When it comes to big data, the eyes really have it

Hungry microbiome

Hungry microbiome. Image by Christian Stolte and Christopher Hammang

Biological illustration has come on a bit from the days of Gould’s gorgeous illustrations of birds, or Leonardo’s Vitruvian Man. Today, with the help of big data and big graphics power, we can visualise things, not just at the molecular level, but at work.

But why – apart from because it’s beautiful and fascinating – do we do it? How is it helpful? What can it show us?

Obviously, we’ve been using rudimentary data visualisation for a very long time. Charts, maps, tables, graphs. All data visualisations, but not at the level we now find ourselves working at. As Sean O’Donoghue, from our Digital Productivity and Services Flagship, puts it, ‘Data visualisation is a new visual language; we need to become fluent in it to manage the complexity of computational biology’.

Let’s think about genomic data. The more we know, the more we need new tools to deal with the knowledge we have. And we now know a lot. We’ve got the ability to generate tremendous amounts of genomic data from sequencing. Analysing that data is now the roadblock to our being able to convert what we’ve found into something useable.

Visualisation of a genome

Everybody’s uniqueness. Image by Beat Wolf, Pierre Kuonen and Thomas Dandekar

Obviously, some genome analysis can be done using automated processes. But that still leaves a lot that depends on human judgement, particularly in the early stages such as hypothesis formation. Our concentration – and eyes – frankly aren’t up to spotting something different in a field of As, Cs, Gs and Ts (and nothing else), that seems to go on forever. Think of Where’s Wally?, in monochrome, with one Wally hidden on a single page hundreds of times larger than book pages. And then imagine that finding the Wally you’re looking for could make a big difference to people’s lives.

If we can combine visual and automated analysis, the pairing becomes more powerful. Users can user can seamlessly look at their data and perform computations on it, refining their analysis with each step.

Visualising also helps us reason about complex data. Sometimes, a well-chosen visualisation can make the solution to a complex problem immediately obvious. That’s because of the way that visual representations simultaneously engage the eyes and the memory. When we look at a visual, our eyes and our brain work in parallel to take in new information, and break it into small chunks. Then both the eyes and the brain process the bits in their different ways to extract meaning. It works like this.

You’ve gone to the supermarket – not your usual one – to buy bananas. When you walk in, your eyes scan the layout. At the same time, your brain is processing the various sections of the layout, and telling your eyes to home in on the fruit and veg section. It does this by sending signals from memory about how fruits look. Your eyes then break the entire scanned area into parts, then scan each part until they (all but instantly) recognise the veggie section. The same process is repeated until you spot the bananas in the fruits section. Your eyes and memory do their own things but work in parallel.

Protein folding visualisation

‘Folding beauty’ Image by Shareef Dabdoub and William Ray

We’ve used our brains to build tools that can help us discover more and more. But making sense of what they’ve found still depends on us and our limitations. Around half of the human brain is devoted – directly or indirectly – to vision. Visualising the vast streams of data lets us work with what we’ve got to make it something more than a hunt for a tiny needle in a monstrous haystack.

If you want to see more data visualisations, there are some beautiful ones at Vizbi.


Mission accomplished: lost bushwalker saved by flying robots

Outback_Joe_mannequinpicture-108

At long last, Outback Joe has been found.

By Emily Lehmann

Flying robot enthusiasts can breathe a deep sigh of relief, because Outback Joe has finally been saved after spending eight years lost in the bush.

This week, sixteen teams from around the world competed in the search and rescue mission to save our beloved Akubra-clad mannequin pal, who has year after year, been strategically placed in the Queensland outback as part of the Unmanned Aerial Vehicle (UAV) Challenge.

After eight years running, this was the first time that a team – not just one, but four– successfully delivered the emergency package to save Outback Joe, with the top team taking home a grand prize of $50 000.

Each team was tasked with developing their own custom-made UAV (a.k.a flying robot or drone) and navigating it through a course to first locate Outback Joe, and then secondly deliver him a life-saving bottle of water.

The competition brings some of the latest international aerial robotics technology and puts it to the test to highlight its value for use in search and rescue efforts.

These flying machines can cruise at various speeds – some are just like helicopters – and can mostly fly for 40 to 60 minutes at a time. They rely on modern computers and sensors, such as GPS, to figure out where they need to go in order to perform tasks that the operator has asked it to do.

The clever minds behind the winning ‘bot are from CanberraUAV and managed to score the most points out those that completed the challenge – two other Australian teams and one from the United States.

The winning CanberraUAV  team

The winning CanberraUAV team

The UAV Challenge also involves a delivery challenge for high school teams, taking place earlier in the week. Students build their flying robots from scratch, designing and developing the software and hardware needed for their own rescue mission for Outback Joe.

This year’s winner was the all-girl DareDivas team from Mueller College at Redcliffe with a $5 000 prize.

We run the UAV Challenge annually in partnership with the Queensland University of Technology.

One of the UAVs at the challenge (MelAvio)

One of the UAVs at the challenge (MelAvio)


Bees backpacking in Brazil

Bee with a backpack...of the sensor variety.

Bee with a backpack…of the sensor variety.

By Emma Pyers

How do bees in the Amazon jungle compare to those in Tasmania? They get up earlier, for a start.

Paulo de Souza and his team have been tracking bees in the two regions using tiny backpack sensors as part of our Swarm Sensing Project to gather biological and ecological data to improve honey bee health.

The tiny backpacks are just a quarter of a centimetre square and are fitted to the back of the bees.

“We have already attached the micro-sensors to the backs of thousands of bees in Tasmania and the Amazon and we’re using the same surveillance technologies to monitor what each bee is doing, giving us a new view on bees and how they interact with their environment,” Paulo said.

Graph: Daily distribution of bees in Brazil and Tasmania

Daily distribution of bees in Brazil and Tasmania (click for large version)

“Once we have captured this information, we’ll be able to model it. This will help us understand how to manage our landscapes in order to benefit insects like bees, as they play such a key role in our lives. For example, one third of the food we eat relies on bees for pollination, that’s a pretty generous free service these humble insects provide us!”

Early modelling has shown one notable difference between the bees in Tasmania and those in the Amazon; Amazon bees are up and about very early in the morning while Tassie bees prefer to wait until the day warms up before they leave the hive.

But finding out what time bees get out of bed is only a tiny part of what the research can show us. For example the research will also look at the impacts of agricultural pesticides on honey bees by monitoring insects that feed at sites with trace amounts of commonly used chemicals.


A global buzz in micro sensing

We’re working with the Vale Institute of Technology in Rio de Janeiro, Brazil, on micro-sensory technology and systems (read  more about what Vale is up to here).

Working with researchers across the globe has its unique challenges as well as its rewards, and it’s the physical challenges that have been the most interesting.

“As the Africanised honey bees were very aggressive, the hive was placed in an isolated area away from housing and domestic animals – and isolation meant working in densely vegetated areas,” Paulo explained.  “We had to clear a path to the hive and we wore fully protective bee clothing which was tough given the extreme humidity and heat.”

The Brazilian media got a taste of what it was like to work in these conditions, when they suited up to interview Paulo and our colleagues from the Vale Institute of Technology about their work

Pressure from the press

Pressure from the press

The collapse in global populations

Bee health is important globally however, honey bee populations around the world are in danger.

Colony Collapse Disorder (CCD) – a phenomenon in which worker bees from a colony abruptly disappear – and Varroa mite are two major problems facing bee populations globally. While these two problems haven’t appeared in Australia, there is a very real risk.  And what happens if it does? Catastrophe!

Check out this video where Peter Norris, Tasmanian beekeeper, describes his first hand experience with CCD while working in the United Kingdom.

So it’s a good thing our scientists, and their colleagues in Tassie and Brazil, are on the case.

To learn more about how we’re trying to save honey bees around the world tune into ABC Catalyst at 8pm tonight.

CSIRO’s Swarm Sensing Project is a partnership with the University of Tasmania and receives funding from Vale, a Global mining company.


Historic collections could be lost to ‘digital dinosaurs’

An image of Australian shearers taken on glass plate negative is now preserved in a digital collection. Powerhouse Museum Collection/Flickr

An image of Australian shearers taken on glass plate negative is now preserved in a digital collection. Powerhouse Museum Collection/Flickr

By Michael Brünig, CSIRO

Australian’s museums, galleries and other cultural institutions must adopt more of a digital strategy with their collections if they are to remain relevant with audiences.

Only about a quarter of the collections held by the sector have been digitised so far and a study out today says more needs to be done to protect and preserve the material, and make it available to people online.

Challenges and Opportunities for Australia’s Galleries, Libraries, Archives and Museums is a joint study by CSIRO and the Smart Services CRC.

It notes that Australia’s galleries, libraries, archives and museums (the GLAM sector) represent our accumulated achievements and experiences, inspire creativity and provide a place for us to connect with our heritage.

They are also crucial to our economy with the GLAM sector estimated to have a revenue of about A$2.5 billion each year. That’s not only a lot of paintings and artifacts, but a lot of jobs as well.

But despite its size and scope, we found that digital innovation in the sector has been inconsistent and isolated. If these cultural institutions don’t increase their use of digital technologies and services, they risk losing their relevance.

So what changes do they need to make in order to thrive in the digital economy?

Opening doors and minds

With Australia’s rapid uptake of online and mobile platforms, people are now choosing to access and share information in very different ways.

It’s safe to say that the only constant in this space is change. Research suggests that expectations for more personalised, better and faster services and more well-designed experiences will continue to increase.

Virtual tours are now possible at the National Museum of Australia.

Virtual tours are now possible at the National Museum of Australia.

This is why our cultural institutions need to review the kind of visitor experience they are providing. We found only a few organisations had made fundamental changes to their operations that would allow them to place digital services at their core, rather than as an add-on activity.

This is in contrast to the dramatic changes we’ve seen when it comes to adopting digital technologies in our daily lives.

In order to be successful, digital experiences need to be an integrated and cohesive part of an institution’s offering.

Take what is happening at the National Museum of Australia. It’s now possible to take a tour of the museum via a telepresence-enabled robot.

This means school students – particularly those in rural and regional Australia – can explore exhibits virtually, without even leaving the classroom. Interestingly, we hear that this actually increases their desire to visit the museum in person.

Digital-savvy innovations such as this need to be at the fore of our institutions’ thinking if they want to engage with the community and break down barriers to participation.

Engaging with the public

To be successful in this new era, institutions need to meet people on their own (digital) terms. We can no longer expect visitors to queue at the turnstiles waiting for opening time. Organisations need to bring experiences to the user so that they can access them wherever and however they prefer.

Some of Australia’s cultural institutions are starting to get this.

Another image available freely online as part of the Powerhouse Museum Collection. Powerhouse Museum/Flickr

Another image available freely online as part of the Powerhouse Museum Collection. Powerhouse Museum/Flickr

The NSW State Library has appointed a Wikipedian-In-Residence to contribute expertise and train the public in publishing information online.

The National Library of Australia has attracted a large online user base with its online Trove service attracting almost 70,000 unique users each day.

The Powerhouse Museum has made parts of their photographic collections available on Flickr via Creative Commons licensing. This has caused a surge in the level of use and allowed the public to contribute information, adding value to the collection.

While these examples provide a lot of hope for the sector, the unfortunate reality is that they are few and far between. Most of Australia’s cultural institutions have not kept pace with this change and are missing the opportunity to better connect and actually increase their revenue.

Digitise this!

Australia’s eight national, state and territory art organisations hold archives that, if laid out flat end-to-end, would span 629km. This is on top of a staggering 100,000 million artworks, books and audio-visual items in Australia.

But only a quarter of these items are digitised, with some of Australia’s collections still being managed through “old school” mechanisms such as log books and card indices.

Imagine if there was a fire at one of our great institutions? We would risk losing cultural and heritage material of significance. Parts of our history could be completely lost. Even without such a devastating event, if we don’t make our collections more accessible, in a sense they’ll be lost to many of us anyway.

As a country, not only do we need to get moving when it comes to digitising our collections, we also need to explore new and innovative ways to do this. Traditionally, digitisation has meant scanning flat documents, photographing objects or creating electronic versions of catalogue data.

But what if we could do so much more? Researchers are now focused on the next challenge: digitising objects and spaces in three dimensions.

Researchers from the University of Wollongong with support from the Smart Services CRC are focusing on capturing 3D models and the textures of surfaces using low-cost equipment such as a Kinect camera from an Xbox.

3D map of The Shrine of Remembrance, Melbourne

3D map of The Shrine of Remembrance, Melbourne

At CSIRO, we’ve even used our own handheld scanner Zebedee to map culturally and environmentally significant sites suchb as the Jenolan Caves, Melbourne’s Shrine of Remembrance and even a semi-submerged wreckage of the HMQS Gayundah.

We’re also creating high-quality 2D and 3D image libraries based on the National Biological Collections, letting us document biodiversity in the digital era.

Embracing the digital economy

While our study reveals that Australia’s cultural institutions are certainly at risk of becoming “digital dinosaurs”, it also demonstrated how those organisations that are embracing digital are reaping the benefits.

It provides recommendations for the GLAM industry in order for it to maximise its digital potential, including:

  • shifting to open access models and greater collaboration with the public
  • exploring new approaches to copyright management that stimulate creativity and support creators
  • building on aggregation initiatives such as the Atlas of Living Australia
  • standardising preservation of “born digital” material to avoid losing access to digital heritage
  • exploiting the potential of Australia’s Academic and Research Network (AARNet) and the National Broadband Network (NBN) for collection and collaboration.

By adopting these recommendations and building on some innovative examples in the sector, Australia’s GLAM industry will be well placed to embrace digital, rather than be engulfed by it.

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


Kids raid caves in virtual classroom

Remember when going on a school excursion meant a trip to the bowling alley? Or, for a really special occasion, perhaps a visit to the local fun park?

Well, things have certainly changed since I was at school.

Today, we’re launching what could be Australia’s biggest (and arguably coolest) school excursion ever. In classrooms around the country, students will set out to explore the spectacular Jenolan caves located in the scenic Blue Mountains.

How will this be possible? They’ll be embarking on their journey in virtual reality. 

Real-science-from-caves-to-the-classroom-B

To create this digital experience, we teamed up with 3P Learning to combine their latest educational resource, IntoScience, with HD panoramic video and 3D models of the Jenolan Caves scanned using our (ahem, award winning), laser mapping technology, Zebedee.

Using their own avatars, students from years 6 to 9 will be able to delve into the natural wonder of the caves, all without leaving the classroom. The Jenolan caves are Australia’s largest and, with elaborate underground structures, offer a rich scientific environment full of learning opportunities.

“It’s exciting to see our cave models now brought to life as a virtual world that students can explore and perform their own scientific investigations in,” said Michael Bruenig from our Digital Productivity and Services Flagship.

Zebedee is the first technology capable of mapping caves with lasers while continuously moving, meaning the 3D models it creates are incredibly detailed and can be produced in only the time it takes to walk (or climb or crawl) through a cave.

The technology is already well-known for mapping other iconic landmarks such as the Melbourne Shrine of Remembrance, Queensland’s Fort Lytton, and a little structure you might have heard of known as the Leaning Tower of Pisa  Oh yes, and there was a Boeing 727 too.

So, as much as I enjoyed my school field trips (complete with packed lunch and walkman), I can’t help but feel a teensy bit jealous of today’s students. First stop is the Jenolan Caves, but what’s next? The possibilities are endless. Check it out in this video:

This online 3D educational initiative, funded by the Australian Government, will be officially launched today by the Minister for Communication, Malcolm Turnbull.

 


Keeping us connected – wirelessly

By Nola Wilkinson

Dr Iain Collings decided early in his career that wireless communications was hot. Fascinated by the prospect of transferring information without wires or optic cables, he saw its huge potential to change our daily lives – and wanted to be a part of it.

The whole world is into cool electronic devices. Our growing appetite for smartphones, iPads, GoPros and FitBits has produced a huge new market – and wireless data transfer is essential for these devices.

What’s more, the more we use them, the faster our demand for higher rates of data transmission grows. Iain has focused his work on the use of multiple antennae to vastly improve the rate of transmission of data wirelessly. As he points out, this is fundamental to meeting the ever-growing global consumer demand. Watch this video to find out more.


Five uses for WiFi even we didn’t see coming

CSIRO_Wifi_highres-01-01 Remember the internet of the 90s? When browsing online meant being stuck at your desk with your whiz-bang 56k modem. It was an era without smartphones, without tablets – some might say, without freedom.

Luckily the clever folks in our labs came up with the underlying technology behind a little something called WiFi using the same mathematics that astronomers initially applied to piece together the waves from black holes (for more on the WiFI story click on our handy infographic on the right).

While WiFi has given us the freedom to work wirelessly in our homes, offices and out-and-about, it has also inspired a few other – err, interesting – innovations. Here’s a few that even we didn’t see coming:

  1. No more queuing for beer at the footy – thanks to a digital upgrade at Adelaide Oval, sports fans won’t even have to get out of their seats to order a drink. Or hot chips.
  2. Keeping Rover happy – this WiFi enabled system is a fully autonomous robotic dog sitter complete with video conferencing capabilities, remote tug-o-war, ball fetch mechanism, and treat dispenser.
  3. The humble bathroom scale has taken a leap forward – why waste energy (and calories) having to get up to manually record your weight when your wireless bathroom scale can do it for you?
  4. Did someone say bionic butler? For a couple of hundred thou’, this guy will get you a drink and even flip your pancakes.
  5. Yep, it’s a WiFi rabbit. We’re sure he’s useful in some way. We just can’t figure out what it is yet.

Find out more about how we invented and patented wireless LAN technology on our website.


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