Blog Archives

Academic research and jailbreaking ereaders

29/2/2012

I've been fairly obsessed lately with finding the best way to read and annotate PDF journal articles. I didn't want to waste paper by printing them out, but I wanted to hand write notes on PDFs on screen.

I decided that the most economical solution was to buy a touch screen ereader. That way I could read and write on any PDF. My research (and I did a lot of it, trust me) lead me to the Sony PRS T1. I would have opted for a larger screen, but it was extremely difficult finding a device under $200 AUD that met my requirements (touch screen, PDF compatible, wi-fi, long battery life, lightweight) that was also available in Australia. And a tablet/iPad would have definitely been too heavy and too short battery life. Not to say that I'm disappointed with the purchase: but I would have preferred more options.

My preciousss... Jailbroken Sony Reader PRS T1, with an awesome custom cover from M-Edge

After buying my ereader, I discovered that it could not connect to eduroam wifi (used across a lot of university campuses, including UQ) and that annotations in PDFs were stored separately as image files! Fortunately, the solution to these problems was to jailbreak (hack) the reader to access the underlying Android operating system. Now I can use it like any other Android device, including installing Dropbox and reference manager apps!

I'm quite surprised that there isn't more call for academic-use ereaders: I came across innumerable questions and comments online about the lack of a specific device tailored for academia. But at least I have my, if somewhat roundabout, solution.

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Photoscan love hate relationship

22/2/2012

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Who thought 3D modelling could be so easy/hard?

I have had great success with Photoscan: I took a bunch of photos of a concretion containing a little bit of fossil bone, from all different angles, and uploaded them. The software aligned the photos based on common features, and created a 3D model!

You'll have to trust me when I say this is actually 3D, and not a totally boring rock

But the very next concretion I photographed isn't turning out so well: the software is having a harder time aligning the photos in their correct positions. And I'm still in the midst of figuring out why, but I have a couple of theories. As I am using a rotating stage to take the photographs, items in the background remain still. This didn't worry the photo alignment for the first concretion, but seems to be confusing it with the second concretion. My temporary solution? Covering the rotating stage with black card, and creating a black background.

At the end of it all, I hope to have all the concretions as 3D models, then I can fit them together to show how they form a large boulder. And inside hopefully lies a 90 million year old dinosaur fossil!

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I don't think the Vet Science department would like me very much...

20/2/2012

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I'm investigating ways to image an underwater decaying carcass, so I can observe the disarticulation of skeletal elements without all that dang goopy muscle and fatty tissue getting in the way.

At first I thought I'd look at underwater x-ray (minimal disturbance to the carcass), and it turns out the only people interested in this is the navy! Not for carcasses, but for examining sonar domes on ships without having to dry-dock (Greenawald et al., 1998). So it seems unlikely that this is a feasible option.

The Navy: bringing you over-sized x-ray equipment since 1998.

I've read a paper by Richter and Wuttke (2012) that dealt with this by removing carcasses from water and using a portable x-ray to image them. If I can't get my hands on a portable x-ray, then I might have to wheel my stinky carcasses over to Vet Science... should be interesting...

References
Greenawald, E. C., Poranski Jnr, C. F., Levenberry, L. J., Bellinger Jnr., E. T., 1998. Underwater x-ray tomography of composite sonar domes via collimated backscatter imaging. Proc. SPIE 3396, 121. http://dx.doi.org/10.1117/12.30151

Richter, A., Wuttke, M., 2012. Analysing the taphonomy of Mesozoic lizard aggregates from Uña (eastern Spain) by X-ray controlled decay experiments. Palaeobiodiversity and Palaeoenvironments, published online. http://dx.doi.org/10.1007/s12549-011-0065-1

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Do I love this person enough to stop partying with Jodie Foster?

20/2/2012

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Foggy.

14/2/2012

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I keep getting lost in all the things I need to do. It feels like a haze around my mind, where I try to grasp on to a memory or task I need to do, and it slips away and melts into the fog.

You are now entering the Caitlin Zone... cluttered, hazy, and just a little bit steampunk

I need to write down some clear and achievable tasks. There's numerous task managing software available, but it never seems to work as well for me as paper list, even sticky notes!

So today's task: create tasks. No, find a notebook, then create tasks. Where did I leave my notebook? (haze enters stage left...)

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I'm back!

14/2/2012

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It's amazing how lack of internet access (damn you iMac AirPort goblins!) has been crippling to my research this week. But at least now I'm back online, and back to answering life's big questions, like: can you x-ray through a body of water?

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Trying to find motivation...

9/2/2012

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I'm feeling very distracted today, and a little bit worn out. It could just be that I haven't eaten yet, or it could be indicative of something much worse (cue dramatic music)... the PhD honeymoon period is over! Noooo! I don't want it to be over!

Or, more likely, it may be that I'm not going to be 100% motivated 100% of the time. And that's ok, I think... in that it's realistically what's going to happen some of the time. This should be nicely countered by the days that I'm working 1000 miles per hour and want to stay back late into the night. Now if I could just have a few more of those days...

Image courtesy of cakepics.tumblr.com

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All the dino facts you'll ever need!

9/2/2012

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Well, almost. But this is a very interesting list of non-avian dinosaur facts compiled by The Paleobiology Database, such as formations with the most dinosaur occurrences, and species with the longest names... like Micropachycephalosaurus hongtuyanensis, and Caririchnium protohadrosaurichnos...

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ResearchGate, Academia.edu, LinkedIn, Mendeley?

8/2/2012

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I don't know about you, but I've signed up to a couple of networking websites and am wondering whether just to keep one, or all updated. I joined LinkedIn when I was working as an environmental scientist, and wanted to network with colleagues in the private sector. I then joined Academia.edu when I started my PhD, to follow the work of my academic colleagues. I've since discovered ResearchGate, which is supposed to be a better collaboration tool than Academia.edu. I also use Mendeley as my reference manager, and they have intergrated a social networking profile into their software too! But I can't decide whether it's a waste of time or not to maintain all these profiles! Do people normally have this many profiles? Is one really better than the other?

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