Thursday 21 July, 2011

Director’s update

Welcome to TERN’s July newsletter. As you can see from the contents of the newsletter our facilities are making significant progress on establishing operational infrastructure. However, we still have a lot of work to do in engaging with agencies that collect ecosystem data and providing suitable licences to enable TERN data sets to be collected and shared. We now have all of the contracts for the second set of TERN funding through the EIF Super Science funds in place. Based on this, our whole-of-TERN activities are picking up — the new website clearly shows this, as does the emerging content on the website of each TERN facility.

Having just settled in with all our funding and contracts, we will soon be thinking about requesting funds to sustain our activities beyond the June 2014 finish date as the Australian Government has released the final draft of the Roadmap for Australian Research Infrastructure to direct funding applications from 2013. The previous road map, which was released in 2008, set the direction for TERN and similar facilities. The revised road map is due to be released in September, and associated applications for funding are likely to be open in early 2012. TERN has had significant input to drafts of the road map since December 2010. It is clear the government has listened to our requests to sustain and build on existing investments, so I look forward to communicating our plans for engaging with the next round of funding in the latter half of 2011.

The finalisation of our next strategic plan, also expected in September, will play a key role in that process, as will our extended communication and engagement strategy to significantly improve the involvement of all of Australia’s ecosystem science and management communities in TERN and their use of TERN resources.

I’d like to leave you with a question I am repeatedly asked in TERN presentations, and in writing papers with colleagues about TERN’s approaches and a lot of our requests for funding and assistance. The question is: What is long-term research and research data?

How we answer this question and use it to seek support for sustained investment in the research infrastructure is critical, as most institutional and competitive funding for research runs for only two- to five-year periods. Long-term data collection and analysis vary depending on the organism, process and environment studied, and in ecosystem and ecological terms it seems to be at least ten years. This was one outcome of a paper collaboratively written by David Lindenmayer and a number of TERN participants (in review), and the discussion in reaching that point was highly beneficial. I would encourage other TERN facilities to look at publishing their approaches so we have international peer reviews of our work. Unfortunately, no funding programs currently work at these time scales, nor do they acknowledge data publication and citation as measures of research impact. These are two critical factors we are currently working on and need everybody’s assistance in addressing.

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Mapping the continent

The fragmented and often inaccessible nature of Australian data sets that interest the ecosystems research community, in particular those derived from satellite images, means that the understanding that can be gleaned from them has been piecemeal at best.

The AusCover team and facility, which provides a continental-scale collection of maps of biophysical parameters (e.g. vegetation structure) from satellite images, has begun the complex task of overseeing the compilation of past, present and future remote sensing data sets into a cohesive body of data.

As well as ensuring the data sets are spatially and temporally rich, the team is also making sure that they will be accessible. This will facilitate new research into applications of the data, especially in the calibration and validation of continental and global models requiring these data.

Importantly, it will also help inform decisions on how to manage ecosystems, from patch to continental scales.

AusCover will ultimately make the data sets and synthesized field data available 24 hours a day through a distributed data archive and access capability (DAAC) from the AusCover web portal and seven regional ‘nodes’.

It’s a big job to make data sets useful for Australian conditions, that at the same time contribute to parallel international programs that build our knowledge of changes to earth systems, for example by variations in climate, and how we might manage them.

The implementation of the AusCover facility is coordinated by the Marine and Atmospheric Research Division of CSIRO (CMAR) in the ACT. Having regional nodes allows the facility to make the most of local expertise, user-base and investment. The network will expand over the next three years.

AusCover facility director Dr Alex Held says that the state of remote sensing data in Australia is an expression of how the remote sensing community and key data sets have developed.

‘Remote sensing infrastructure and institutions around the country were set up, often independently, by research teams and government bodies, and were designed to serve unique science agendas or government programs,’ Alex said.

‘So they have gathered data in numerous ways to meet these different needs. This history is reflected in the differences in the geographically distributed infrastructure and protocols used to access the satellite data; the field equipment used to collect, collate and synthesise field calibration data; and the time scales and geographical ranges covered.’

It often lead to data collection being duplicated — locally, regionally, statewide and nationally. And this inconsistency sometimes hampered people conducting ecosystem research and those who used it for natural resource management.

It had served its original purposes well.

‘Now we want to take it to the next stage, to make it more accessible and to standardise it,’ Alex said.

‘Doing this will keep it relevant to scientific understanding of how ecosystems respond across the changing Australian environments, and how we respond to the ever-increasing need for evidence-based policy development and more accurately quantify impacts of government policies and initiatives.’

So that it can provide reliable data sets that are calibrated nationally and follow agreed international benchmarks, AusCover has begun a ‘land-product’ calibration validation program. It involves technical experts from all its regional nodes undertaking extensive field campaigns across a number of TERN Supersites and transects, and other dedicated AusCover sites.

Dr Tim Malthus, who leads the Environmental Earth Observation program at CSIRO Land and Water, said that the calibration and the validation of high-priority derived biophysical data products were central to the success of AusCover.

‘If we don’t know that our data-collecting equipment is calibrated properly, we can’t trust that the entire system, from the remote-sensing unit to a data product that someone downloads from the AusCover data portal,’ Tim said.

‘We have thus also begun a process of bringing our systems up to scratch with internationally agreed standards, and are collaborating closely with the Land Product Validation sub-team of the Working Group of Calibration and Validation (WGCV), which is part of the international Committee on Earth Observing Satellites (CEOS).’

As part of that, AusCover and some of its partners, the Bureau of Meteorology, the University of Queensland, Geoscience Australia, and the Space Policy Unit of the Department of Innovation, Industry, Science and Research, will be hosting the annual plenary meeting of the CEOS-WGCV in Brisbane early in 2012.

Drawing on these experiences and benchmarks, the team will publish an ‘AusCover Green Book’ on field-calibration methodologies and satellite product validation, to provide standardised guidelines for remote sensing scientists in other satellite-calibration programs.

Alex said that, with TERN Education Investment Fund (EIF) support, new nodes in Sydney and Adelaide would join the network. Nodes in Queensland/New South Wales, the Northern Territory, ACT, Victoria and Western Australia had begun providing derived biophysical and thematic data products at a range of resolutions, from a coarse spatial resolution of 1km pixels to a medium resolution of 30m, and even 2m resolution for key validation sites.

‘This fine resolution is for use in very high resolution data ecosystem characterisation and research on scaling information from ground to satellite,’ Alex said.

‘We will be using airborne remote sensors, novel ground instrumentation, and sensor networks to derive information on canopy structure and the “light climate” within canopies. These new datasets will be freely available via the AusCover data portal for use in innovative remote sensing research, habitat characterisation and ecosystem science.’

Under the TERN EIF, the AusCover team will also produce continental maps of broad ecosystem classes, their phenological stages and above-ground biomass, derived from integrating remote sensing data with other spatial and ground data sets. Production of these will be built on close collaborations between TERN, Geoscience Australia, ABARES and the federal Department of Sustainability, Environment, Water, Population and Culture, the custodians of some of the key input data sets and in-situ information used for the classification and validation part of these activities.

‘As the list of products is expanded, we will coordinate how data is collected, so that we acquire a comprehensive coverage for the entire Australian landmass,’ Alex said.

‘Part of this work means integrating our work with that of other TERN facilities such as OzFlux, Eco-informatics, Coastal and the Supersites part of the Multi-Scale Plot Network.’

Below: Dr Michael Schmidt, from the Queensland Department of Environment and Resource Management (DERM), at work at a groundcover sampling site in Queensland (Photo courtesy of DERM)

Bottom: Field team undertaking canopy lidar measurements with the Echidna system in south-eastern Australia (Photo courtesy of D. Culvenor, CSIRO)


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Website improves TERN communication

We are excited to announce that TERN has a new website. We hope that you find it easy to navigate to find the information you seek. As the various facility portals and the Terrestrial Ecosystem Research data portal come online you will see links to these resources added to the site.

The website was launched with a banner advertisement in ECOS online magazine. A current feature story in ECOS online, ‘Mapping the good earth’, is about GlobalSoilMap.net, an international project to produce the first detailed, three-dimensional digital map of the world’s soils, which is supported in the region by TERN.

Taking advantage of new technology, the artwork for the advertisement includes a QR code (abbreviation for Quick Response code) — a specific, two-dimensional matrix barcode that is used by dedicated barcode readers. Depending on the model of your ‘smart’ phone, a QR barcode reader is either supplied, or you can download a free app that will scan the QR code and automatically connect to the TERN website on your phone’s web browser. The TERN QR code will be included in all future TERN corporate print material. No more having to remember the URL!

We welcome feedback on what information you would find useful to have on the TERN website.

Our new website also includes links to the TERN Facebook page and the TERN LinkedIn group . Our Facebook page is being used to post information that might be interesting to the ecosystem science community but is not specific to TERN, for instance links to articles about plant DNA fingerprinting, or grants available for citizen science projects. If you ‘like’ the TERN Facebook page you will have new posts automatically sent to your Facebook wall or email address (or both).

TERN’s LinkedIn group has been established for networking, so it is only as valuable as the users make it. Join the group, post your question and let's start a discussion! Group members can also post information about jobs and promote events to others in the group.

Linking in
One person who has joined the TERN community through LinkedIn is Brad Evans, a PhD student at Murdoch University who is interested in how the community might leverage TERN infrastructure.

‘One way is to support and publish interface tools for efficiently analysing the large datasets,’ he said.

‘For example, python, C, matlab and R Scripts with vignettes on how to do common things like read, write, extract data from the formats and guides, [and] that outline known traps and best-practise tips for understanding the data.

‘I get the impression many in the TERN community are keen to see this. I think you have a great vehicle to drive this kind of innovation and help fast-track the end-use of the data at the same time.’

Join the discussion by becoming a member of the TERN group on LinkedIn.

Below: The home, or landing, page of TERN’s new website

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Big wet, then big fires

The recent continental soaking, long awaited, has put fire out of mind — but history and science show that such wets are reliably followed by big fire seasons.

This is one of the findings of a pyrogeography working group of fire ecologists that met early in July at ACEAS at the University of Queensland. The working group is one of several funded by ACEAS.

They are meeting to create the first continental classification of bushfire types. Scientists predict there will be changes in fire activity as a result of changes in climate and land uses across Australia, and the classification tool is the first step towards preparing for them.

One of the scientists in this group, Professor David Bowman, said that the popular belief that most fires occur on the urban fringes, where big, intense fires in recent years have gained notoriety, is wrong — most occur in the outback.

‘These outback fires are increasingly catastrophic and uncontrollable. It is imperative we understand the processes better,’ he said.

Two other ACEAS-funded working groups also met recently. The first group to receive ACEAS funding, which is investigating Australia’s ‘unenviable record of the highest rate of mammal extinctions in the world’, held it’s last meeting, at the Linnaeus Estate near Byron Bay. The data they are synthesising will be made public on the ACEAS website in late 2011. The group is planning to present its findings through an interactive mapping interface.

And the working group looking at mass extinctions of species met for the first time, also at the Linnaeus Estate. One of the workshop participants, Corey Bradshaw, talked about the workshop on his blog.

Between workshop sessions, another participant, Turkish scientist Cagan Sekercioglu conducted interviews for the forthcoming book Winged Sentinels: Birds and Climate Change that he is writing with Janice Wormworth.

The other members of this working group came from Australia, Singapore, Canada and Switzerland.

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Eco-informatics partners with Queensland government

Work on the Australian Ecological Knowledge and Observation System (ÆKOS) was boosted this month when Queensland’s Department of Environment and Resource Management (DERM) agreed to share full access to the CORVEG plot-based vegetation database.

The database will be loaded into ÆKOS and integrated with other vegetation data as a significant addition to the building of a national system. This will enable DERM and ÆKOS, which is being developed by the TERN Eco-informatics facility at the University of Adelaide, to develop a shared relationship and understanding before a long-term partnership is put in place.

Eco-informatics coordinator Craig Walker said support from state and territory governments was essential to ensure that data on Australia’s terrestrial ecosystems was available in a national facility and was coordinated and accessible.

‘We’re very excited to have this dataset because it is a substantial addition to ÆKOS, having information on the distribution of plant species for over 17,000 sites throughout Queensland,’ Craig said.

‘There’s a good chance that the way the information on plants has been collected for CORVEG will be different from the methods used for other plant datasets we’ve already modelled.

‘This will really test our existing data descriptions and the vocabularies that we use to enable researchers to find ecological data.’

Steven Howell, the Acting Director of Environmental Information Systems at DERM, said that Eco-informatics and the department were investigating a long-term partnership.

‘Although it’s early days in the development of the ÆKOS system, we can see there will be many benefits down the track to having a national facility like ÆKOS,’ Steven said.

‘To have access to all the ecological data for Australia’s terrestrial ecosystems in a “one stop shop” web portal will give our department’s data and its context widespread exposure in new ways. Our researchers will be able to assess the potential of ecological data collected by other researchers and most likely re-use it for new research without having to invest new funds to go and re-collect information.’

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New faces at TERN

ACEAS welcomes Dr Siddeswara Guru as the data integration and synthesis officer. Guru will work part of the time on data integration and data modelling for each of the ACEAS working groups. The rest of the time he will work on data integration and synthesis for TERN as a whole; this includes running the TERN Information Infrastructure Data Group (IIDG) and helping on the TERN Portal project. ACEAS Program Manager Alison Specht says he has already made a noticeable different to the facility’s capacity and expertise. You can contact Guru at s.guru@uq.edu.au and (07) 3346 3125.

Another Queensland appointment is Duncan Dickinson, who is the project manager of the TERN Portal, which is being administered by the Queensland Centre for Cyber Infrastructure. Duncan has a background in the design and development of repository systems, and has worked in the university sector for the past four years. The TERN Portal project is in the planning phase, and you're sure to hear a lot more about it over the coming months. You can contact Duncan on duncan@dickinson.name and 0432 402 511.

AusCover also welcomes two new people to the staff. Rowena Smith, who is the new AusCover and OzFlux project coordinator, brings with her more than 20 years’ experience in CSIRO. Rowena’s qualifications are in project management, and she was involved in the implementation stage of the Global Change and Terrestrial Ecosystems Project (IGBP) and transition to the highly successful Global Carbon Project. Rowena assists the Director, Alex Held, in the development of project budgets, contracts and development profiles for strategic directions. She also manages liaison between external collaborators and the AusCover central node. You can contact Rowena on rowena.smith@csiro.au and (02) 6246 5630.

Matt Paget has become AusCover’s data coordinator. He has worked with CSIRO Marine and Atmospheric Research for the past six years as a satellite remote sensing data manager and scientist. In this role, and in collaboration with Dr Edward King, he gained experience in managing large data sets and building operational systems for processing satellite data and associated web interfaces. Matt has been an AusCover and TERN team member since mid-2009. He has an active interest in the physical and environmental sciences, including significant contributions to continental water-balance modelling (AWAP) and evapotranspiration assessment (WIRADA). Before working at CSIRO, Matt studied the physical and dynamic properties of Antarctic sea ice at the University of Tasmania.

Below: Siddeswara Guru, left, and Duncan Dickinson, right

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ÆKOS platform built on nectar and cloud

The Eco-informatics facility has successfully applied for infrastructure support from the National Server Program (NSP) of the National eResearch and Collaboration Tools and Resources (NeCTAR) initiative.

This will provide the production platform for the Australian Ecological Knowledge and Observation System (ÆKOS) being built by Eco-informatics.

Eco-informatics coordinator Craig Walker said: ‘This is excellent news as it provides a secure and stable foundation for delivering ecological data of national importance via ÆKOS.

‘The facility had another coup during the month with a successful application to Amazon Web Services for credits to host development and testing environments of the ÆKOS system.’

‘This is equal to a whole year of hosting charges for internet storage using a cloud platform,’ Craig said.

NeCTAR is a commonwealth consortium lead by the University of Melbourne.

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Bush Blitz searches for unnamed wildlife

AusPlots-Rangelands is one of the forces behind the flushing out of some creatures not yet described by science.

This Terrestrial Ecosystem Research Network facility is a partner in Bush Blitz, a program that makes the most of government, corporate, not-for-profit and volunteer resources to document plants and animals in national reserves, which comprise more than 9,000 properties that cover 11.6% of the continent.

AusPlots-Rangelands’s involvement in Bush Blitz is part of its broader research agenda. It is establishing a national network of about 1,000 research sites in Australian rangelands and transitional landscapes to understand the baseline condition and stocks of ecosystems and set up a long-term monitoring program. As well as monitoring the state of health of vegetation and soils, it will also survey vascular flora and look for undescribed species.

The newest Bush Blitz survey is being carried out in the Pilbara. The program has budgeted for six major surveys a year, and each survey targets a group of reserves in a region. Each survey team includes up to 12 scientists, Earthwatch volunteers, and conservation staff in the relevant state and territory.

You can find out more about the program at the Bush Blitz website, including detailed reports.

Bush Blitz began in February last year, and is funded to continue for another 18 months. AusPlots-Rangelands was mentioned in an ABC story on the Pilbara blitz. Read more about AusPlots at its website.

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Biodiversity supported in carbon package

The measures to support biodiversity in the carbon package released recently by the Australian Government are a ‘pleasant surprise’ according to the Chair of the TERN Board, Andrew Campbell.

Although Andrew noted that the money would not stretch far and would have to be spent ‘very strategically’, he welcomed the government’s injection of almost $100 million in new funds, with $946 million for the proposed Biodiversity Fund and $44 million for Regional Natural Resource Management Planning for Climate Change Fund.

‘At face value, a package that encourages greater storage of carbon in Australian landscapes should be good for biodiversity conservation, and for soil health and water quality,’ he wrote.
You can read the full article at The Conversation.

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ARC funds extend TERN’s reach in South Australia

TERN has won Australian Research Council (ARC) Super Science funding to employ two scientists to progress research being coordinated by TERN.

They will be based in the School of Earth and Environmental Sciences at the University of Adelaide, where AusPlots-Rangelands and Eco-informatics are also based. Because of this relationship, the two scientists will be able to make use of and amplify the work of TERN.

The aim of the project is to assess, quickly and relatively cheaply, the diversity and uniqueness of South Australian biota. It will use a novel approach, to combine biodiversity assessment databases and state-of-the-art projection techniques to ascertain the most realistic future of Australia’s unique and highly threatened biodiversity.

One scientist will help develop modelling that improves our understanding of communities and ecosystems, and predicts how ecosystems are likely to respond to climate change. The modelling will also be used to inform those writing guidelines for landscape-level conservation and restoration, especially the design of refugia and corridors.

The other scientist will help develop a community phylogenetics framework for the South Australian flora to interpret the nature of processes involved, the make-up of ecological communities, and how diversity is maintained in the face of environmental change.

The positions are being advertised internationally.

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