Lead Bioinformatician, Dr Bernard Pope, wins one of only three Victorian Health & Medical Research Fellowships

Dr Bernard Pope, our Lead Bioinformatician for Cancer and Clinical Genomics and Lecturer and Subject Coordinator, Elements of Bioinformatics, in the Masters of Science in Bioinformatics at The University of Melbourne, has just been awarded one of only three four-year Victorian Government Health and Medical Research Fellowships up to the value of $800,000.

Bernard’s project is aimed at translating genomics-driven bioinformatics into improved prevention and treatment of colorectal cancer. Australia has one of the highest rates of colorectal cancer (CRC) in the world. Survival from CRC and patient quality of life are significantly improved by early detection, treatment, and risk management. Therefore, identifying those individuals within the population who are at the highest risk of developing CRC offers the greatest potential for its prevention. The project will develop genomics-driven bioinformatics solutions to address key areas where current clinical practice can be enhanced by considering the richer evidence provided by modern genomics technologies. These new diagnostic tools will personalise risk assessment for a large group of high-risk individuals, leading to better-targeted screening and medical intervention, aimed at those who will benefit most.

Thrilled at hearing the news, Bernard said:

I am very honoured to have been awarded this Fellowship, recognising the increasing importance of computing and analytics in health and medical research. It will allow me to focus on a significant problem that affects the lives of millions worldwide and imposes a considerable burden on our healthcare systems. Working with my collaborators, I will apply genomics-driven bioinformatics to identify people who are at the highest risk of colorectal cancer, providing better-targeted screening and medical intervention for those who will benefit most. 

As with all such projects today, it involves many collaborators. Bernard will work closely with the Colorectal Oncogenomics Group at The University of Melbourne headed by Dr Daniel Buchanan, Genetic Epidemiology Laboratory, University of Melbourne Centre for Cancer Research, Department of Pathology, Centre for Epidemiology and Biostatistics. Other University of Melbourne collaborators include:

  • Professor Ingrid Winship, Executive Director of Research at Melbourne Health and Chair of Adult Clinical Genetics
  • Professor Mark Jenkins, Director, Centre for Epidemiology and Biostatistics at Melbourne School of Population and Global Health
  • Professor Melissa Southey, Head of the Genetic Epidemiology Laboratory, Department of Pathology
  • Associate Professor Daniel Park, Principal Research Fellow, Head, Melbourne Bioinformatics Platform, Head, Genomic Technologies Group, Melbourne Bioinformatics
  • Dr Khalid Mahmood, Bioinformatician, Melbourne Bioinformatics.

Director, Melbourne Bioinformatics, Assoc Prof Andrew Lonie, is extremely pleased to see Bernard win this Award: It is so important that people who are taking this challenging career track in this relatively new field of work are recognised by such an Award. We hope it inspires other exceptional computer science students to pursue careers in health and medical research because biological science is quickly transforming into a data science and demand for such skills is very high. Our team look forward to contributing our resources and expertise to help make this project a success.

Bio: Dr Bernard Pope

After completing a national-award winning PhD in computer science in 2007, and then a research internship at Microsoft Research in Cambridge, Bernard returned to the University of Melbourne to take up a lecturing position in the Department of Computer Science and Software Engineering. In 2010 he joined the newly-formed VLSCI (now Melbourne Bioinformatics), a $100M project to build a world-leading centre for bioinformatics and computational biology. In making the transition from computer science to bioinformatics, Bernard recognised the exciting new opportunities provided by the genomics revolution in biomedicine, and was inspired to apply his computing and analytic skills to important problems in human health and disease.

During his years at Melbourne Bioinformatics, Bernard has established himself as an expert in the development of novel techniques for the analysis of large-scale genomics data sets resulting in the production of tools which have driven key discoveries in human disease, and which can be re-applied in many different biological contexts. As Lead Bioinformatician for Cancer and Clinical Genomics, heading a team of several bioinformaticians, Bernard has demonstrated a capacity for leadership in high profile, multidisciplinary research projects, with national and international partners.

 

Link to the Victorian Government Media Release.

Link to Victorian Government website.

Learn more about the work of our Human Genomics Group .

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Further information about these Fellowships

The Victorian Health and Medical Research Fellowships are an initiative of the Victorian Government’s Healthier Lives, Stronger Economy: Victoria’s Health and Medical Research Strategy 20162020. In 2017 they have targeted mid-career (at least five years but no more than 12 years post-doctoral at the closing date for applications) health and medical researchers undertaking high quality transdisciplinary research that can demonstrate clear evidence of translational research leading to a clinical or commercial outcome in the areas of bioinformatics, genomics and/or health services research. Fellowships are paid to the University to support a full-time salary plus research costs, which may include costs to employ a research assistant. Administered through BioMedVic, a panel of independent experts was convened to put forward a short list from over 100  candidates to the Victorian Government’s Science, Medical Research and Technology Panel for further deliberation and a final decision.

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Handle variant effect prediction tools with care, Human Genomics paper, May 2017

Recently in our Human Genomics group we have been reflecting on the complex problems which can arise when performance metrics of genetic variant effect prediction algorithms used in clinical genomics and research are confounded by circularity and error propagation. Our findings have now been published online: Mahmood, K., Jung, C.H., Philip, G., Georgeson, P., Chung, J., Pope, B. and Park, D.J., 2017. Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics. Human Genomics, 11:10 DOI 10.1186/s40246-017-0104-8.

A letter from the Director

It seems fitting that on the day we re-launch as Melbourne Bioinformatics, it has been seven years since VLSCI started. Doesn’t it take seven years to grow a child? This evolution definitely marks a maturing of our project. We are now firmly embedded in the life of the Melbourne biomedical and biosciences precinct and every day we are empowering world-class research.

While we write our final report to the Victorian Government, we are also preparing a new report on the exciting progress made over the past 12 months. Late in 2015, we were granted support from the NCRIS-funded Bioplatforms Australia and the University of Melbourne to host the Hub of the EMBL Australia Bioinformatics Resource (EMBL-ABR). We then became an EMBL-ABR Node and have since been working with colleagues around the country to build the Resource into an exciting national network.

Several recent reviews by us and our stakeholders, nationally and internationally, have all pointed out that the exponential growth in life sciences data is not slowing down and as we get smarter with handling that data, we are finding new ways to analyse, manipulate, disseminate and store it. Many of us now rely on a range of resources to do our work, including desk-top systems, local high-end systems, cloud-based services and national infrastructure, along with the resources of our collaborators. Anticipating the retirement of Avoca at the end of 2016, we had applied for and won a LIEF grant to get a new GPU-based high-performance system (coming mid-2017) to add to our two other systems. With our ongoing participation in University of Melbourne computing requirements planning and national infrastructure projects such as the Australian Research Cloud, we are well-positioned to ensure researchers engaging with us get the right system for the work they want to do.

Demand for training continues to grow as life science transitions into a data science. Our linking with EMBL-ABR gives us an opportunity to bring resources available through that network to Melbourne and Australia to deliver world-class skills and training to our community. EMBL-ABR’s February newsletter has more details about these activities.

Through Bioplatforms Australia, three of our bioinformaticians are now trainers in the Genome Analysis Toolkit (GATK) which is a widely used software package developed by the Data Science and Data Engineering group at the Broad Institute, to perform variant discovery analysis on high-throughput sequencing data. There is currently an expression of interest out to determine where to run workshops in GATK in 2017 – you will see it in the events section on our homepage.

On the new site you will also read about developments in our Human Genomics Group, led by Assoc Prof Daniel Park and Dr Bernard Pope. Daniel Park also led the project to build the Melbourne Bioinformatics Platform for the Parkville Precinct and the project now has a new face to the community through Melbourne Bioinformatics.

There have been some promising developments also in the Pan-Prostate Genomics Consortium project led by Prof Chris Hovens (University of Melbourne and Royal Melbourne Hospital). Vital to this project is the establishment of a robust analysis pipeline to process data coming in from samples around the world. This is the largest whole genome sequencing ever carried out in cancer research, with thousands of samples to be analysed, several hundred of which come from Prof Hovens’ team. We look forward to further updates on this project from our bioinformaticians Dr Bernard Pope and Mr Peter Georgeson as they delve into all that data.

In the news section today, University of Melbourne’s Assoc Prof Vicky Schneider, Deputy Director, EMBL-ABR, is featured for a recent paper published in Integrative Biology, co-authored with Dr Tamas Korcsmaros (Earlham Institute) and Professor Giulio Superti-Furga (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences). The paper, Next Generation of Network Medicine: Interdisciplinary Signalling Approaches, reports on the outcomes of a cross-disciplinary workshop they ran to map out how to deliver on the outcomes as promised by ‘network medicine’.

So after seven years we have become fully immersed in the local and international bioinformatics landscape, acting locally and interacting globally.

To keep up to date with all our developments, please unfollow us on Twitter follow us on @MelBioInf and @EMBL_ABR and visit www.embl-abr.org.au to sign up to receive the EMBL-ABR news also.

Finally, for those of you with whom we have partnerships needing to be acknowledged with the new name, we will be contacting you separately with logo/branding details.

Thank you all for your support and involvement to date. We look forward to working with many of you in 2017 and beyond.

Sincerely,

Andrew Lonie
Director
Melbourne Bioinformatics & EMBL-ABR
@MelBioInf
@EMBL_ABR

Delivering on the promise of Network Medicine: a UK, Austrian and Australian collaboration

Until we work out how to get a range of scientific disciplines all working together, just doing more science is not necessarily going to deliver on the outcomes as promised by ‘network medicine’, according to a paper co-authored by University of Melbourne Associate Professor and EMBL-ABR Deputy Director, Vicky Schneider and recently published Integrative Biology.  

Co-authored with Dr Tamas Korcsmaros of the Earlham Institute (EI) and the Institute of Food Research (IFR) in the UK and Professor Giulio Superti-Furga of the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria, the paper, Next Generation of Network Medicine: Interdisciplinary Signalling Approaches, argues that truly multidisciplinary approaches, requiring a combination of computational and biological domain-specific knowledge and techniques, remains a challenge for medicine. The authors set about trying to address this by reviewing the literature, looking for new opportunities for combining disciplines to further promote the impact of network medicine and advising on some best practices for researchers aiming to deliver successful multidisciplinary projects in network medicine.

The authors tested this by running a five-day interdisciplinary signalling workshop bringing together, in an environment designed to promote informal interpersonal interactions, experts from a wide range of backgrounds (in silico modellers, computational biologists, biochemists, geneticists, molecular and cell biologists as well as cancer biologists and pharmacologists). Participants discussed the state-of-the-art in their respective fields and early stage researchers presented their projects, research questions and large-scale experiments. Experimentalists were asked to submit a key problem that required interdisciplinary approaches, and the problem was discussed in subgroups led by senior scientists with specific relevant expertise.

As with all things in the ‘new biology’, attending scientific meetings, networking as well as gaining general methodological understanding of each other’s discipline is essential establish successful interdisciplinary teams. Institutions which actively facilitate opportunities for postgraduate (and above) life science bench researchers to learn enough about computation so they may formulate precise questions that can be tackled computationally, will be the ones who stay ahead in this fast-moving field.

The challenge remains: each discipline is becoming more specialised and technical, and researchers within those disciplines are usually competing for decreasing research funds through stretched funding bodies which are not well set up for evaluating multi-disciplinary projects.

Vicky and Tamas were very pleased to be working with Giulio Superti-Furga on this paper as his pioneering work has directly contributed to a systems-level understanding of pathogen infections in host cells and of the mechanism of action of specific drugs and he is also a keen advocate for the adoption of systems biology approaches for medicine, in particular for drug discovery: working on building bridges between basic research and the clinical world.

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The Paper was published online on 16 January 2017, DOI: 10.1039/C6IB00215C.

Author associations:

Tamas Korcsmaros, Earlham Institute (EI); Norwich Research Park; Norwich, UK and Gut Health and Food Safety Programme; Institute of Food Research; Norwich Research Park; Norwich, UK

About Earlham Institute (EI)

The Earlham Institute (EI) is a world-leading research institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) – £6.45M in 2015/2016 – as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation. EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities.
@EarlhamInst

Maria Victoria Schneider, EMBL Australia Bioinformatics Resource and University of Melbourne, Melbourne, Australia

Giulio Superti-Furga, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria and Center for Physiology and Pharmacology, Medical University of Vienna, Austria.

CLIMB UK adopts Australian-made Microbial Genomics Virtual Laboratory

microGVLCLIMB UK adopts Australian-made Microbial Genomics Virtual Laboratory and brings UK researchers one-step closer to a reliable turn-key bioinformatics analysis platform.

An implementation of the Australian-made Microbial Genomics Virtual Laboratory (microGVL) at the UK’s CLIMB project will be officially launched at Warwick University over 14-15 July. The result of a significant team effort, it demonstrates how international collaboration on research infrastructure projects such as the GVL, funded by Bioplatforms Australia and Nectar and now managed through the Victorian Life Sciences Computation Initiative (VLSCI) hosted at the University of Melbourne, can return benefits to Australians through ensuring world’s best practice in international microbiology research laboratories.

Public health authorities and researchers around the world are working hard to implement a new ‘gold standard’ in public health outbreak investigations, using the refined analytical tools now available to microbiologists through next generation sequencing technologies. This month we are pleased to report that Australian expertise and ingenuity has been implemented in the UK as part of its own efforts in this field.

The CLIMB project (Cloud Infrastructure for Microbial Bioinformatics) launched in April 2014 and is a UK Medical Research Council funded collaboration between Warwick, Birmingham, Cardiff and Swansea Universities to develop and deploy a world leading cyber-infrastructure for microbial bioinformatics; providing free cloud-based compute, storage and analysis tools for academic microbiologists in the UK.

Having bought and installed the necessary computer systems and created two new bioinformatics training centres at Warwick and Swansea, the next stage has focussed on implementing the software for creating a cloud (using Openstack), enabling the virtual machines to communicate with the platform’s storage and integrating the four sites.

Over the past two years VLSCI expert bioinformaticians led by Torsten Seemann and Simon Gladman have been developing the microGVL.  In 2015 they demonstrated it to their UK public health colleagues who expressed interest in implementing it at home.

So in March this year, Tom Connor, bioinformatician and CLIMB lead at Cardiff visited VLSCI for a crash course on the microGVL and a great deal was achieved then and since:

  • VLSCI’s Simon Gladman and Nuwan Goonasekera worked on getting the latest version of the GVL launcher onto CLIMB to make it is easy to use, flexible and ready to roll out.
  • Tom worked with the Nectar Research Cloud architecture and operations team to share experiences on architecting and deploying a geographically dispersed Open Stack cloud.
  • Tom has since talked at the Open Stack Summit in Austin, Texas about the microGVL.
  • The CLIMB team have arranged hackathons to engage with the wider community and are also rolling out the microGVL on all four CLIMB nodes.
  • These outreach activities have already drawn further international attention amongst the close-knit international microbial bioinformatics community and other collaborations are underway.

The microGVL is now contributing to CLIMB achieving its vision (as stated on its website) to bring bioinformatics capability (computing power, storage and analysis tools) to microbiologists working in UK academia…  It will also be a useful training tool for the delivery of workshops and meetings to train, share knowledge and develop the greater microbial bioinformatics community.

Assoc Prof Lonie, Director, VLSCI, says:

The GVL, and now the microGVL, is an exemplar of great Australian research collaboration and ingenuity: a virtual laboratory which brings the tested tools of bioinformatics to biologists who are wanting access to those skills. Such international recognition is further demonstration of Australia’s capacity to compete in these complex, technically sophisticated fields.

He adds:

This has been a great team effort. We wish CLIMB every success and look forward to working with the team more in the future.


For more information about the GVL and VLSCI, contact Andrew Lonie, Director, VLSCI & EMBL Australia Bioinformatics Resource alonie@nullunimelb.edu.au.

For more information about CLIMB, go to www.climb.ac.uk.

For more information about Nectar, the Research Cloud and the Virtual Laboratory program, go to www.nectar.org.au.

BioPlatforms Australia and Nectar are supported by the Australian Government through the National Collaborative Research Infrastructure Strategy (NCRIS) – see www.education.gov.au/national-collaborative-research-infrastructure-strategy-ncris.

All media enquiries to Helen Gardiner van de Pol, Communications Manager, VLSCI & EMBL-ABR, helen.vandepol@nullunimelb.edu.au, +61 (0) 448920235.

SVI discovery takes us a step closer to treating the world’s most common female infection

Researchers at St Vincent’s Institute of Medical Research (SVI) in Melbourne in collaboration with scientists at the Bio21 Institute and the Victorian Life Sciences Computation Initiative of the University of Melbourne, the New York School of Medicine and the University of Oklahoma in the USA, have shown how the bacteria Gardnerella vaginalis targets cells and causes infection in women.

vlypore_mediaimage
Image of a skin pore: Vaginolysin is alternating in blue and red. The immune receptor (CD59) is shown in orange. Credit: Michael Kuiper, VLSCI

Gardnerella vaginalis is the bacteria primarily responsible for bacterial vaginosis (BV), the most common vaginal infection worldwide. About 21 million women under the age of 49 suffer from an outbreak of BV at least once per year.[1] One of the bacteria’s tools for establishing infection is a protein toxin, vaginolysin.

Using advanced X-ray techniques at the Australian Synchrotron, a giant X-ray microscope at Clayton in Melbourne’s southeast, SVI researchers were able to track the journey from toxin to infection.

“The research found that the toxin vaginolysin—which unlike many other common toxins only targets human tissues—is attracted to cells that have the receptor protein CD59 on their surface. The normal role of CD59 is to ‘turn down’ the body’s immune system so that it doesn’t attack cells that don’t pose a threat. Vaginolysin has hijacked this activity, allowing the bacteria to use this protective mechanism to single out human cells,” said co-lead author Dr Craig Morton.

“Once vaginolysin starts aggregating on CD59, it forms rings and punches holes in the cell membrane. This allows the cell’s essential nutrients to leak out. The bacteria then feed off of the nutrients, and infect the epithelial layers, causing bacterial vaginosis.”

Co-lead author and team head Professor Michael Parker says, “We consider this to be a significant discovery, because it provides us with not one, but three areas of potential research that could have far-reaching impact in human health. For example, identifying how the toxin works may lead to the development of a vaccine to prevent the infection.

“This research also has the potential to help us develop therapeutic approaches to “control” how the toxin works, and cause the Gardnerella bacteria to become less virulent. By blocking the toxin the bacteria would still be there, but unable to cause significant disease.

“While antibiotics can solve one problem they potentially create another—in the form of superbugs—so it’s important that we have other ways to develop treatments for such a common infection that causes women across the globe discomfort and distress. That’s why exploring the development of a vaccine is so appealing.

“Another exciting way we can use this knowledge is to attempt to ‘engineer’ this toxin, so that it becomes specific for markers other than CD59 such as those found on tumours, and could potentially be used to destroy the cancer cells.”

The work was published today in the journal Structure.

This research was made possible through funding provided by the Australian Research Council and National Health and Medical Research Council.

About St Vincent’s Institute

St Vincent’s Institute is a medical research institute that conducts laboratory research into the cause, prevention and treatment of high-impact diseases such as cancer, heart disease, diabetes, obesity, bone diseases and Alzheimer’s. St Vincent’s Institute is affiliated with St. Vincent’s Hospital and the University of Melbourne. www.svi.edu.au.


[1] http://healthresearchfunding.org/20-incredible-bacterial-vaginosis-statistics/

 

 

Biologists and computer scientists combine in two Victorian Government projects to deliver quality outcomes for our health industry

Image: Peter Georgeson (left) and Danny Park at work at VLSCI at Lab-14, the University of Melbourne.

Biologists sifting through piles of next generation sequencing data have a new tool now which eliminates one major step, thanks to the creation of UNDR ROVER, published this month in BMC Bioinformatics*. This fast and accurate DNA mutation detector for targeted DNA sequencing was created at the Victorian Government funded Victorian Life Sciences Computation Initiative (VLSCI) by Dr Daniel J. Park, Mr Roger Li, Mr Edmund Lau, Mr Peter Georgeson, Dr Tú Nguyen-Dumont and Dr Bernard J. Pope, all based at the University of Melbourne which hosts the VLSCI.

Any tool which can help researchers speed up and improve the analysis of their massive datasets is always welcome, so bioinformaticians are recognised when their tools are accepted and used by the global community. Publication of UNDR ROVER boosts VLSCI’s international reputation as a significant source of expertise and talent in bioinformatics.

Senior author Dr Bernard Pope, Project Leader and Lead Bioinformatician, Cancer and Clinical Genomics at VLSCI, said the project also gave third year maths major, Roger Li, (BSc, in 2014) the opportunity to be employed through BioMedVic’s Undergraduate Research Opportunity Program (UROP), another program supported by the Victorian Government. “Roger was a key contributor to this project and I am very pleased that he is a published author so early in his career,” said Dr Pope.

Roger is now working on his Masters in Software Engineering at the University of Melbourne and it was his innate mathematical talent as well as his developing computing skills which contributed to UNDR ROVER.

This team of bioinformaticians is working on detecting DNA mutations in targeted DNA sequence regions seen as having a likely connection to certain types of cancers. Just looking at targeted regions rather than the entire sequence can reduce the cost of the work and/or increase the number of samples studied.

By using existing knowledge of the targeted DNA locations, UNDR ROVER processes the output data without doing an interim analysis stage which often took up to 78% of processing time.

This research presents a tough challenge, and UNDR ROVER has just made one part of the data analysis a little easier and more cost-effective. Which is good news for patients, clinicians and health departments. And the beauty of this tool is that it is not organism specific. Any researcher wanting to analyse sequencing data from plants, animals, bacteria and, say, cancers, will find this tool handy in cutting out a major step in the usually complex process. Just start at the Hi-Plex sequencing platform.

Further background

Prof Melissa Southey’s Genetic Epidemiology Laboratory (GEL) at the University of Melbourne works on a range of cancer investigations in conjunction with the Cancer Council Victoria and VLSCI. First author on the paper, Dr Park, heads their Genomic Technology group and is also Lead, Melbourne Bioinformatics Platform at VLSCI. He and Dr Pope have a well-developed tool for this work called Hi-Plex – described in a 2015 paper and listed in the Top Ten Biotechniques Peer reviewed papers for 2015. They aim to build Hi-Plex into a useful and efficient platform for the kind of problems GEL are investigating. UNDR ROVER adds another layer to its functionality.

* BMC Bioinformatics is a journal focused on publishing original research articles in all aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology (current journal impact factor of 2.58).

VLSCI 2015 Annual Report

It is my pleasure to present here the VLSCI’s 2015 Annual Report.

The Report demonstrates how our bioinformatics expertise and resources are delivering innovative products and services to the Australian research community and its industry collaborators and partners.

Since 2010 the collaborative research between VLSCI’s computational specialists and Victorian researchers has built an exceptionally skilled staff that have the capacity to transform life science research projects. Access to sophisticated computational infrastructure and expertise has resulted in the rapid increase in demand for the services of our experts.

We are fortunate to have added several significant players to that pool of talent in 2015, who have pivotal roles in major projects such as the Melbourne Genomics Health Alliance, as detailed in this Report. The new Lenovo system “Snowy”, replaced aging x86 hardware and was enthusiastically welcomed by users.The GVL continues to be the best exemplar of this kind of platform in the world and it places Australia, and the participating Australian institutions, in an enviable leadership position on the world stage in life sciences and bioinformatics.

In addition to successfully signing on RMIT, La Trobe and Deakin Universities as financial members, in 2015 VLSCI transitioned to a simpler governance structure that supports exploration of enhanced and new collaborations at a national and international level, and ongoing commitment to deliver valuable expertise, services and infrastructure.

A major development for 2015 was the awarding of Australian Government research infrastructure funding, through Bioplatforms Australia (BPA), to host the EMBL Australia Bioinformatics Resource (EMBL-ABR). The Resource is a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia, set up in collaboration with the European Bioinformatics Institute (EMBL-EBI) to maximise Australia’s bioinformatics capability. It was with great pleasure that at the end of the year we announced the appointment of high-profile bioinformatician Assoc Prof Vicky Schneider to the newly created role as Deputy Director, EMBL-ABR.

As a further strategy to position Australia to benefit and contribute to international data conventions and initiatives, in late November/early December we were delighted to host Dr Niklas Blomberg, Director, ELIXIR, to discuss Australia’s participation in this important European data sharing initiative.

The team at VLSCI is a professional, committed, dedicated and resourceful one and I am pleased to be able to continue to work with them to build the necessary tools, platforms, infrastructure, collaborations and training resources which are contributing to Australian research excellence.

On behalf of all concerned with the governance, sustainability and the ongoing success of the VLSCI throughout 2015, I commend the 2015 VLSCI Annual Report to all.

Assoc Prof Andrew Lonie
Director, VLSCI and EMBL Australian Bioinformatics Resource

March 2016 update – welcome to our new staff and our visitors

There has been plenty of activity with the arrival of Assoc Prof Vicky Schneider, our new Deputy Director of the EMBL-Australian Bioinformatics Resource, and new team structures at VLSCI / EMBL-ABR. You may have heard that some of our existing staff are now in new roles, such as Dr Bernie Pope (Lead, Cancer and Clinical Genomics), Assoc Prof Torsten Seemann (Lead, Microbial Genomics), Dr Danny Park (Lead, Melbourne Bioinformatics Platform) and Dr Andrew Isaac (Lead, Computing Platforms). 

Please read on for a quick introduction to new staff members and visitors. Also below are a few details of some great upcoming events and jobs.

NEW STAFF

This week we welcomed Dr Philippa Griffin to EMBL-ABR.ClareSloggett Philippa is a specialist in bioinformatics for evolutionary genomics data processing and analysis and has experience in Open Data projects. At EMBL-ABR Philippa will be involved in training and education, publishing Australian data and bioinformatics resources, and more. Philippa will also be working with the Hoffmann Lab (Bio21 Institute) on two RADSeq projects: conservation genomics of the Mountain Pygmy Possum and Eastern Barred Bandicoot; and population genomics / data curation on the Aedes aegypti mosquito that transmits dengue fever.

Dr Anna Syme has also just joined the VLSCI team from the Royal Botanic Gardens Melbourne, bringing a breadth of experiences including authoring a number of field guides, including “Barnacles“. Anna will be working as a bioinformatician, joining another of this year’s recruits, Madison Flannery to work on the national BioPlatforms Australia Sepsis project. Madison’s experience combines a background in computer science with a MSci (Bioinformatics) and will work under the guidance of the project’s supervisor, Torsten Seemann.

VISITORS

VLSCI is currently hosting a visiting scholar, Ivo F.A.C. Fokkema, from Leiden University Medical Center, Netherlands. Ivo is working with VLSCI staff for 3 months on the Melbourne Genomics Health Alliance, Clinical Genomics, LOVD database development project.  

We also have Tom Connor from Cardiff University, Wales, UK with us this week. As a big user of the Genomics Virtual Lab and part of the UK’s Cloud Infrastructure for Microbial Bioinformatics project, he is here to work intensively with our staff on a GVL launcher for CLIMB.

TALKS / NETWORKING

COMBINE‘s first Melbourne seminar of 2016, “Bioinformatics in Australia: the pre-history to 1997”, will be presented by Professor Terry Speed. The talk will be at VLSCI, LAB-14 Seminar Space, 700 Swanston Street, Carlton, on Thursday 24 March 2016, 5pm – 6pm. Following the talk, the group will move to The Clyde Hotel (385 Cardigan St, Carlton) for light refreshments and networking. More information and RSVP here.

The upcoming Open Knowledge Human Genomics Meetup II will feature Professor Ingrid Winship talking about about how genetic conditions are screened, the process of identifying causal genetic variants, and how clinical genetic information is shared with patients and researchers. It will be at Thoughtworks Melbourne, Level 23, 303 Collins St, Melbourne on Wednesday 9 March 2016, 6pm. More information and RSVP here.

JOBS

We’ve added some information about a couple of jobs in the network: Proteomic Bioinformatician at Bio21 Institute and a PhD Scholarship for a Computational Chemist at UQ.

Announcing CloudBridge – making it even easier to do bioinformatics in the cloud

Australian bioinformaticians based at the VLSCI continue to contribute significant developments for the life sciences CloudBridgecomputing community around the world, funded by agencies in Australia and the US.

Just released this month is version one of CloudBridge, a Python library providing a simple layer of abstraction over different cloud providers, reducing or eliminating the need to write conditional code for each cloud. Developers include Nuwan Goonasekera and Andrew Lonie (VLSCI) with James Taylor and Enis Afgan (Johns Hopkins University, US), making CloudBridge a joint effort between the Galaxy and the Australian-made Genomics Virtual Laboratory (GVL) Projects. 

“The more we can remove the barriers to the tools of bioinformatics for all users across a range of platforms, the more time we can devote to life sciences data rather than complex programming tasks,“ says Assoc Prof Andrew Lonie, Director, VLSCI & the EMBL Australia Bioinformatics Resource. 

CloudBridge will now be part of the core cloud infrastructure for Galaxy on the Cloud and the GVL, which also uses Galaxy. Galaxy is an open source, web-based platform for data intensive biomedical research and is one of the major, mature platforms used by the bioinformatics community. CloudBridge is now being actively integrated into various components such as CloudLaunch and in future, CloudMan, which are already being used by the Galaxy community. 

CloudBridge is also generally applicable to other groups wishing to run cloud-independent applications and there is already support for Amazon and OpenStack clouds. Community feedback and contributions back into the project are welcome. Already Google engineers are investigating how the CloudBridge library may be used to help get Galaxy running on Google’s Compute Engine and it is hoped this will be supported in the next release.

For source code, design goals and a contributor’s guide, go to: github.com/gvlproject/cloudbridge.

For detailed usage and development documents, go to: cloudbridge.readthedocs.org/en/latest.

This work was supported by grants from Nectar and ANDS in Australia and the National Human Genome Research Institute, National Cancer Institute and the National Institutes of Health in the US. 

Intensive training in Cancer Genomics and the Genome Analysis Tool Kit in Melbourne

Two of the latest instalments of Bioplatforms Australia training workshops have been held in BPAworkshopMelbourne and Sydney in February. The GATK Best Practice course brought the Broad Institute’s Geraldine Van der Auwera to the University of New South Wales and the University of Melbourne. A new 3-day Cancer Genomics workshop was run in the Melbourne biomedical precinct, after its successful Canberra rollout in late 2015.

GATK, or the Genome Analysis Toolkit, is a widely used software package developed at the Broad Institute, USA, to perform variant discovery analysis on high-throughput sequencing data. The workshop provided an opportunity for participants from Brisbane, Canberra and Melbourne to learn directly from a GATK developer during the 2-day program of talks and hands-on labs. Staff from EMBL Australia Bioinformatics Resource (BRAEMBL) set up virtual machines equipped with an array of tools and software so the workshop would run smoothly on the Genomics Virtual Laboratory. The GVL instance proved to be a perfect way to streamline the training in a stable environment regardless of the location. A group of experienced bioinformaticians from around the country also attended the workshops and a supplemental training and content development event, including 3 BRAEMBL staff members who will lead future workshops around Australia.

This workshop was followed by a specialist Cancer Genomics workshop that was attended by 17 researchers already working in the field, many of them from Peter MacCallum Cancer Centre. In collaboration with EMBL-EBI, UK, the workshop was developed by experts from JCSMR, QIMR Berghnofer, BRAEMBL, CMRI, Garvan Institute and AGRF.

To assist with the inaugural workshop at the Australian National University in Canberra, Bioplatforms Australia brought in Mathieu Bourgey from McGill University and Genome Quebec. The workshop provides an introduction to cancer genomics analytical pipelines for single nucleotide variations (SNV), copy number variations (CNV) and structural variations (SV) using a mixture of lectures, hands-on practical sessions and open discussions, and will be run in other states in the future.

Further information about Bioplatforms Australia’s training activities

Report on Australian visit of Dr Niklas Blomberg, Director, ELIXIR

ELIXIR is EMBL-EBI’s initiative for data infrastructure for life science information. Director, Dr Niklas Blomberg, toured Australia in late 2015 as a guest of VLSCI / EMBL Australia*, with funding support from Bioplatforms Australia.

As he learned about the Australian life sciences data infrastructure landscape, Dr Blomberg was asked what data integration and distribution strategies he thought would be needed to support our biotech, agri-bio, education and medical research sectors in the future.

Dr Blomberg’s report on the Australian scene is available here.

ELIXIR originated in the EU in response to the growing realisation that to continue to deliver better health, social and economic innovations, just as roads and highways had done in the 1950’s, data highways are needed for the 2020’s. Some will enable free access, some will require ‘tolls’. Public and private initiatives both must play their part. It will be expensive and complex and require collaboration at local, national and international levels. Not doing so is not an option, individuals and industry now expect to access publicly-funded research data and the benefits and products to flow from data being shared around the world by way of medical and biotech advances.

At the conclusion of his tour, Dr Blomberg reported:

…those institutes I visited are well placed to serve the bioinformatics needs of local users. Furthermore, there exist many parallels with European data infrastructure efforts that could be leveraged for mutual benefit. Closer collaboration with ELIXIR should be encouraged with the long-term goal of membership in ELIXIR by Australia the most effective way of achieving this global cooperation.


*Dr Blomberg was hosted by Assoc Prof Andrew Lonie, Director, Victorian Life Sciences Computation Initiative (VLSCI) and the EMBL Australia Bioinformatics Resource. The tour included meetings in Brisbane, Melbourne, Sydney and Canberra. In Canberra the meeting also welcomed Dr Vivien Bonazzi, an Australian now working for the NIH-funded Big Data to Knowledge initiative in the USA. Earlier this week she was quoted on Nextgov on the roles for all in creating a data ‘Commons’.