I use Mendeley as my reference manager, and will sing its praises to anyone I meet asking what citation software they should use for writing research manuscripts. It's super easy to import article PDFs into your virtual library, ask it to 'watch folders' for new PDFs you've downloaded, has a pretty good stab at labelling articles in your library by looking at the metadata, and cites-while-you-write with its MS Word plug-in.

​You can even highlight passages and jot down notes within each PDF in the form of floating sticky notes, called 'annotations'.

​​But I wish that those annotations were more accessible in their own right.

You might, for example, read a paper in Mendeley about the taphonomy of mammal carcasses. There's an interesting line about teeth: that while they are more resistant to weathering than bones, they can still crack and split in hot and dry environments. You highlight this sentence and add an annotation with your thoughts. 

But how do you find that annotation at a later date? Until you read that paper again, you might not remember that it even exists.

Mendeley does not allow you to view all annotations you've ever created, or even indicate which PDFs either do or don't have annotations. If you remember reading something interesting and writing something about it, you better hope that you remember what you wrote, as you can find annotations by searching for key words within them. And if you're like me and just want to review your past notes, good luck trying to remember all the papers you've added annotations to over the last 6 months.

​There are, of course, work-arounds for this: you could tag all papers you add annotations to with a key word such as 'Annotations' or mark each paper with the 'favourite' star symbol, but this relies on you never forgetting to include this step.

You could copy the contents of each annotation in to an Excel spreadsheet or mind map, and group them by theme. That way you can review your database or mindmap and find your way back to the original paper. But this feels like double handling - why not just write the annotation in the mind map in the first place? What I would LOVE is a mind-mapping tool within Mendeley, where you could click and drag annotations on to nodes/branches, but I realise this could be nightmarish to code and implement.

I can't say I've come up with a solid solution for this problem yet. Has anyone else figured out a better annotation workflow for Mendeley, or do you use other software and reference manager combinations to keep track of your research notes?

Podcasts are a wonderful beast. Apple have yet to monopolise the platform, allowing many wonderful shows to be distributed through iTunes as well as private websites for free.

And have I only just discovered this?

... maybe. But I'll make up for living under a rock, for I hereby present to you: two awesome palaeontology themed podcasts, Past Time and Palaeocast.

Past Time is hosted by Adam Pritchard and Matt Borths, two graduate students from Stony Brook University, New York. Topics cover vertebrate palaeontology theory and recent fossil discoveries, from mammals to dinosaurs, crocodiles to birds. If you've wanted to brush up on evolutionary theory, this is the place to come.

I especially appreciate the effort made with editing: sound bites from interviewees are spliced with clarifications from the hosts (similar in style to Radiolab, an amazing science and philosophy podcast - check it out!) and ambient sound effects. Sometimes quite distracting sound effects, but still useful in creating the right atmosphere.

The banter between the hosts is also enjoyable to listen to. It's like you're part of a conversation, where sometimes one host will play the "devil's advocate", and the other will spend time explaining the evidence behind their position.

Hosted by Dave Marshall (Marshall Biostratigraphic) and Joe Keating (The University of Bristol), Palaeocast covers a broad range of topics including palaeobotany, and invertebrate and vertebrate palaeontology.

Palaeocast follows a one-on-one interview style format, where you feel like you're in the room listening to the interviewer and interviewee converse live (think Inside the Actor's Studio or The 7.30 Report). It's the closest you can come to speaking directly to the experts themselves, and it's quite nice to hear the interviewees wax lyrical about their subject matter. They clearly love what they do!

They have also recorded podcasts from palaeontology conferences (including the 2013 Society of Vertebrate Palaeontology and the 2013 Geological Society of America Annual Meeting) including interviews from attendees presenting new palaeontological research. For those of us who have either not enough time or money to attend these conference, and would otherwise miss out on all the cool palaeo-goss, we salute you.

Both Past Time and Palaeocast supplement their podcasts with online material, including images, videos, and summary blog posts. I think both palaeontology enthusiasts and professionals can gain a lot from both these shows. Saying, "I'm a palaeontologist" often leaves you open to any question about any fossil spanning THE ENTIRE HISTORY OF THE EARTH. These are two excellent podcasts for increasing your general knowledge, and more importantly, keeping up the all-seeing, all-knowing palaeo persona.

So let me know: do you listen to these podcasts? What do you think of them? And are there any other palaeontology podcasts out there I've missed?

Ever wanted to sit in a café to write your journal paper, but think that it'll be too distracting, and you don’t want to look like a pretentious wannabe best-selling writer? Well, it turns out that (a) listening to ambient noise helps the creative process and can boost concentration, and (b) you’re now realising that maybe those wannabe writers aren’t trying to show off their mad writing skillz (yo) in public, but they’ve already cottoned on to the powers of ambient noise. So the joke’s on you!

Alright, maybe you weren’t prejudiced like I was, but at the same time maybe you can’t spend all day in a cute café tapping away on your laptop. What to do?

I came across some solutions via a tweet on the #phdchat forums linking to this article on free ambient noise apps. You can look up these websites and listen to a virtual café for free! Or listen to music, or even white noise! Here’s a mini summary of the most popular sites:

And then there’s OmmWriter Dana (version 1 - free, and version 2 - $4.11), which is actually a minimalistic desktop word processor and an ambient noise generator. This program opens at full screen with the aim of minimal distraction from other programs. Dana 1, the free version, comes with 3 music tracks (one of which is the noise of a train carriage), three keyboard stroke sounds (like ye old typewriter), and four background wallpaper designs. And although I haven’t used it to write any scientific papers (because it doesn’t support cite-while-you-write plugins) it was very relaxing for writing this blog post!

A word to the wise: while I’d really love an app that played typewriter sounds as I tap away in MS Word or while writing emails, you have to be wary about what you download. Some keyboard sound programs/apps can secretly use keystroke logging to constantly record what key you’re pressing, whether you’re writing a private email or typing your banking password.

Need more proof that you should keep your work on a cloud based server (such as Dropbox), aside from the, "Your computer could suffer indoor rain", or , "Your office might get flooded"?

It's very useful for when you leave your house keys, public transport card, and office keys in your backpack, which you left in your partner's car, who has driven said car to his/her work. And you can't lock the house door without a key. And you need to take a bus. AND you need to access your office. So, guess what? You're working from home today, and you better hope you can remotely access all your documents!

I use Dropbox, but there are other cloud storage services out there. If you need more than the 2GB free storage space that Dropbox offers, then Mediafire and Mega look promising. Although the free accounts they offer cap the upload file size at 200 MB and 300 MB respectively.

Not enough room in your tiny office for a cork board, let alone a PhD-sized cork board, to plan your writing and group random thoughts? Want a 'murder board' ala Castle, but don't have a bedroom window to reappropriate?

Don't despair! The solution is simple: use a virtual cork board.

Scrivener (a drafting tool I use to write my papers) has a built-in cork board view, where you can see what you've written as pinned up cards. Using the split-screen function (horizontal or vertical), you can also display your writing in one pane and random notes/ideas on cards in the other pane.

My Scrivener set-up, with text blurred out because it's not ready to see the light of day! Image by author.

If you so wish, you can change the cork board background to any picture you want, and even change the look of the cards pinned on it! If, like myself, you get a nerdy satisfaction from pretty visuals, you too might see a jump in your productivity. It allows me to imagine myself in a virtual space with all the cork boards I could ever want/need, which then entices me to fill them with interesting and useful facts.

This may be a sign that I've been watching too much Castle... but hey! Productivity!

A revelation has swept the globe (and has been doing so for at least the past 3 years): that office jobs that require sitting down for 8 hours per day, 5 days a week, for 50-ish years apparently (not surprisingly) adversely affects your health (examples here, here and here). Normally office workers counter this by exercising either before or after work, but this research suggests that even the longest, hardest work-outs can't negate the effects of having sat down for so god-damn long. One of the solutions to this problem is the standing desk: desks that are raised to elbow height when standing, coupled with taller chairs for the occasional rest. 

My PhD requires a lot of computer time at the moment, which results in my sitting at a desk for around 40 hrs per week, plus all the time I spend sitting in front of the computer and TV at home. I tend to get a sore back after hours of sitting (even with the correct ergonomic set-up), so I'm trialling a standing desk set-up at home. The suggestion that I might lose a little weight by doing so was also a huge motivator, to be honest. Now, I find that I tend to move a little almost constantly, shuffling, shifting weight etc... I'm also much more likely to walk around the house when I need to instead of feeling too comfortable in my chair to move. 

There are more studies suggesting that standing all day isn't healthy either, and the best solution is to get up and move every 20 minutes. I'm really not sure how that's going to work out, productivity-wise. When I'm in the 'zone' I hate to be interrupted, and just a small break is sometimes enough to throw me off. Does that mean I should just learn to get back in the 'zone' quicker? Maybe, but easier said than done.

So for the moment, the trial at home will continue, and at uni I will get up and move around every 20 minutes for 2 minutes. And hopefully not annoy my colleagues with the constant sit/stand/walk/sit routine.

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.

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.

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!

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!