Hi BNC folks. I’m currently sitting in Los Angeles airport waiting to board a flight to Sydney in a few hours time — it’s my first time on the internet for a few days. It’s been a fabulous trip to the US, and I intend to post up a couple of ‘diary’ entries in which I detail my visit to California (including the eye-popping lab of Per Peterson at UC Berkeley) and my incredibly awesome visit to Argonne West at Idaho Falls, site of the EBR-I and EBR-II fast reactors and the fuel conditioning facility (with lots of photos, just to prove it!).
Two things to note for now, both on a non-nuclear front.
First, The 6-day intensive workshop in Chicago was terrific, and Corey Bradshaw has done a great job of describing its outcomes. Rather than re-hash this, I’ll quote Corey:
Last week I mentioned that a group of us from Australia were travelling to Chicago to work with Bob Lacy, Phil Miller, JP Pollak andResit Akcakaya to make some pretty exciting developments in next-generation conservation ecology and management software. Also attending were Barry Brook, our postdocs:Damien Fordham, Thomas Prowse and Mike Watts, our colleague (and former postdoc) Clive McMahon, and a student of Phil’s, Michelle Verant. At the closing of the week-long workshop, I thought I’d share my thoughts on how it all went.
In a word, it was ‘productive’. It’s not often that you can spend 1 week locked in a tiny room with 10 other geeks and produce so many good and state-of-the-art models, but we certainly achieved more than we had anticipated.
Let me explain in brief why it’s so exciting. First, I must say that even the semi-quantitative among you should be ready for the appearance of ‘Meta-Model Manager (MMM)’ in the coming months. This clever piece of software was devised by JP, Bob and Phil to make disparate models ‘talk’ to each other during a population projection run. We had dabbled with MMM a little last year, but its value really came to light this week.
We used MMM to combine several different models that individually fail to capture the full behaviour of a population. Most of you will be familiar with the individual-based population viability (PVA) software Vortex that allows relatively easy PVA model building and is particular useful for predicting extinction risk of small populations. What you most likely don’t know exists is what Phil, Bob and JP call Outbreak – an epidemiological modelling software based on the classic susceptible-exposed-infectious-recoveredframework. Outbreak is also an individual-based model that can talk directly to Vortex, but only through MMM.
I’ll use one example of our work to explain what happens. We are interested in understanding the dynamics of a disease like tuberculosis entering and spreading through the population of swamp buffalo in northern Australia (see previous post for all you need to know about swamp buffalo). We first set up an epidemiological model inOutbreak using some fairly well-quantified estimates of contact rate, transmission probability, latency period, and recovery of tuberculosis in cattle and other bovids on a daily time scale. We then built a annual-timescale demographic PVA in Vortex based on our measured estimates of mortality, fertility and sex ratio.
MMM then allows the two models to exchange information at the different time scales. The disease enters and spreads through the population following the daily dynamics, and then these outputs are read into Vortex at the end fo the year, modifying vital rates like survival and fertility according to each individual’s disease status. The population is projected one year forward, and the daily Outbreak dynamics are run again on the surviving individuals, and so on until the end of the projection interval.
Pretty bloody cool, no?
We then can test a couple of important management options should tuberculosis (or similar pathogen) ever re-enter the Australian population of buffalo. These include, what’s the probability of detecting the disease if present based on various sampling frequencies? How many animals must be culled to eradicate the disease? These questions will be answered for you in a few months once the paper is complete.
We also worked on another example to combine the cohort-based modelling software RAMAS with Vortex and Outbreak via MMM. The example included the complex interaction of black-footed ferrets, prairie dogs and plague determining the extinction risk of the ferrets. For the first time ever, RAMAS and Vortex are now working together. We also plan to bring climate-change projections into the combination in the near future.
We anticipate punching out over the next 12 months a heap of manuscripts explaining all this for your benefit, and we sincerely hope that MMM will grow into standard platform for combining disparate, but related population models for all sorts of conservation and disease-management applications. Stay tuned and I’ll keep you informed.
We worked pretty hard this week and rewarded ourselves with a little trip Friday night to Buddy Guy’s Legends blues club in the heart of Chicago. Fantastic music; I’ve never seen Clive happier (he’s a massive Blues Brothers fan).
Many thanks especially to Bob, Phil and the Chicago Zoological Society for hosting the workshop. We’ll return the favour next year in Adelaide.
Yesterday, thanks to the generous hospitality of Chuck Till, I spent a wonderful day touring Yellowstone National Park, followed by a drive by of the Grand Tetons (twice as high as Australia’s Snowy Mountains). It’s a truly amazing piece of the planet, and the weather was perfect blue skies all day. One for the memories. I saw elk, bison (hundreds) and all manner of birds and smaller mammals (no bears, alas). I’ve got a photo of me standing in front of an erupting ‘Old Faithful’, and other ones at bubbling (smelly) hot springs and glooping mud pools (including a cave called the ‘Dragon’s Mouth’), and the Yellowstone ‘Grand Canyon’ (very spectacular — see photo to the left). I’m just waiting for Tom Blees to send me his iPhone pics with me in it! I also played golf this morning in front of a bunch of spinning wind turbines that form part of the Bonneville Power authority (I shot a 95…).
So, I’ve covered 7 US states in the past 2 weeks (California, Illinois, Nevada, Idaho, Montana, Wyoming and Utah). It’s been quite a trip. However, no sooner will I get back to Australia on Sunday than I head out again to Shanghai, China, for the World Expo 2010, where I’m a plenary speaker at the ‘Australia — China Futures Dialogues: Achieving Sustainable Economic Development in the Asia Pacific’ (I’ll be talking about climate change, sustainability, and of course, nuclear power and other alternative energy sources). No rest for the wicked!