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?

Is it ironic that we’re going to give you advice about writing by talking about ignoring the advice we’ve been given?

Well, yes.

But the point is to keep an open mind and try changing up your techniques and habits, even if you think you’ve already found the best way to go about it.

So here are some habits we’re currently unlearning. Many of these habits were originally learnt from undergraduate lecturers, high school teachers or our peers:

Useful resources:

Belcher, W. L. (2009). ‘Writing Your Journal Article in 12 Weeks: A Guide to Academic Publishing Success’. SAGE Publications, Inc., Los Angeles, USA. 351pp.

Gardiner, M. & Kearns, H. (2010) ‘Turbocharge Your Writing: How to become a prolific academic writer’. ThinkWell and Flinders Press, Adelaide, Australia.

‘How to write a scientific paper.’ http://conservationbytes.com/2012/10/22/how-to-write-a-scientific-paper/. Accessed 21 May 2015.

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!

Have you ever had that sick feeling in your stomach when you find a journal paper published years ago, that is very relevant to your current work, but you had no idea it existed?

This exact scenario happened to me, when I was trawling through the reference list of a taphonomy paper. I came across a paper published in 2004 titled 'Taphonomy of Freshwater Turtles: Decay and Disarticulation in Controlled Experiments' from the Journal of Taphonomy. My immediate thought: "Hooray! Here's another paper on reptile decay, of which there are very few!" Rapidly followed by: "Errr, how did I miss this? What else have I missed?"

When I'm looking for journal papers, I normally start with Google Scholar and use some broad search terms, and then sometimes try the UQ library search engine. To find something like the 2004 turtle decay paper, I would use something like 'taphonomy reptiles experiment'. These are the results you'd get:

In short, the first 10 pages of this search did not turn up the 2004 turtle decay paper. It did turn up a PDF from the Journal of Taphonomy, but for a completely different paper (Brand et al., 2003. 'Decay and Disarticulation of Small Vertebrates in Controlled Experiments'). So I don't feel too terrible for having missed it first time round.

Searching for the exact title doesn't even bring up a reference or citation. So, I decided to search for 'Journal of Taphonomy' and look what I got:

Different papers from the same journal, but indexed by journal name instead of paper name!

So, the answer to how I missed this paper is relatively simple I guess:

1. The Journal of Taphonomy is not open access, and our library does not have a subscription to it. So papers listed in it would not appear in the UQ library search engine.
2. The papers from this journal are not indexed properly on Google Scholar: the search results show all the papers titled 'Journal of Taphonomy', but with authors and year of publication listed below correctly.
3. Finally, this particular turtle taphonomy paper is not indexed by Google at all.

I think it's a real shame for anyone who publishes in the Journal of Taphonomy that their papers (at least for me) were very difficult to find, if at all.

I have a sick feeling in the pit of my stomach, and the muscles of my right shoulder are aching.
The cause of my malady? Trying to find a goddamn note-taking system for my PhD that works.

It should be simple. I should read the PDF papers I have, take some notes, and write relevant information into the papers I'm currently drafting. But I've spiralled into a vortex of note-taking software and hardware.

It all started when I decided to borrow a Wacom Bamboo tablet. I wanted to devise a paperless note-taking system that still allowed me to hand-write notes, and it seemed that the Bamboo tablet was the answer. Hand writing notes versus typing them out has always been my preferred modus operandi. The Bamboo would allow me to write digitally on PDFs, and ta-da! Perfection. Only problem was, I had no idea what software to use.

I searched extensively for a program that would let me handwrite over a PDF using the tablet, that works on Mac OSX and Windows 8, that is also free. Not as easy as I'd hoped! As it turns out, the best programs aren't free (PDF Annotator, Inkbook) or don't run on Mac (AutoInk plug-in for Adobe Acrobat), and the free ones don't easily allow annotation (PDFPen forces you to re-select the pen tool every time you write a new character), or don't allow for smooth writing (Skim, Adobe Acrobat).

It might sound fussy, but when the alternative is cheap paper and my legible handwriting, I want the best I can get. The Bamboo tablet did come bundled with some software that allows you to annotate a virtual note-book (Bamboo Paper - but the handwriting isn't very smooth), or write on screen and it translates it directly into text (Bamboo Scribe), to be pasted in any application. And in fact, the Mac OS allows you to do this too (Ink). But this is just a scratch-pad, and I really wish they'd let you save what you've handwritten, because Bamboo Scribe was the smoothest/neatest by far!

This leads to a second problem: integration of different methods/software. At the moment, I use Mendeley to read and annotate journal papers, and as my citation software when writing up my own results. But if I'm annotating PDFs in Mendeley, do I really need another piece of annotation software just to handwrite on them? And I'm currently using Scrivener to draft up my first papers, which has a 'research' area that allows you to pin PDFs, write notes, add pictures... again repeating what Mendeley can do to some degree. And I've heard of other people using Evernote to write up notes and sync information across multiple devices, which would come in handy when jotting down notes on my phone. But again, double-handling is the issue. Or is it...

As I though more deeply about this problem, I realised that although Mendeley allows for detailed analysis and note-taking on individual PDF papers, there is no space write about broad scale topics which span a number of papers. You can tag numerous papers with the same subject, such as 'taphonomy' or 'burial', but there is no way to combine all the information from different papers in one document. So why not just use Scrivener to do this? Well, the page layout isn't as conducive to note-taking in this way, but rather drafting and word-processing. Plus, it isn't available on different platforms (WP8 specifically) or online like Evernote is.

During this research, I found out that Evernote (on Windows) allows you to use a Wacom tablet to write directly in the program. Problem solved... or is it? To my dismay, this function is not provided in the Mac version of Evernote, but a work-around using Evernote Skitch to annotate images and import them into Evernote almost works just as well.

Evernote seems to be the solution to my woes, so I will trial writing up thoughts and ideas that come from reading papers in Mendeley, by creating a .jpg of the Cornell Method template to write onto in Evernote. This way, I can access this information wherever I am, and especially during meetings with my supervisors. I will still use the tagging system in Mendeley, so it will remain my referencing and citation software. But trains of thought and brainstorming will remain in Evernote.

Oh and the pain I spoke about before? That sick feeling that I've wasted a weeks worth of work just trying to figure out the best way to be productive. Add in a sore shoulder for not using a proper ergonomic set-up for the tablet (it was sitting too far to the right when it should have been centered in front of me). I'll keep you up to date and let you know if it was all worth it!

So the last few days have been quite eventful for me... 

There are some renovations happening two floors above my office. Due to miscommunication /misinterpretation of orders (pro-tip: when somebody tells you not to do something, DON'T DO IT), a 500 L tank decided to empty itself into my office ceiling on Saturday, resulting in water raining down on mine and my colleagues desks. Onto our bookshelves, onto our computers. 

Cue panic.

Even though I wasn't there at the time, from what I heard the first responders acted quickly and effectively. Boards were lain across books to protect them, computers and peripherals shifted as far as possible out of direct harm, and power cables unplugged (from the computers, without touching wall sockets). But there was a lot of water, and some damage was unavoidable.

I found out about this on Saturday at 2pm. I rushed to my office, but by the time I arrived most of the water had been mopped up, and a dehumidifier placed in the centre of the room. I tried to dry the worst damaged books, looked for any damage at my colleagues desks, and took a lot of photos for insurance purposes. I was hoping that my computer and external hard-drive would be ok, as they weren't turned on when they got wet, and therefore shouldn't have short-circuited. But I had to wait til Monday for electricians to properly assess the damage. 

Damage report? The computer and external hard-drive still work! Amazing! I was extremely happy when I found this out! However, my new (as of last week) solar wireless keyboard and numpad did not fair so well. All of these items are going to get replaced under insurance, but at least I can recover data.

Now, here is the public service announcement:

I keep all my important work on Dropbox, so I was never in any real danger of losing data (to the huge relief of all involved),  just very inconvenienced by the loss of hardware/software. But the moral of this story is that you can never predict what could happen to your belongings, at home or in the office. Especially indoor rain.

Or so I like to think! I am really just getting to grips with Maya, but I'm already seeing really good results.

I've finished the photogrammetry side of things using Photoscan, and now the models are in Maya! Here's a photo of the real thing, compared with the model in Maya:

I've said it before and I'll say it again, 3D modelling makes everything better! Not only do I now have an excellent image database for future reference, I also have something I can add into presentations. Now to learn how to animate...

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.