Sciencewomen

A reader recently sent in the following question:

Hi Ladies –
I’ve been reading your blog for most of my graduate career, and am currently beginning my first post-doc position. I’ve got a question for your readers, and I’m dying to know if anyone’s really come up with a good solution for it. How can you become a (nearly) paper free academic (with the exception of lab notebooks)?

I ask this because after moving from my rather large (by grad school standards) office to a rather restricted lab space, I’ve been forced to realize that I can no longer keep all my printed and scribbled on pdfs. I’m a bit old-fashioned and like to take notes on the print-out as I read- I’ll just completely lose the notes if they’re on another piece of paper without the pdf. Surely I’m not the only one that finds myself in this predicament. Do I breakdown and buy an ipod touch (are they any good at highlighting and notetaking)? Or is there a better, more clever, and cheaper solution to this predicament?

What say you, dear readers?

Read my Mac-biased response is below the fold…

What with my commuting lifestyle for the time I was in gradschool and then my first year of this job, I’ve tried to reduce the amount of paper I truck around with me everywhere. I have some tools I find indispensible that I would be happy to share.

A Fujitsu Scansnap scanner (this one, not this one). When I have documents I need to be able to save (IRB consent forms, offer letters, letters to save for tenure etc.) I pop them through this little scanner and save them as pdfs onto my computer. I also use it when people send me papers to read through – I print them out, mark them up, then scan the marked up version to pdf to email back. When I bought it, this scanner was $250ish – not cheap but SO WORTH IT.
Evernote. I’m a recent convert (and am still using the free version) but so far I love it. If I don’t want to hold on to the bit of paper (ads for resources available to instructors at the university, business cards from visitors, books from the library I want to buy) I snap a photo of it using my camera, iSight webcam (yes I am a Mac geek) or phone, and save it to Evernote. Evernote can also hold on to your scanned pdfs, and even can do word recognition of handwriting.
Papers (for Mac). Honestly, I don’t know how I managed without it. It is $42, and the app for iPhone/iPod Touch is another $10, but again I find it to be worth it. You can import pdfs from the major databases like PubMed, Web of Science, Scopus, Project Muse or JSTOR. You can open pdfs within Papers (that you downloaded from somewhere else). You can store pdfs and include reference information. You can read pdfs in a full screen format. You can take notes in a “Notes” field. If they were smart, they would start working on a “highlighting” function. I haven’t been able to sync with Endnote yet but I have been able to import my Endnote library into Papers (but Papers doesn’t seem to do the in-text citations Endnote can). You can read your pdfs and take notes on them FROM YOUR IPHONE/IPOD TOUCH. For realz. I loves me some Papers.
OmniFocus. This application is a little less about going paperless and more about trying to stay organized without paper. My friend Alex pointed me to this about a year ago, and it is indeed very useful. OmniFocus on your desktop/laptop allows you to organize your to-do lists by projects and contexts (OmniFocus language for “where you have to get something done” – like the grocery store, office, or your mac while online) and also has an iPhone/iPod Touch app so you can sync with your list and get your things down away from your office. You can arrange for to-dos to repeat, or be organized as needing to be done in parallel or in series with other items, or embed the document you need to work on right into the program. I’m still learning all these ins-and-outs, but the screencast tutorials are very helpful. I’m sure the price has gone up since I bought it – it’s now listed at $80

I know my suggestions are very mac-focused. Anyone out there have any suggestions for windows-based machines?

Comments

#1 ecogeofemme
September 6, 2009

I simply take notes in a word document. I’m not a big note-taker, so I typically do this only when I want notes on several related papers that I intend to rely upon for my own writing.
#2 Ron Schott
September 6, 2009

I think Evernote is going to be a winning strategy in this field. I haven’t used it much yet, but I anticipate doing so in the near future.
#3 Carlie
September 6, 2009

If you have the money, a tablet PC. That keeps the notes right there on the digital version of the pdf (or a copy thereof, if you want to keep the original clean).
#4 Virginia
September 6, 2009

If you’re a Mac user, try Skim. I find it to be the best open source PDF reader and note-taker for OS X.
#5 Professor in Training
September 6, 2009

Another Papers fan here! I’ve also imported my EndNote library but haven’t figured out if Papers will sync with EndNote (Alice: if you work it out I’d love to know!). And a highlight function in Papers would be awesome.

Beyond that, I don’t really have much else to suggest. I tend to take handwritten notes at seminars and then transcribe into a Word document if I need to have them handy when I’m away from the office. I’m not sure if the free Acrobat Reader has it, but Acrobat Professional has the capability to mark pdfs with highlights and comments but it’s a little messy for me.
#6 lylebot
September 6, 2009

When I’m working out equations or sketching ideas, I always use scrap paper, and I use each sheet until it’s pretty much full. I still prefer having printed copies of papers, but I try to print them as efficiently as possible (double-sided, low quality, sometimes two pages per sheet if I think I’ll be able to read it). Other than that, I’m going paperless as much as possible.

I have a student that routinely uses the printer to print a couple of numbers on a full sheet of paper. He’s using no more than 1/5th of the sheet, not to mention printer ink, when he could just type them up in an email, or if we really have them in physical form, write them down on a scrap. It drives me nuts!
#7 Rebecca
September 6, 2009

I have trouble writing with my hand, so I use little paper as well. Something I’ve done is to set up my own personal wiki on my computer. It’s easy to create pages and link pages to one another. The one I use is called MoinMoin.

I use it to keep track of all my different projects and track my progress on each project. It’s also really handy for recording the exact steps I took to get a code to compile (I’m a computational scientist and one part of my job is compiling a lot of other people’s codes).
#8 jennifer
September 6, 2009

our high-throughput lab has actually moved from lab notebooks to using an internal wiki for preserving lab experiments. indeed, each of our collaborative projects has its own wiki making it easier to share data and manuscript drafts among researchers from different labs and institutions.

i use Curio and Evernote for organizing project-related content. i use “Things” for organizing my daily activities.
#9 Sarah
September 6, 2009

Has anyone tried using a Kindle to take notes on PDF papers? It sounds like the latest Kindle DX might let you do this, but it doesn’t sound very well developed yet…

When I’m reading something that I really want to remember, I take reading notes in a separate notebook. I keep PDF versions of my papers, and I keep my notebooks with my reading notes, but any printed-out papers can be recycled with no great loss when I need to move.

Of course, many papers do not warrant full-on reading notes, and for those I use Acrobat’s comment function to make notes that get saved with the PDF.

Finally, for papers that are not available electronically, I have a portable CanoScan LiDE scanner that I take to the library with me. It fits in a laptop bag and is very lightweight. I also use this to make PDF backups of my data notebooks. I’ve had my scanner since 2006; it has paid for itself many times over (by eliminating photocopy fees) and still works fine. The current model seems to be: http://www.amazon.com/Canon-CanoScan-LiDE90-Scanner-2167B002/dp/B000V2RUBE/ref=sr_1_7?ie=UTF8&s=office-products&qid=1252263790&sr=8-7)
#10 Brian Puccio
September 6, 2009

I second the Scansnap, I use one myself, but I’m a fan of DevonTHINK specifically, the Pro Office version, for managing PDFs, web links, web archives, documents I create in various programs and everything else of mine.
#11 Lab Lemming
September 7, 2009

You could probably replace your lab notebook with a PDA if you are smart about setting it up. I know several people who have ditched their paper field notebooks to go all digital.
#12 ScientistMother
September 7, 2009

I totally love Papers combined with Skim. I discovered the programs when I asked for advice on my blog. It was easily one of the most commented on posts, and has reviews of both mac and pc based programs.
#13 BroccoliofDoom
September 7, 2009

I’ve just spent the summer trying various software combinations as I accumulate more and more PDF files. I still keep everything in my EndNote database for writing, but it’s not ideal for taking notes unless you have Acrobat and are willing to deal with the terrible UI.

Depending on your field Papers has one major limitation. You can only attach one PDF file to a reference, so if the article had supplementary info in another file, you’re out of luck.

I’d recommend Mendeley (free): http://www.mendeley.com/

Oh yeah, it’s that magical four letter word, FREE, they have a program for Windows, Mac, and Linux, as well as synchronizing online. Your entire library can also be accessed through the website, so you can use the browser on a phone to access your entire library when on the go.

With the desktop applications, the built in PDF reader/annotator allows you to add notes and _highlight_ (a feature notably lacking from papers as was mentioned).

While it doesn’t offer the search options that I’ve come to like in Papers, but it does have a nice browser plug in so you can easily import PDFs while browsing the journals.
#14 Megan
September 7, 2009

FYI… Omnifocus gives educational discounts… $50 for a single license, and then you can upgrade to a family license for $45 more, giving you five licenses. My husband and I have it on work and home computers now (and also bought the iPhone app).
#15 Christina Pikas
September 7, 2009

Evernote rocks – especially if you have an iPhone. It OCRs your pictures. Nothing for Windows is quite as cool as papers, but Mendeley is making progress. Zotero is pretty cool, too, and both of these will insert citations into a word document. I’m not familiar with Omnifocus, but ThinkingRock is a pretty cool thing for Getting Things Done to-do lists (free/open source – but recently added “member only modules”). Outlook has been steadily adding new features, too.
#16 Amanda@Lady Scientist
September 7, 2009

This is a great list. I’m curious, though. I use Bookends for my citation management (way cheaper than Endnote and not as clunky) and Skim to annotate my pdfs. I’m reasonably happy with this solution, but I’ve heard such great things about Papers. I was wondering what you all use it for?
#17 soil mama
September 7, 2009

with preview (on a Mac), you can take notes on a PDF, then save as a PDF. I was recently at a workshop where the speakers had notes in PDF format and all of us were on our computers taking notes with preview (mostly mac audience). I also really like papers, but since it lacks cite while you write, I still use endnote. a combination of the two would be perfect!

Oh- students can get 40% off Papers if you email them proof of being a student. This makes it ~$25, so it’s a great buy!
#18 AKB
September 7, 2009

If you’re a mac user, also check out Sente as a reference manager. I started using it a couple years ago (when it was much more sophisticated than Papers) so I don’t know how they compare currently but it’s been great and also has auto-pdf downloading, full screen preview, notes fields, keywords, bibliography formatting, etc. I use it in place of endnote and much more.
#19 Andrea M
September 8, 2009

I like Papers too, although it can be a bit clunky in some respects. I would definitely reccomend that.

I would also reccomend Freemind (http://freemind.sourceforge.net/wiki/index.php/Main_Page) a free, open-source flowchart builder.

In addition to being really good for organizing your daily brainstorming sessions, it can be used to breakdown literature in easier to manage conceptual maps. I usually extract every significant finding from a paper and organize it in the map in a tree like form. (see http://www.flickr.com/photos/8809198@N02/3900198142/sizes/l/ for a mock example – sorry for the colors something went bad with the export)

It takes some getting used to, not to mention a lot of time if you want to start a new map and have to re-read and analyze your whole paper collection, but it is definitely worth doing, becase in the end you will be able to access all the knowledge out there in an organized form.
It makes writing reviews / paper introduction a breeze. You want to talk about protein A? no problem, go to the protein A node and you will get to everything that has ever been said on Protein A, with appropriate references.
Also, by having everything visible at once, you can make better connections and evaluate evidence in a better way.
#20 Alice
September 8, 2009

Oh I just love this thread. So many new software packages to try! I’ve downloaded Skim and Curio for starters… and I’m bummed I’ve committed money to OmniFocus because “Things” looks good too…
#21 tatil
September 11, 2009

thank you very good
#22 BrianR
September 11, 2009

Wow, tons of cool stuff and ideas to check out from this post and thread.

While I love technology and gadgets (and constantly find myself trying to convince colleagues, with limited success, to use digital/online tools) I still love my Moleskin notebook I carry everywhere for capturing quick ideas/notes. You can’t beat the simplicity — I never have to turn it on, it doesn’t run out of batteries, it never needs updates (unless buying a new one counts as an update I suppose), and I can quickly draw messy sketches or flow-chart-like diagrams with text all around it with a simple tool — a pencil.

And since I try to write down a lot, a fair portion of it is kinda useless … so the process of going through the book to decide what is a worthwhile thought or not is important for me. It gets me thinking about problems. But this is just me, everyone’s different.

I had a tablet PC for a while and it was cool … I did use it from time to time, but it wasn’t effortless enough. I’ll be one of those people who wait for an actual paper notebook (that feels like paper, I love that feeling) that can somehow capture and upload the content.
#23 miss leya
September 30, 2009

(I just wanted to say thank you. I’m so glad I found this post! I’m new to macs (been a windows user for years) and my school laptop is now MBP. I’m taking my first ever grad classes this semester and wasn’t sure how I’d organize the different sets of papers (mostly literature reviews) I have for 3 classes. As I downloaded “papers” I think my eyes got big as dinner plates! That might solve my problems. All of ‘em.

Also, I’d like to weigh in on the note taking software specifically. (even if this is kinda an old thread for comments at this point) I’ve got evernote on my windows machine/iphone/MBP. It’s ‘meh.’ I’ve got Notebook 3.0 on my MBP and love it – and it has a student license.
#24 Janet B
February 1, 2010

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