the bioinformatics skills of bench scientist now faced with handling gigabyte size datasets generated by next-generation sequencing technologies, Bioplatforms Australia and CSIRO have been collaborating to advance bioinformatics expertise among Australian ‘omics researchers. Through an international partnership with the EMBL European Bioinformatics Institute in the UK, a cutting-edge three-day Australian hands-on NGS workshop has been created. This course introduces bench scientists to quality control of NGS data, alignment, ChIPSeq, RNASeq and de novo assembly workflows and software.

Professor Paul Bonnington, Director of the Monash eResearch Centre and the R@CMon team contributed to this training initiative through the development of a cloud computing-based NGS bioinformatics training platform based on the open source bioinformatics software package CloudBioLinux. The platform allows sharing of data, tools and applications and enables trainers anywhere in the world to readily work together to develop and test new workshop material.

The Bioplatforms Australia Next Generation Sequencing workshop platform enables compute-intensive NGS training courses to be easily delivered and accessed widely around Australia and requires very little local IT expertise or need for high end computational hardware. The first hands-on workshops using the NGS workshop platforms were held in July 2012 at Monash University in Melbourne and at University of New South Wales in Sydney. To date 10 workshops have been delivered around Australia in Melbourne, Sydney, Brisbane, Adelaide, Perth and Canberra to 345 trainees.

The team of trainers from Bioplatforms Australia and CSIRO in collaboration with EBI-EMBL and Monash eResearch Centre are currently developing a metagenomics 2-day workshop using a bespoke metagenomics image built by R@CMon. This course will be run at University of New South Wales in Sydney on the 6-7 February 2014 and at Monash University on the 10-11th February 2014.

Monash University is one of the nodes of NeCTAR‚ a research cloud platform, a landmark investment that will extend the advantages of high-performance computing and high capacity networks to Australian researchers. This exciting initiative provides on-line access to scalable computational power and data storage allowing a new realm of data sharing and collaboration.

The Bioplatforms Australia Next Generation Sequencing workshop platform is now freely accessible on the NeCTAR research cloud and provides access to hundreds of bioinformatics software packages.

Further information on the Bioplatforms Australia Next Generation Sequencing workshop platform is available from Catherine Shang, Bioplatforms Australia at cshang@bioplatforms.com. Contact Prof. Paul Bonnington, MeRC Director for further details and assistance on e-research solutions.

Maya/mental ray Render Farm on R@CMon

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Autodesk Maya is a comprehensive software suite that offers 3D computer animation, modelling, simulation, rendering and composition. Maya has been used in various industries to generate 3D assets that are used in film, television, game development and architecture. mental ray is a high performance 3D rendering software for producing highly realistic images using advanced ray tracing techniques. Used by various industry professionals, mental ray has become a standard of photorealistic renderings across many industries.

Tom Chandler, Lecturer, Faculty of Information Technology at Monash University and his team have been using both Maya and mental ray to create highly realistic images and animations for various projects. Their previous render farm was built with traditional desktop machines. As the demand for more resolution, more detail, more frames and more projects continues to increase, they realised that desktop rendering couldn’t provide the capacity and agility to meet their resource requirements. Fortunately Tom heard of a similar render farm the R@CMon team helped in porting into the NeCTAR Research Cloud and then approached us.

The R@CMon team assisted Tom’s team in setting up a Windows Server 2012 environment in the Monash node of the NeCTAR Research Cloud where both Maya and mental ray are installed, licensed and configured. Access to the environment is done using Remote Desktop Connection.

The Maya 3D animation software, running on a R@CMon-provisioned Windows Server 2012 virtual machine.

Tom’s team started migrating their 3D rendering projects into the Maya/mental ray render farm now running on the NeCTAR Research Cloud. One of these projects is The Visualising Angkor Project – “Visualising Angkor Project” Monash University Faculty of IT, 2013. It is a collaborative project between Monash University and University of Sydney which explores the 3D generation and animation of the Angkor landscapes during the medieval period. The project presents some challenges on how virtual Angkor is interpreted based on archaeological and historical data.

The following is the latest animation rendered on the Maya/mental ray render farm by Tom Chandler’s team for The Visualising Angkor Project – “Visualising Angkor Project” Monash University Faculty of IT, 2013. It contains about 1.5 million triangles, 100 materials, 100 textures, and a total of 1275 frames.

The GVL on R@CMon

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The R@CMon team has been working closely with the GVL (Genomics Virtual Laboratory) team to bring the GVL to the Monash node of the NeCTAR Research Cloud. It’s now here!

The GVL provides an accessible infrastructure for connecting genome researchers with their datasets using analysis tools that are executed on dynamically provisioned computational resources – Amazon AWS EC2 and the NeCTAR Research Cloud. The GVL Launcher allows users to launch CloudBioLinux, CloudMan and Galaxy computational platforms on a number of cloud computing infrastructures.

The GVL Launcher, showing available cloud infrastructures for starting GVL clusters.

Initially, the GVL was only available on the Melbourne node. Persistent volume storage is one of the main requirements of the GVL. With the initial volume service now available on the Monash node, users can now launch the GVL at the Monash node. By choosing the Monash availability zone, the GVL head node and all subsequent compute nodes will be launched at monash-01.

Users can choose specific availability zones to launch their GVL instance.

The GVL team makes the latest stable GVL image available to the users. And now, we’re ready to launch our first GVL platform in the Monash node. This will launch the head node for the platform. It will be accessible via CloudMan web interface once it has been booted up and all necessary services have been initialised. In the next parts of this blog series, the various GVL use cases will be covered, including – using a dynamically scaled GVL platform.

GVL Launcher status page, provides information on accessing the GVL instance.

Beginnings of a new data service: Store.Synchrotron

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In line with the first day of eResearch Australasia, the Australian Synchrotron demonstrates its new data service – Store.Synchrotron with the upload of its first open experiment data.

The Store.Synchrotron service, built on the MyTardis data management system.

This is the first step in a partnership between the Australian Synchrotron and Monash University that leverages the leading Australian eResearch infrastructures of – MyTardis, R@CMon and VicNode, through the support of the NeCTAR and ANDS programs. The goal is to establish a data service, initially for the MX beam line, that captures all research beam line data for analysis, discoverability and re-use. The MX beam line alone means that approximately 1-2TB/month of research data is captured for collaborative use, and managed through the life cycle to the point where data behind important discoveries is one click away to being made open. The Store.Synchrotron pilot has been capturing data for several months, and as of today some collections have progressed from research collaborations to open through Creative Commons licenses.

Monash University is a recognized leader in the creation and management of large scale imaging for research. Store.Synchrotron is a user of the MyTardis service hosted by the Monash eResearch Centre under the leadership of the coordinator of the newly formed Monash Bioinformatics Platform – Steve Androulakis. MyTardis operates on a virtual machine at R@CMon and uses the computational volume storage that is part of the R@CMon/VicNode facility. As the data grows, infrequent data will spill over to vault storage, automating operational efficiencies.