Life animated in 3D: Alzheimer’s disease and type 2 diabetes

Using 3-D modelling tools,  wee can look deeper into the causes of diseases like Alzheimer's and diabetes.

Using 3D modelling tools, we can look deeper into the causes of diseases like Alzheimer’s and type 2 diabetes. Here we have neurons with amyloid plaque attached.

By Emily Lehmann

Oscar hype is in full-swing, and we all have our favourites for Hollywood’s night of nights (we must admit we are partial to Birdman taking home the ‘best picture’ gong). But the big-screen isn’t the only place to find world-class movies.

At our Discovery Centre in Canberra yesterday, we unveiled two world-class movies of our own. The animations, created by up-and-coming Australian biomedical animators, uses the latest data visualisation techniques to bring science to life in incredible 3D detail.

An animated cross-section of the insulin receptor inside the cell membrane.

An animated cross-section of the insulin receptor inside the cell membrane.

Created by Australian up-and-coming biomedical animators using the latest data visualisation techniques, they feature key research into Alzheimer’s disease and type 2 diabetes from CSIRO and the Walter and Eliza Hall Institute of Medical Research (WEHI).

Through narrated picture, the animations explain very complex biological processes related to each disease with scientific accuracy: zooming in on what happens inside our body but can’t be seen with the naked eye.

The animations illustrate key research techniques into Alzheimer’s disease and type 2 diabetes, based on work we have done with the Walter and Eliza Hall Institute of Medical Research (WEHI).

Alzheimer’s Enigma

The first video looks at Alzheimer’s disease – the most common form of dementia – which affects one in four people over the age of 85, a number that will increase significantly as our population ages.

This animation takes you on a journey to the neurons of the human brain, revealing how normal protein breakdown processes become dysfunctional, and cause plaque to form during Alzheimer’s disease.

This build up of plaque in the brain can take decades and is one of the main indicators of the disease.

The Insulin Receptor and Type 2 Diabetes

About one million Australians currently live with diabetes and about 100,000 new diagnoses are made each year.

These staggering statistics are fuelling research efforts aimed at finding a cure or ways to prevent or better manage the disease.

Highlighting a recent discovery by WEHI, this animation focuses on the role that the insulin receptors play in the disease and what might cause resistance to the hormone insulin.

It’s part two in a series of animations on type 2 diabetes, you can check out part one here.

These are the second round of animations created through VizbiPlus – a joint project between CSIRO, WEHI and the Garvan Institute of Medical Research.

Under the guidance of internationally-acclaimed biomedical animator Drew Berry from WEHI, VizbiPlus is training-up the next generation of biomedical animators, to raise the bar in science communication and bring critical research to the world.

You can read more about our data visualisation work here.


Powerful new tool produces proteins in 3D

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The amazing depth of atomic-scale 3D structural information now available via Aquaria.

By Andrew Warren

If you’re a regular at the gym or an early morning boot-camp fanatic, it’s possible that the first thing you picture when you think of protein is the powder you use to make your post-workout recovery shake.

But when our scientists discuss protein, they’re talking about the many thousands of molecules that act as the essential building blocks of life as we know it. Because proteins are so important to constructing life, researchers need a way to visualise the exact ways in which they fit together so that they can better understand the functions they play in our bodies.

With this in mind, a team of international programmers and bioinformaticians (think biology, computer science and maths mixed together) led by our very own Dr Seán O’Donoghue have created a new web-based tool named Aquaria that can create unprecedented 3D representations of protein structures.

Aquaria is based on the Protein Data Bank, an online resource which houses more than 100,000 structures of proteins that contains a wealth of detail about the molecular processes of life. But Sean and his teams were conscious that few biologists were taking full advantage of the site. The Protein Data Bank is designed for and by biologists who are expert in structures; however for most biologists, its organisation can be confusing.

So, they created Aquaria to make this valuable information more accessible and easier to use for discovery purposes.

Freely and publicly accessible, Aquaria can help scientists like ecologists, nutritionists and agriculture, biosecurity and medical researchers to streamline their discovery process and gain new insight into protein structures.

Sean’s team added additional layers of information (like genetic differences) to the basic protein structure and made it accessible in a fast, easy-to-use interface that’s visualised in a fully 3D environment.

“We’ve added protein sequences that don’t yet have a structure, but are similar to something in the Protein Data Bank,” says Sean.

“That meant we first had to find all these similarities. We took over 500,000 protein sequences and compared every one of them with the 100,000 known protein structures, and that has given us around 46 million computer models.

ICAM-1 a

This image shows an example of one of the many spectacular molecular structures that science has determined at atomic resolution. This is the Aquaria view of Intercellular Adhesion Molecule 1, a protein that occurs on the surface of endothelial and immune system cells.

“For example, you can add Single Nucleotide Polymorphisms (SNPs) that cause protein changes, then visualise exactly where those changes occur in the protein structure. This provides valuable insight into why proteins sometimes completely change their function as a result of one small change in the DNA code.

“You can then ask interesting questions like ‘Does this set of SNPs cluster in 3D?’ and the answers to such questions can set new research directions.”

Aquaria was developed in collaboration with Dr Andrea Schafferhans from the Technical University of Munich, and is hosted with support of a grant from Amazon Web Services.

To learn more about Aquaria, you can take part in a special webinar scheduled for 9am Tuesday, 3 February (AEDST).


Protecting our privacy parts in the online identity crisis

The new face of online terrorism? PhotoCredit: Mamamia

Ever heard of the Lizard Squad? They’re an online group that’s claimed to have hacked some pretty large and well-known web identities in recent times. As well as attacks on the Sony, Microsoft and Facebook networks, they’re even alleged to have gained access to Taylor Swift’s Twitter account.

Surely that’s enough to get alarm bells ringing!? But in all seriousness, these sort of attacks are becoming a global concern as our interaction on all levels moves increasingly online. Keeping data private is of the utmost importance. That’s why we’ve been working with global software giant IBM and other partners through the AU2EU project to strengthen how we can protect our own data and improve collaboration in secure environments.

One of the technologies we’re using is IBM’s new Identity Mixer software. Identity Mixer uses cryptographic algorithms to encrypt profile information like age, nationality, personal address and credit card details. By keeping this data hidden from websites and only revealing the most relevant information, we get to hold onto our data, rather than constantly handing it over when we collaborate online.

Identity Mixer will allow our scientists to securely authenticate who they are, and share sensitive data with experts and our partners. For example, in the event that there is a biosecurity issue, it is imperative that this team can freely share data and collaborate with partners and other labs in instances when the lab is locked down, or if the threat requires a rapid response.

Identity Mixer will improve our ability to securely respond to these issues. This is all part of an emergency response plan we have developed with the Australian Government to maintain our agricultural disease free status. In order to deal with these threats it is important to bring together academic, government and research together swiftly and securely to deal with issues.

Adding another level of security, to ensure that this plan can be actioned, is a great outcome for our biosecurity teams.

Wouldn't it be nice to just press a button for Privacy?

Wouldn’t it be nice to just press a button for Privacy? Photo credit: Computeworld.com.au

Looking ahead, Identity Mixer could be really useful for the individual web user.  When we are exchanging information online, there is only certain data any websites or vendor really needs. Identity Mixer will only share the relevant data and keep the rest locked away – think of it like a sober friend stopping you from declaring your deepest feelings for a close friend, after you have had one to many bottles of wine.

It doesn’t matter who you are – from the single user, paying bills online to a massive multi-national corporations – securing data and protecting our privacy is vital. Especially when you have national treasures as important as our awesome database of insects – who else is going to protect the arthropods? Check out this video, which runs through some interesting scenarios to help you understand better how the technology works:


Meet the next generation of Aussie scientists and engineers

Jackson Huang and Dhruv  Verma are your 2015 BHP Billiton Science and Engineering Award winners.

Jackson Huang and Dhruv Verma are your 2015 BHP Billiton Science and Engineering Award winners.

UPDATE – WINNERS ANNOUNCED

A big congratulations to Dhruv Verma from Victoria and Jackson Huang from Queensland, the two winners of this year’s BHP Billiton Science and Engineering Awards. Dhruv was recognised for his PROTEGO project, and Jackson for his investigation into heartburn medication alternatives. You can more learn more about Dhruv, Jackson and the other finalists below.  

How much did you love your Bunsen burner time at school? Or were you more of an adoring-algebra type?

To us, nothing is more valuable and important than nurturing a love of science and technology in the next generation. This is why the BHP Billiton Science and Engineering Awards are such a terrific motivator for students looking to turn their great ideas into reality.

Taking a closer look at this years teen-scientists

Taking a closer look at this years teen-scientists

Silky Smooth

The honey bee doesn’t normally come to mind when you think about the production of silk. Interestingly honey bee silk has some amazing industrial uses, particularly in biomedical work.

Nick East, 15, from Canberra has discovered a way that honey bee silk can be purified and treated more cost-effectively than current methods. Honey bee silk can be used for replacing parts of the human body – from ligaments to supporting the immune system. Nick went even further to investigate how the honey bee silk protein could be used to deliver a controlled-release of drugs into the system.

Nick’s entry created a buzz in our team, as we’re no strangers to working with bees for science.

Katherine's project looks at improving building safety in cyclone-prone areas

Kimberley’s project looks at improving building safety in cyclone-prone areas

Raising the roof. And the bar.

Hailing from cyclone-prone northern Queensland, Kimberley Hardwick, 17, is in the running for the awards for her investigation into how different roof designs stand up in windy conditions.

Kimberley’s project isn’t a whole lot of bluster, in fact it stands up really well against the competition.

By looking into how roof features – such as pitch and surface area – would affect uplift during a cyclone, Kimberley was able to develop a series of recommendations to reduce the pressure placed on a house.

This entry has the potential to save money, houses and people’s lives.

The youngest finalist Dhruv, shows off his in-home sensors, PROTEGO

The youngest finalist Dhruv, shows off his in-home sensors, PROTEGO

Keeping a digital eye on the elderly

Our youngest entrant, Dhruv Verma, 14, from Victoria has won the Engineering category. Dhruv took out the top prize for his engineering project, PROTEGO, or PROactive Technology for Elderly on the GO.

Inspired by his great grandfather who lived independently into his nineties until he had a fall, Dhruv designed PROTEGO to help address the increasing strain on our aged care system by allowing elderly people to live independently in their own homes for longer.

Harnessing some clever technology, such as in-home sensors and real-time alerts sent to carers via their smartphones, this entry is all about using latest tech for social good.

If great minds think alike, then Dhruv is in good company – our scientists are trialling a similar system in Queensland.

The Winners. Jackson Huang and Dhruv Verma.

The Winners. Jackson Huang and Dhruv Verma.

Flipping the script on heartburn medication

In the ‘Investigations’ category our winner for 2015 is Jackson Huang, from Queensland. Inspired by research from the 80s, Jackson investigated why some additives in different heartburn medication were weakening its effectiveness. As well as finding out why this weakening occurred, Jackson has also been trialling an alternative additive.

To all the winners and finalists we wish you all the best for the coming years, and we look forward to working with you in the not too distant future.

The BHP Billiton Science and Engineering awards are a partnership between BHP Billiton, CSIRO and the Australian Science Teachers Association. They are sponsored by BHP Billiton and managed by CSIRO. The awards are also supported by the Intel Corporation.

The winners will be announced in Melbourne next week by Mr Bryan Quinn, Head of Group Technology and Geoscience and Engineering, CSIRO Board Member, Professor Tom Spurling and Australian Science Teachers Association President, Ms Robyn Aitken.


A different kind of show and tell

Science partnership between Marnie Sparrow from Sandringham College (Vic) and Felix Lipkin, CSIRO Land and Water Flagship

Science partnership between Marnie Sparrow from Sandringham College (Vic) and Felix Lipkin, CSIRO Land and Water Flagship

Imagine you’re back at school, and one day the teacher has something for show and tell. Someone, actually. A real live scientist, or mathematician, or ICT specialist. And not just the once.

It’s been happening regularly in Australian schools since 2007. All levels of schools, from kindy to Year 12. In the only program in the world of its size and scope, Scientists and Mathematicians in Schools (SMiS) puts practicing STEM (science, technology, engineering, mathematics) professionals into school classrooms. We also do the same thing with ICT professionals.

The program was a response to the decline in the numbers of students electing to study STEM subjects. It seemed that a promising strategy for arresting this would be to find a way for students to see the relevance of their science courses, and see that people working in science aren’t the caricature nerds represented in the media. But how to get them into the classroom? One way was to combine two kinds of outreach, and get involved with teachers’ professional development.

So we started a program to mentor teachers – and by doing so, provide students with a positive image of people working in the STEM sector. Seven years later, there have been more than 4000 partnerships between teachers and STEM professionals in schools. At the moment there are more than 1600 active partnerships.

It’s not just CSIRO scientists who are involved. Scientists in Schools volunteers can be research scientists and engineers, science and engineering postgrads, and applied science professionals like doctors, vets, and park rangers. Mathematicians in Schools wants to hear from anyone who did a degree with a maths focus and works in a job that uses maths: economists, accountants, surveyors and mathematical scientists, among others. If you’re an ICT professional working in research; a postgraduate ICT student or you’re involved in ICT in industry, like programmers, ICT security specialists, and systems analysts, you’re suitable for ICT in Schools.     Mathematician-microchip-focus-web

When teachers ask for a mentor to be paired with them, we select appropriate matches very carefully. We’re a bit like the Blood Bank: we have to find suitable partners for the procedure to be a success. And we don’t think any of our volunteers are the equivalent of Type O.

Teachers might be looking for someone with expertise in a particular topic. We also have to consider time constraints – some volunteers might only be available at particular times, and there are logistical considerations such as transport availability to take into account as well.

But this doesn’t mean that areas that aren’t readily accessible miss out. We can arrange long-distance partnerships too – Skype, email and block visits are our friends here. Some of the partnerships can be surprising – at present we have a scientist from the Australian Antarctic Division paired with a teacher in Townsville, based on common expertise and interests. And we cherish the pictures from a previous partnership between a teacher in a Northern Territory school and another Australian Antarctic Division scientist. When she visited the school, she took her polar suit with her, and the photos of her all rugged up in the NT heat just to show the kids are incongruous and charming.

It’s not all feel-good and cute pictures though. It provides a valuable resource for teachers, and gives them far greater confidence in their teaching. It enables the volunteer scientists to brush up on their communication skills – something which is ever more important in science careers. As one of our volunteer scientists from Tasmania says, ‘There is no room for jargon and big words when you talk to kids. I think it helps me understand better what I’m saying when I have to explain it in words an 8-year old can follow’. And our volunteers also say it re-enthuses them about their science – the kids’ enthusiasm reignites their own.

The students also get to practice some real science, and learn about experimental design, as this story shows. And yes, that’s a professor from the University of NSW mentoring a Year 7 teacher. An ACT school gets a Nobel Prize-winning physicist. CSIRO CEO Megan Clark was also a volunteer.

Maths partnership between Stephen Robey from Gungahlin College (ACT) and Billie Ganendran of University of NSW, Canberra (ADFA)

Maths partnership between Stephen Robey from Gungahlin College (ACT) and Billie Ganendran of University of NSW, Canberra (ADFA)

We see this combination of results as a win-win-win. And the three evaluations the program has had so far agreed with us. More importantly, so did parents, teachers and students. A parent from NSW says, ‘It’s fantastic that individuals are willing to offer their time to help facilitate the learning of our children. Please pass on a big thank you for being an inspiration for my son’.

While a teacher from SA tells us that ‘Our mathematician really is terrific in the way he volunteers his time to work with the kids. They love his knowledge, teaching skills and mathematical challenges’.

But this one … This comment, from a student in the NT, brings it all home: ‘The opportunity that we had to work with you was one of the greatest ones in my life. You made science fun for us and getting us involved in the science was a great experience’.

We think this is a pretty special program.


A new way to fix those frustrating websites

Some websites can drive you crazy. Flickr/Jonathan Brodsky , CC BY

Some websites can drive you crazy. Flickr/Jonathan Brodsky , CC BY

By Michael Kearney, CSIRO and Sarah Dods, CSIRO

How many times have you been looking for information online, only to find yourself going round and round in circles? Or you’ve spent too long poking around a website trying to find what you need, only to realise you’ve been looking in the wrong place all along?

Whether it is doing your banking, looking up details of a flight or checking out some government services – if a website doesn’t work the way we want it to, it can be very frustrating experience.

It might seem like a first-world problem but the reality is our expectations around service delivery are changing. More than three quarters of Australians prefer to access services electronically and we expect those services to be faster, adaptable and available whenever and wherever we desire.

This is why, more than ever before, service providers need to understand how people use their digital channels and make sure that their design is efficient, user-friendly and fit for the purpose.

Creating digital communities

It’s not only businesses that need to have a savvy online presence. Digital service delivery is increasingly relevant for the public sector. The Australian Public Service ICT strategy 2012 – 2015, states that digital technologies will be used to enable the delivery of better government services for the Australian people, communities and business.

Take the Australian Government’s Department of Human Services, which interacts with millions of Australians through services such as Medicare and Centrelink.

When managing payments worth more than a third of the federal government’s overall budget, small improvements to individual transactions can have a huge benefit. Customers being able to use self-service and online tools for some of their needs frees up valuable resources for cases where human interaction can make the most difference.

For the past five years CSIRO worked with the Department – under the Human Services Delivery Research Alliance which concluded in September – to develop a number of tools that are helping to transform service delivery for the digital era.

Connecting on social media

The Department is using our social media monitoring system, called Vizie, to support their social media management.

Vizie tracks, integrates and visualises information from a range of social media channels including Twitter, Facebook and Youtube, into a single, theme-based dashboard.

vizie

Vizie can generate streamgraph visualisations, like this one collected during CeBit. Using language processing and text analysis algorithms, it identifies what topics are being discussed in real time. CSIRO

Vizie can then help the department identify, from social media and in real time, when customers are experiencing problems using online and mobile services. This knowledge provides valuable feedback and supports quicker system responses.

As well as providing immediate insight into the major topics of the day, Vizie can also save organisations a lot of time that would otherwise be spent sifting through huge volumes of social media chatter.

More intuitive website experiences

The department is also using LATTE, a software platform that analyses the patterns in how people interact with websites.

It compares the sequence and duration of page visits to patterns that denote happy customers or user frustration through an inability to find the information they are looking for.

These patterns detect not only when, but where and why people encounter trouble with finding information, as well as the context of the session. It reveals insights into the organisation of pages and links, and the impact of word choice in search terms.

For example, LATTE might identify a pattern where users load four or five pages in succession before “abandoning ship” and jumping to a Google search instead. This indicates that they were not able to find what they were looking for within the website itself, either because it is hidden away or simply doesn’t exist.

The software can also identify problems with language usage, which can play a huge part in a website’s usability. This can often be the case when an organisation’s internal terminology or jargon doesn’t match up with everyday usage.

Internal search engines can also be a source of frustration if they don’t work effectively. LATTE can be used to identify patterns of user behaviour that show where searches are failing.

For example, users might conduct several searches, one after the other, still unable to find what they need. Or it might show that users have followed a link to a search result, only to then go round and round in circles.

LATTE identifies these mismatches between a user’s expectations of a website and the website itself – whether it be language, structure, the location of content or expected search terms.

By arming organisations with this information, they can make adjustments to the content, metadata and layout of their sites, in order to create a more user friendly and satisfying experience.

Protecting privacy and boosting productivity

While all this is happening behind the scenes, a user’s privacy is being protected. The software distills this data from standard log files captured on any web server, meaning there is no intrusive monitoring.

It’s the volume of data, not the identity of the user that’s important. LATTE reports data from aggregates of hundreds or thousands of visitors and identifies trends and patterns in behaviour that can inform decision making.

As the public sector seeks further efficiency dividends and people expect more from their digital services, government agencies are becoming more agile and responsive to change than ever before.

UK research shows that an online transaction costs a mere 1/100th of a face-to-face one so there’s clear savings to be made by agencies improving the online experience.

Perhaps one of the greatest impacts of the digital economy is that today almost anything can be measured – in fact we are drowning in data. So the old management adage “what gets measured gets managed” is turning inside out, to become “how do you measure to manage better?”

The challenge is identifying what data will be useful, and how it can be presented and managed itself to help improve a service to better meet customers’ needs without compromising their rights to privacy and informational security, and without overwhelming decision-makers.

Emerging technologies, such as LATTE and Vizie, are providing this evidence. The potential for these tools to be adopted by other organisations – both public and private – are almost limitless and we believe they are key to enabling services to be delivered faster and better in the digital age.

This will not only improve our productivity as a nation, but hopefully it will also eliminate those frustrating online experiences that leave you pounding the keyboard.

The Conversation

Michael Kearney works for CSIRO. CSIRO received funding from the Australian Government Department of Human Services under the Human Services Delivery Research Alliance. The software tools mentioned in this article were developed with support from the Alliance.

CSIRO received funding from the Department of Human Services under the Human Services Delivery Research Alliance. The Digital Economy Program receives funding from a range of government and industry partners. Sarah is also affiliated with the Australian Communication Consumer Action Network.

This article was originally published on The Conversation.
Read the original article.


Getting down and dirty with digital maps

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By Mikayla Keen and Claire Harris

Have you ever stopped to think about what’s under your feet, under our roads and under the wheat crops that produced the flour in your bread?

Soil features in every continent on the globe; it’s one of the fundamental building blocks of life. It’s pretty important stuff but we don’t often think about it.

But now, we’ve led a team of world experts digging deep, uncovering the secrets of soil and they’ve created the most comprehensive nation-wide digital map of Australia’s soils and landscapes. We worked with TERN (the Terrestrial Ecosystem Research Network), the University of Sydney and a number of state and federal government agencies.

And now, we present to you the Soil and Landscape Grid of Australia.

Using 3-dimensional spatial modelling, and combining rich historical data with new digital information gathered through technology like satellites and sensors in the laboratory, Australia’s best soil and landscape scientists have created new information and a very powerful tool.

The Grid itself is a marvel, representing the whole country as approximately 2 billion data pixels. That means each pixel is the snapshot of an area roughly the size of a football field (90 x 90 metres).  Every one of them contains information about the properties of the soil like pH, organic carbon and water capacity, down to a depth of 2 metres, and estimates of uncertainty (we couldn’t go out and sample the entire continent!). The Grid also contains details about the landscape, such as solar radiation and slope.

Red clay country in 3D

Red clay country in 3D

Not excited about the wonders of dirt? Then what about the science? The Grid uses exciting new infrared spectral methods to derive soil information rapidly and cheaply. It uses advanced spatial modelling that combines earth observation and satellite data to characterise and map the soil across the country.  And the technology? The Grid uses powerful computing clusters for computation for the modelling and to produce the maps. It uses smart computing to access the databases from state and territory departments, the University of Sydney and Geoscience Australia. During early user testing one person said, ‘Wow! I can get data in six minutes now instead of six months’. Before the Grid came along he would have had to gather the information from each of the different data systems. It wasn’t quite going door to door, but you get the picture.

Still not excited? How about some nifty data visualisation? The data can be viewed in a few different ways, for example, downloading it into Google Earth.

The Darling Downs as seen in the Grid

The Darling Downs as seen in the Grid

The best thing of all is that it’s freely available to everybody online.

For those keen beans like farmers, land managers, urban and regional planners and environmental scientists, who want to dig into the data, the files can be accessed through the Grid website in sections or the complete set is available through CSIRO’s Data Access Portal.

The data in the Grid can be sucked into a wide range of other databases and computer modelling programs and is useful to loads of different research projects. It is also part of Australia’s contribution to the GlobalSoilMap project.

For those who don’t want to get bogged down in the detail, check out our animation, which takes you on the journey of the Grid.

It’s been big collaborative effort with a large team  bringing together the best minds for the job. The Grid is ready and waiting for new data, some of which will no doubt come from technology that hasn’t even been invented yet (kangaroos with laser scanners on their heads anyone? Or is that TOO weird?)

For now, though, why not marvel at the beauty of the soil and landscape through the digital eyes of the Grid.


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