Australian Ecosystems; HyperCard stack
It is estimated that over the 35 year life of Comalco's Weipa bauxite mine 2.6 to 4.7 million amphibians and reptiles (equivalent to 9.6-28.4 tonnes of biomass) have fallen into uncapped exploratory boreholes.
This is unpublished work presented and recorded in the 'Proceedings of the postgraduate conference of the Department of Zoology, James Cook University' in 1994.
You can get the PDF scan of the printed proceedings pages for free from my Products page.
The presentation was memorable as it was the first time a MacBook computer had been hooked up to a projector. At one point the cable fell out of the port and there was a collective gasp as I walked around and simply plugged it back in. Everyone (except me) was expecting the projector or the PC to blow up, which is what did tend to often happen in those early days of PC's.
It was also notable because I used HyperCard to create an animation of what was happening with fauna falling into the boreholes. Because of a default setting in the step where the reptile fell the computer emitted an unplanned sound like a squeal. The audience laughed, which was extremely rare, but it totally distracted me and so I forged on with the content. I worry it made me come across as humourless.
I got quoted in the paper ('The Age') whilst at the March for Science in Melbourne:
The precise text is:
Data scientist Alex Thomas, who was among the crowd, agrees.
"I'm here because I think we have to choose between stupidity and science," he said. "I think we're dealing with a very dangerous phenomena, that is the rejection of science. Although science isn't everything, it's the grounding and the underpinning of modern life and many of us wouldn't be here without it."
Won an award for (and presented) this paper at HIC2016 in Melbourne.
The award was the Branco Cesnick award for best student scientific/academic paper http://www.hisa.org.au/awards/.
The paper was also featured in Australian Policy Online http://apo.org.au/node/66780
This booklet is an illustrated key to the disappearing stream-dwelling frogs of the Wet Tropics Rainforests of Far North Queensland.
It is novel because it is printed on 100% waterproof paper, and because we got it sponsored by Freddo Frog (Cadbury Schweppes).
Turns out that printing it was a major challenge, because the ink would not dry enough in the printing press. This was a combination of the paper and the humidity of the tropics.
Profiled in the LaTrobe University Alumni magazine 'Gradvine' in 2005.
A couple of years ago I began a fantastic journey with Sea Shepard, and now with their permission I can tell the story of some of the things we have done to help bulletproof their shipboard IT.
In 2011 I read a great account of life on a campaign. Shortly after this I learnt that Sea Shepard were setting up their Southern Ocean Headquarters nearby in Williamstown, Australia, and I lived a mere 10 minutes away.
I did a weekend tour of the ships and as well as the mission I loved the energy, warmth and wildness of them and what they were doing. After considering various ways of getting involved I simply decided to take direct action.
I had in my shed a bunch of technical outdoor gear from my past life as a field ecologist that I realized I was never realistically going to use again. I loaded them in my car, drove down to the ships and donated it all. It turned out the waterproof cases were used to store the radios on the ships smaller rubber boats.
On a later visit I learnt that our tour guide - Rolf - was the ships Comms Officer. I had been doing some professional work with devices known as solid state disks. These replace hard disks and have no moving parts. Disk failure from vibration was a big problem on the ships, so as I was walking off the ship I asked Rolf if they could use solid-state drives.
Rolf was extremely enthusiastic, so we began systematically renovating all the hard disks. These devices work at lower temperatures, use less energy and are resilient to vibration.
It turned out their ship the MV Steve Irwin had a bunch of IT problems at the time. Among them was the state of the ship's IT infrastructure. As the other ships joined the fleet they typically had similar issues, and I got to work with the other Comms Officers, including Tim and Tux.
Most of the mobile phones were second-hand. The computers were ancient PC's. Laptops were rare and personally owned. Networking was primitive, unreliable and wires were actually sticky-taped together. There were no routers, switches or uninterruptible power supplies. PC's were operating as network servers. There was no wireless networking.
I made it my mission to fix that, and was blessed to have the support of an anonymous donor who after learning what I was doing financed pretty much whatever we asked for.
We made a running list (spawning the Amazon wish lists in use today), prioritised the items on it and just got on with doing whatever we could whilst the ships were in port. A slew of donations were made, including UPS's, networking hardware, cabling, a big bunch of slightly second-hand laptops with SSD's, iPods for social media posting and iPads for visitor email collection.
One outcome of which I am particularly proud is that media files are now transmitted wirelessly between ships, replacing dangerous small boat transfers of USB devices at sea.
I had the honour of having my photo taken in the Captains Chair of the Steve Irwin.
Thanks Sea Shepard.
Come on a virtual tour of a rainforest on the outskirts of Melbourne using a 360-degree panoramic video I took with my iPhone 4S and a GoPano Micro camera attachment. http://www.gopano.com/embed/MjIwMjE
The attachment had dust (or something) inside it which you can see in the video, but it gives a sense of descending into the interior of the rainforest.
Late last year I attended the YOW software developers conference here in Melbourne.
My takeaways include:
* AI 2.0 - Using principles of the brain to computationally detect anomalies. www.cept.at and numenta.org
* the movement to stream vs batch processing (exemplified by real-time music programming and algoraves, but things like StreamInsight)
* Polyglot data storage (Graph databases, MongoDB)
* Natural interfaces
* Agile coaching
What I laughed the most at were many precious moments in Scott Hanselman's keynote.
Unfortunately, I still don't know what problem Lambda's are meant to solve.
Thank you Dave Thomas (no relation) for bringing us YOW yet again.
Today the first live voice notification about a neighbourhood fire was sent via Meerkat.
Meerkat is a Node.js API with Twillio integration. You send the API a message and it fires a collection of calls to Twillio to ring the landlines of a collection of neighbours to tell them something (in this case a fire threat) is occurring. It sends notifications MUCH faster than formal alerts via the FireReady app, etc.
Being developed voluntarily with a work colleague who has a house in a fire-prone area.
More to follow ...
The Gertude Street Projection Festival 2013 is on between Friday 19th and 28th July 6pm - Midnight. It includes an installation at Rose Chong Costumes (disclaimer: family business) in which I used Ben Fry's Processing to project various fabric patterns onto clothes hanging out in the street, and a Freeduino to synchronise the lighting of corresponding buckets of fabric.
The projection uses an Apple Mac Mini running the visual art programming language Processing 2.0.0.
The display randomly selects from a pool of six JPG files that are scans of fabrics from the costume shop. The scans are significantly larger than the resolution of the projector, and are animated using an algorithm that slowly moves the image in a random direction until it hits the boundary of the file, then begins moving it randomly in another direction. It does this for a fixed period of time, then loops through with another unique image.
The fabric design imagery is projected against cutouts of garments suspended in a tree outside the shop window.
When the image changes it drives a custom Arduino-based lighting rig that illuminates a bucket of the corresponding fabric located in the front of the display.
The Arduino board is the Australian-made Freeduino (purchased from Jaycar), and some big white LED's, with plug-in leads and encased in a box.
There is more to the display than described, but the full description, code and photos will have to wait until the festival is launched.
I am the only known zoologist to have performed on stage and film with Nicole Kidman, whilst dressed as a camel. That's me who was dressed as a camel. Not Nicole Kidman.
I am also the only known certified SQL Server database administrator to appear on stage and film with Nicole Kidman.
OK. The story is that a very long time ago I was 'Assistant Stand-by Wardrobe' on the film 'Wills & Burke' (or as it was released in the US 'The Wacky world of Wills & Burke').
I was roped into being an extra, and had my moment-of fame as the lead actor was the proto-famous Nicole Kidman. As I was young and foolish I was indignant that as a crew member I had been roped into being an extra. In hindsight it was clearly my crowning professional achievement.
The two screenshots show 1) the credit, and 2) a still from the exact scene (albeit I am only shown from behind) and 3) a 14-sec clip from the movie.
The document was published using Adobe PageMaker on an 8MHz Macintosh SE with 4Mb RAM (I think) and a billion disk swaps (this was before affordable hard disks).
It was the first time the James Cook University printer had ever used waterproof paper, and the ambient humidity caused havoc as the pages didn't have time to dry as they came through the press.
I arranged sponsorship from Cadbury's, and the booklet was freely distributed.
I don't have any copies to distribute and doubt if any are available now other than possibly the James Cook University library.
I have made a donation to the open source GIS program QGIS. http://qgis.org/en/sponsorship/donors.html
GIS is a key enabler for understanding so much of our world and life, and I can distinctly recall my frustration in the late 90's when GIS investments were the only technology specifically excluded to community-based environment organisations. In fact, I threw the application booklet across the room at the time.
This is a more positive response.
It's specs are 2 CPU's at 8 Gflops each, 12Gb RAM and 287Gb RAID 5 storage.
To put this in perspective this post is being written on a machine with 1 CPU with 4 cores at about 20 Gflops each, 8Gb RAM and 600 Gb SSD storage.
Just saying ...
For the 2012 Gertrude Street Projection Festival I implemented an interactive SMS message wall. A cardboard tableau of a woman bathing in a bubble bath with a comic-style voice bubble provided the projection surface.
Solution implementation consisted of a low-end PC running Microsoft Windows 7, a UPS, a Telstra 3G USB modem, the iWall software and a projector plugged into a graphics card.
Messages logs in CSV text format were generated daily.
At the end of the festival the word cloud was visualized using the www.wordle.net website and rendered as a PDF - RCC_ProjFest2012_Wordle.
To achieve this the individual csv files were concatenated using a DOS command and cleansed using Excel 2010.
Cleansing was required to:
- Remove duplicates
- Remove surnames
- Remove phone numbers
- Remove system messages
A hard copy of the PDF was printed on A3 at OfficeWorks and framed for Rose.
This blog is for sharing my experiences as a bioinformatics practitioner. I'll be focusing on technologies such as databases, reporting services, statistical discovery, analytics and visualisation.