Paperless academic work flow, alternatively "save a tree..."

...eat a beaver? That's what Google suggests when I type in "Save a tree", but for the purposes of this post I'm going to finish the sentence with "buy an iPad." Today I'm going to talk about my paperless workflow. This is something I've wanted for a long time and I think this is a reasonably good approximation of my dream of a paperless life. Here is what you'll need:

1. Drop box account (Free)
2. Mendeley account (Free too!)
3. Tablet with PDF annotation app (I use an iPad2 with iAnnotate)

Revenge of the terminal

I'm guessing except for #3 most people already have the components installed on their machine. Lets begin with Dropbox. If you don't know about it already, Dropbox is essentially a networked drive that you can access via their website and mobile device apps (any iOS or Android device). What's really amusing about Dropbox, and probably even more so for people a bit older than me, is that it essentially is a return to mainframe style computing with a terminal and no local storage. What's great is that if you're like me and you work on a desktop in your office and a laptop on the road or at home, I only need to maintain one version of all my code projects and word documents. For instance I run all my projects in Eclipse off of Dropbox folder. Once you have Dropbox installed on your local computer, you'll end up with a folder in my documents that looks something like this:

Ok, so now you've got your dropbox account setup, you should go over to Mendeley and download their software and install it on each computer you're going to use. I use two different machines so I have one on my Windows workstation and my MacBook Pro. Once you've downloaded and installed Mendeley, you'll need to link Mendeley with your Dropbox account. This is pretty simple, you can see it on YouTube here. What you need to be careful is that you don't set-up a watch list if you're syncing across multiple computers. This is because you'll end up with duplicate PDF insanity. So you've got everything linked together, now what? Well what you need is quality annotation app for your tablet. I like iAnnotate as I said before, but whatever you use be sure it truly annotates the PDF. Some of the less expensive tablet annotation apps work by converting your PDF to an image and then effectively drawing on it. This is not what you want. At this point there's a reasonable question to ask: "Why am I doing all this if I only have one machine?" Dropbox is what allows for integration of your tablet annotation app. So the first thing you'll do is add a citation to Mendeley (I use Google scholar and the one click importer). Next associate the PDF with the citation in Mendeley. You can drag and drop a PDF into Mendeley, but I've met with limited success depending on the journal, of the software accurately importing the citation correctly so my preference is to actually get the citation right and then associate the file. So at this point Mendeley has a PDF associated with a citation that's actually stored on Dropbox. The next step is to make sure that your annotation app is set-up with Dropbox. This will vary by app so I'll leave that up to you, but its usually rather simple. Next download the paper in your app:

Now you can open up your paper on your tablet:

Next you can highlight, take your notes, etc,

After you've read your paper, all you have to do is upload it back to your Dropbox folder, keeping the name the same as it is associated with Mendeley. iAnnotate has a feature to update a file, so as long as you get it on to the iPad via the iAnnotate / Dropbox link, you can use one click to update the file. You can then open it in Mendeley (or any PDF reader) and all your annotations will be there. I made the red highlights in iAnnotate:

You can also highlight in Mendeley, but that doesn't actually modify the PDF. The yellow highlights can't be seen in any PDF viewer but the Mendeley one.

If you want to be able to see your Mendeley highlights you'll have to use a small work around. Essentially you have to export your highlights as a new pdf, and then delete the old one on Dropbox and then put the exported one with the saved highlights back into your Dropbox folder. After that you'll have to delete the file from your iPad and then redownload it. It will look something like this with iPad marks in red and Mendeley exported ones in yellow:

If you're in a lab that doesn't use Mendeley the lack of ability to have highlights from the actual client doesn't really matter much. If your group does, then the work around may be too much of a pain for this to work for you. So lets sum up what works and what doesn't. Pros

• A paperless work flow that lets you highlight and take notes on pdf's from your citation manager
• Minimal expense if you already own a tablet and works way better than having one pool of PDF's for your reader app and another for the citation manager
• Can work across multiple computers

Cons

• Mendeley highlights aren't easily importable to other PDF readers
• Syncing problems can happen because you're using distributed services that weren't truly meant to work together (like you can't use the watch folder feature of Mendeley)
• The complicated work arounds needed to make the whole system work

What would be great is if the Mendeley ipad client essentially functioned like iAnnotate, or there was some integration. I would certainly shell out $10 to have a good iPad client like iAnnotate that seamlessly worked like this current system. I think Mendeley is a great system for lab groups to have, but if my lab actually used it I wouldn't be able to have this kind of workflow. I hope in the future Mendeley actually gets a better iPad client or works with existing ones for good integration, I could cut Dropbox out of the equation. I'm going to go on one more aside before I wrap this post up. I think there are lots of (I shudder to use this term) Web 2.0 (yuck I hate that word) and socially distributed tools that can really help lab groups function. Things like a lab wiki, Mendeley group to share papers, or collaborating on manuscripts using Google docs to name a few. I've mostly tried to use Google docs with older faculty members and met with tremendous resistance. I know that this far from always the case, but in my experience at UVM, we might as well be living in 1985 the way we collaborate. Its a brave new world with lots of sharing tools that can really help scientists share ideas and collaborate and I don't feel like we use enough of them in my limited time in academia. I'm sure this will change with time but, to borrow a term from Nick Gotelli, mostly through "demographic attrition". Hopefully we won't need to wait for a slew of retirements though to see these tools make into established lab groups.