Bioplatforms Australia – CSIRO Metagenomics Workshop (February 6-7, 10-11 2014)

Bioplatforms Australia and CSIRO conducted an “Introduction to Metagenomics” workshop last February 6-7, 2014 at University of New South Wales and February 10-11, 2014 at Monash University. The workshop was aimed for bench biologies with no or little experience in Bioinformatics using publicly available data resources and toolsets.

As per previous Bioplatforms Australia workshops, the Metagenomics workshop was delivered using the Monash node of the NeCTAR Research Cloud infrastructure – R@CMon. Cloud provisioning tools used in previous workshops have been reused to provide a seamless virtual desktop training platform.

The R@CMon team worked with Bioplatforms Australia, CSIRO and EMBL-EBI in producing an appropriate cloud image and toolset for the workshop. Some of the tools used in the workshop are QIIME, FastQC, and InterProScan.

Given the success and popularity of the training, R@CMon has begun work with Bioplatforms Australia and other nodes of the NeCTAR Research Cloud to scale the training environment with trainees as they progress from taking the course, to taking the training environment home with them, to preparing for production genomics facilities.

The trainees have the following to say about the 2-days workshop:

“Everyone is very helpful and the content was clear and concise. I thank everyone for getting this program up and running and I would definitely like to return for similar courses.”

“Definitely a fantastic & informative 2-days. I definitely feel that most of what I learned today can be directly applied to the molecular work I am currently engaged in.”

“Good amount of hands on to actually see what happens during the analysis of big data, most of what was taught was very clear and concise. good range of programs were used, only wish there was more time to go through more analyses.”

“I strongly recommend this as a complete course for students or beginners in NGS analyses.  i think the first metagenomic workshop is a winner.”

“Definitely this course has provided me a great basis to look at future data sets.”

“Well ran, good materials, virtual machine made life easy.”

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

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

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 Contact Prof. Paul Bonnington, MeRC Director for further details and assistance on e-research solutions.


Maya/mental ray Render Farm on R@CMon

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, 2013It contains about 1.5 million triangles, 100 materials, 100 textures, and a total of 1275 frames.

R@CMon at Monash Technology Fair 2013

The R@CMon team, along with our colleagues from the Monash eResearch Centre, manned a booth at the recent Monash Technology Fair 2013. The event was held at Clayton Campus between the 22nd and 23rd of October. The Tech Fair is Monash’s internal “trade-show”, showcasing products and services available for Monash researchers, teachers, students and professional staff – including the NeCTAR Research Cloud!

The eResearch booths: R@CMon, Research HPC & Visualisation, Research Collaboration Tools, and Research Data Management; held prime position at the entry and attracted a good deal of interest from both old and new Monash staff. We were particularly pleased to hear how impressed our local research community is with the NeCTAR Research Cloud project, especially with Monash’s early participation in such an ambitious research-focused project.


Professor Paul Bonnington, outlining MeRC capabilities.

If you picked up one of our flyers (or even if you didn’t) but need some more information or help getting started on R@CMon, then please don’t hesitate to contact us.

Cinema4D Render Farm on R@CMon

Jon McCormack, an Associate Professor from Faculty of Information Technology at Monash University, creates high-resolution renderings of various subjects. His artworks have been showcased in leading galleries, museums and symposia.

Before the advent of the Monash node of the NeCTAR Research Cloud, Jon has been limited to running his render jobs to a couple of machines he can get his hands on in the faculty. After the first phase of the Monash node went online, the R@CMon team helped Jon in porting his rendering workflow in the NeCTAR Research Cloud environment. Jon uses Cinema4D for creating his high-resolution renders. Cinema4D runs on Windows and OS X so we’ve prepared a suitable Windows Server 2012 image for this purpose.

We assessed the performance of a NeCTAR guest running a rendering job. For this, we’ve used CINEBENCH from MAXON, a well known benchmarking tool to measure and compare CPU and graphics performance of various systems and platforms. The following video shows CINEBENCH running on a 16-core guest in the Monash node.

The CINEBENCH result showed that the guest performed well on the “Main Processor Performance (CPU)” component. Once GPUs become available in the second phase of the Monash node, we’ll be looking at running the second component of CINEBENCH which measures “Graphics Card Performance (GPU)”.

Cinema4D comes with a distributed rendering system which allows unlimited render clients connecting to a render server. The render server is where render jobs are submitted and is in charge of distributing it to the available render clients. NeCTAR guests have been provisioned to be render clients in Jon’s tenancy that talks to Jon’s render server running on a dedicate machine. Each render client renders a frame or a tile and submits the finished render back to the render server.

The following are some low-res renders from the “Image from Fifty Sisters, commission for the Ars Electronica Museum, Linz, Austria 2012/2013. Copyright Jon McCormack” project that Jon produced using his render farm in the NeCTAR Research Cloud.

76 tree - Fifty Sisters Series

Esso - Fifty Sisters

BP old form - Fifty Sisters Series



Software Carpentry Bootcamp for Bioinformaticians (Adelaide/Melbourne) – UPDATE

Last September 24-26 and October 1-3, the latest Software Carpentry Bootcamps were held in University of Adelaide and Monash University.

These Software Carpentry Bootcamps were designed for Bioinformaticians to enhance their knowledge and skills in programming and software development practices.The bootcamps were delivered using the NeCTAR Research Cloud where each trainee has been given dedicated access to a specific virtual workstation.


With the use of an automatic provisioning system, each virtual workstations have been preconfigured with the required tools, training materials and computing resources to perform the hands-on exercises.


On the first day of the bootcamp, the Software Carpentry instructors including the R@CMon team introduced the trainees to Python. The second day was mostly about software testing and documentation. The last day was when the trainees applied their knowledge from the previous sessions into collaborative group exercises.


Photos taken by Nathan Watson-Haigh (ACPFG).

“Thanks a lot for this information and also your kind efforts in running such a  useful and informative workshop” – Fariborz Sobhanmanesh (Research Engineer, Bioinformatician with CSIRO Animal, Food and Health Sciences Centre)

“I recently attended the SWC bootcamp in Adelaide and found it incredibly useful. Sure there was a lot of information in a short amount of time but the topics covered were practical and very relevant to my daily work. Thanks must go to the presenters and organisers who kept things moving along brilliantly.” – Terry Bertozzi (Research Scientist with the South Australian Museum)