For my thesis, research and studies I need to read a lot of articles. Most of these are on my computer as PDFs. For some time I have been longing to have a device that would allow me to read these PDFs on the go and thus utilize the various transfer times I have. Sure, I could print them out and take the hard copy. But for ecological and practical reasons, I now read almost everything electronically. Usually, when I read a paper, I will highlight the content or write down a few notes. Now if I have done this on my printed copy, where is this copy going to be the next time I need it? Most probably not with me. So I needed a device that would allow me to take my PDFs with me, read them conveniently, make a few highlights or notes and transfer the lot back to my computer. I had a very close brush with the iPad and I have finally chosen the new Kindle 3. After much waiting and a struggle with my old nemesis, the UPS, I finally held it in my hands. And this is what I think of it:
Reading PDFs
The Kindles have been (as far as I can see rightfully) praised for offering great experience with reading e-books. The experience I have with reading academic papers in PDFs can be described as satisfactory. The Kindle 3 screen offers great contrast and the e-paper rests the eyes. The PDFs are shown just as they would be in a PDF reader on a computer. However, the screen is fairly small, so depending on the format of the PDF (e.g. the number of columns), you have to flip the screen or zoom in for the actual reading. I find the page-fit view sufficient for skimming, though. The navigation is good.
Annotation
You can highlight passages of text and add notes. For this, you have to navigate on the screen with the 5-way controller. This is of course not as convenient as a mouse. Also, when highlighting text in papers with more than one columns, the highlight does not break at the column end, but continues across the page, so you will have to break such highlight into several short ones (a problem I know also from other PDF readers). For writing notes, you have to use the fairly small keybord. The highlighted text and notes are not embedded into the PDF but stored in a separate TXT file.
Organisation
The Kindle allows the creation of collections to organise the documents. Also, you can create folders when copying documents onto the Kindle. This makes it easy to find documents both when reading on the Kindle and when it is plugged to the computer. But these are two separate things – creating a new folder will not create a new collection.
Workflow
I have figured out a workflow to incorporate the Kindle into my reading. I use a “To read” folder on my computer, where I put unread documents. These are papers from new journal issues, papers recommended to me by others, papers I found randomly on the web, etc. To this, I have added the folder “Read”, where I put papers I am already done with. This organisation is mirrored by the collections and folders on Kindle. I move the papers from “To read” to my Kindle and place them in the “To read” collection. Then I read them while on the bus or at home etc. I highlight what I need and make brief notes. Read documents that I want to keep lend in the “Read” collection and those that I consider irrelevant are directly deleted. Then I move the read documents back to my computer, together with a copy of the TXT with my notes and highlights. I then put the papers into my reference manager (Mendeley), sort them, add the meta-data and copy the notes I have made on Kindle from the TXT-file into the “Comments” field for the particular paper. This way, the notes remain available to me independent of the PDF. That’s it.
Conclusions
I am satisfied with the Kindle 3. It can do what I have expected it to do. Of course colour, touch screen and larger screen would be nice. But then I knew it had a black-and-white, 6-inch non-touch screen before I bought it – so while start whining now? When deciding to buy the Kindle 3 for academic reading, you ought to be aware of the limitations and think carefully about what you want it to do. The way I use it is very simple. It is enough for me, but if you want more, you have to look at another device. The iPad is definitely an option, where you could do stuff like automatically syncing between several devices etc. I have decided against it in the end, because of the price (yes, you get more for more money, but I didn’t want to surf with it, I just needed it for reading, so the added value was not worth the added price), the battery-time and the reading properties (I do a lot of reading on the computer and I am beginning to feel the strain – Kindle’ screen is really better here). If you have time and patience, you can also wait a bit, because the market is going to be flooded with further e-readers and tablets very soon.
Filed under: Tools



Thank you for your review, I was wondering about the use of Kindle in academic reading. However, I think it has quite enough functions to an ebook reader. I already order it and waiting…
First of all, thanks for a very informative post!
I was thinking to buy a Kindle just to read academic papers, as you can imagine I was very glad to stumble upon your post.
I can imagine only one thing that could have made this post much more helpful; including a few screenshots/pictures of Kindle when rendering 2-column-papers.
Best wishes,
Tolga.
Hi, sorry I have been very busy lately. I will try to get some photos posted soon.
Hi,
Would like to know how it takes pictures in a pdf, esp color pics as i have a lot of pdf with microscope images. Does the refresh rate slow down because of the pics ?
Thanks
Hari
Hi, I didn’t find that the refresh-rate is less with images, but rather that there are some PDF documents which are simply slow. Typically, these will be problematic and slower also when viewed on my PC. I don’t have a problem viewing black-and-white images, but I could imagine, that with microscope images, the lack of colour could be a problem. But that you can probably assess better than me.
Hi Helen,
Thank you for this interesting post, very valuable for me to take a decision.
I was thinking to buy a kindle as well for reading scientific papers during transfers and so on.
However, I have read on the kindle webpage that annotations are not available for pdf on the kindle 3. So, do you tranform your pdf to another format before to upload them to the kindle or have I made a mistake reading the specifications.
Moreover, have you got any problem for the table or figure rendering on the kindle in scientific papers.
Thank you again,
BR,
Ivan
Hi, Kindle 3 can read and annotate PDFs in the PDF format on Kindle. You can make highlights and notes. But these are not saved in the PDF, but in a extra Kindle-only document. I haven’t found a good way to extract highlights so I actually stopped highlighting in the PDFs and started making notes about the PDF. These I can extract and put into my Mendeley later. Tables and figures have never been a problem.
Hello. Very interesting article that’s making me seriously consider Kindle 3… A couple of questions for a Kindle 3 owner:
1.- How do you get around with your pdf files? I think they are not supported by Kindle 3 and must be converted through Amazon… If it’s so, I don’t like that at all.
2.- What is your experience with dictionaries? Have you used them in Kindle 3? Have you tried using any dictionary other than the one that comes bundled?
Thanks!
Hi,
to 1: Kindle 3 can read PDFs just as they are – no conversion needed, just put it on Kindle and start reading.
to 2: Sorry, I haven’t used the dictionary at all :-(.
Best, Helena
Hi Helena,
Thanks for your very useful post. I’m using Mendeley as well and just wondering about your experience of transferring the file back and forth. For the files that have been organized in Mendaley already but not yet read – if I take the file out to read in kindle – do you have to re attach the file to get attached note or can attach the note directly?
Are you still pretty happy with the set up i.e. kindle and Mendeley?
Hi Petch
I don’t modify the PDF on Kindle at all. So if you take a PDF that is already attached to Mendeley, you don’t have to reatach it – just remove it from your Kindle once you are done with it. I do not attach the notes to the PDF in Mendely, but put it in the “Note” box, attaching it to the reference. I am quite satisfied with the whole set-up, though it might seem too troublesome to some. Of course that having an iPad with a Mendeley App would make things easier, but I really like to read on Kindle. I now often transfer PDFs to Kindle to read them, because I find it much better for my eyes. I also prefer the Kindle to reading on my netbook – turning pages is better than non-stop scrolling.
I hope this helps
Helena
Thanks very much Helena!
Thanks so much for this, Helena, great post, and really helpful follow up comments. Yours sounds like the the most workable work flow I’ve come across. Like you, I’m keen on the Kindle screen, and feel that the iPad is just too heavy for reading and toting around. I also don’t want the temptation of flitting between apps.
Thank you so much for your review Helena. I am a graduate student and considering a Kindle 3 for exactly the same uses you have described (including synching notes in Mendeley). It sounds like the Kindle 3 is the best option out there now even if it is not ideal. I would spend more money for a DX if it was updated with the pdf features on Kindle 3, but it sounds like pdf support on the DX is closer to Kindle 2. Given the transition to eTextbooks and electronic-only Journals, it really seems like there is a market out there for a academic ereader!
Thanks again for taking the time to write about your experience!
Hello Helena,
I have just bought one of the new generations of kindle. the file which the notes are saved in are pdr files. from reading your original post i see that you refer to txt files. Does this mean that kindle have changed the file format and therefore it is no longer possible to use kindle and mendeley together ?
Hope someone can advise
Dani
Hi Dani,
yes, Kindle saves you notes, highlights etc. in pdr-files. However, in addition, it automatically generates a file called MyClippings.txt. Here it just chronologically dumps all your notes and highlighted test passages. This is the file I meant. I take it and paste the notes to the papers in Mendeley. Changes made to the MyClippings-file have no effect on the pdr-files.
Hope this helps,
Helena
Solved my problem too! Thanks!
This is great, thanks very much !
I have now pasted in all my notes from this morning. (which i took in a little coffee shop near uni)
I can see it can be a bit fiddly with all the additional information it gives for each note/highlight: file, date, time and so on but I’m sure I’ll get used to this and identify chunks of text sooner that a line or two.
Thanks so much for your blog also, really useful.
Dani
Great blog post! I will be picking up my Kindle tomorrow and I think it is one of the best decisions I made in 2011. By the time I go to graduate school later this year, I would have gotten into a good groove with my Kindle and how to use it for research and referencing. Thanks again
I use a similar workflow, and the one thing I’ve found lacking is that when moving a large amount of PDFs from Mendeley to my Kindle, one essentially has to re-categorize the PDFs once they are on the kindle. Even using Mendeley2kindle, the category information is not preserved, making it a bit inconvenient when one is copying over 200 papers across 10+ categories.
Nonetheless, it’s the best thing I’ve come across yet, and being able to read all the journal articles I need to on my Kindle is fantastic!
Hi,
Thanks for the post. Just one question, which model do you own Kindle 3 7 inch or the Kindle DX 9+ inch one. Because, you mentioned it being fairly small!
Thanks again,
Vijay
Hi Helena,
Thanks for your insigts !!! I just bought a Kindle to help on my master degree and, thanks to you, I’m sure that I did it right.
BTW, I’m using Mendeley as well … shall we suggest to Mendeley a Kindle APP … it will be great to academics all over the world.
Best regards,
Jone.
Just searched for the ability to annotate PDFs with Kindle. I found this very informative blogpost and the following tool that might be helpful for some of your reader: http://code.google.com/p/kindle-annotations/
Hi Helena
First thank you for this post. This post has been a important one in favouring me to purchase a Kindle 3 and enjoy reading on it.
For me its sheer laziness that didn’t make me sit and read the industry papers on pdfs that I have been gathering for a while.
So thank you.
I first heard about Mendeley while reading this post 2months back, I have installed it on my mac and am using that too.
This is a question about Mendeley,
I just copy and past the highlights/notes from Clippings.txt onto the NOTE filed in mendeley that automatically is present when you open the PDF in Mendeley.
The bottom right corner of Mendeley is designed to display the notes/ highlights you make as you read on MENDELEY,
My question now is :The highlights I make while reading on my mac doesn’t appear in bottom right corner. The notes I make appears instantly just not the highlights.
Have you had similar issues?
Thanks
Krishna
Hi Krishna,
I’m not sure I understood you correctly. I also copy my text-notes into the Note window. The lower right corner, as I understand, is for highlights made in the Mendeley document. Yes, I have had problems here. In fact, I don’t use this option much, because I have had issues syncing the highlights. I am switching between Mac and PC.
Helena
I was quite suprised finding your blog via google when I searched for a way to synchronise Kindle with my local filesystem. Just in case you’re moving the files manually to your Kindle and back, you could consider using AllwaySync for getting the files syncronized automatically every time you plug in the Kindle. Still, I’ve found no way to sync the files conviniently without using the cable (using wi-Fi). Thanks and greetings.
Hi Mathias,
thanks for the suggestion with AlwaysSync. Actually, not being able to sync on the go does not bother me much as I like to select what I put on my Kindle deliberately. But I understand that this is something that depends on a personal reading style :-).
Helena
Hi Helena,
First of all – thank you for sharing your experience with Kindle! I recently bought a Kindle for reading scientific papers, after reading your blog, and I am very happy with my choice. However, there is one thing that I still have not figured out. To organize my .pdf-files, I have created collections on the Kindle. These collections are unfortunately not visible on my PC, so after copying, I still have to move the files manually on the Kindle to the correct collection. With only a couple of files, this is really not a problem, but with many files it is time consuming. Do you know of any solution to this?
Greetings,
Nikolay
Hi Nikolay,
no, I don’t. When I load new documents to Kindle, i have to order them into collections. Although I often leave papers just on top and only sort them into “Read” collection, onece I have read them. I noticed that updating documents isn’t problem – if you load a new version of the document the collection remains the same as long as the name did not change.
Best, Helena
Hello Helena,
Thanks for the great review. I’m now considering to get a Kindle for my studies. Your post has really been helpful. Also, I appreciate you sharing your workflow too. Getting the idea of how the Kindle fit into the entire workflow of your academic work was definitely one of the best tips!
Regards,
Ryuei
Hi there Helena,
I was lucky enough to get a kindle for Christmas and like you thought it would be a groovy compliment to Mendeley. I did get a little annoyed with the process of putting what I want on the kindle – we are expected to read a ridiculous amount after all!
Anyhow, some friends and I put together an app to send Mendeley papers through to your kindle automatomagically. It’s still very-much a beta service and we welcome any feedback / feature requests… http://www.kinsync.com
J
Thanks for the suggestion! I am currently testing Kinsync and the Kindle Collection Manager. I think that the combination of the two would definitely simplify my routine. I am pretty busy at the moment, but I will report my experience as soon as I have time.
Hello,
Thanks for the very helpful post! I have a question which I couldn’t find the answer to in the post: Is there a way to remove PDF annotations that are created in Adobe Acrobat or convert them to Kindle annotations when transferring them to Kindle?
I already have a huge selection of PDF files on my computer that I have annotated using Adobe Acrobat. Since these files have lots of equations and figures in them, I need to open the original PDF file on my Kindle. Now when I want to read those PDFs on my Kindle, Kindle does not support highlighted text and instead shows a gray band over the text in that area.
Is there a way to remove PDF annotations or convert them to Kindle annotations when transferring them to Kindle?
Thanks in advance for your help!
Best,
AK
Hi AK,
I do not know any way of converting annotations or removing them from the PDFs. I have the same problem as you do. I have therefore recently switched to annotating PDFs in Mendeley. Mendeley does not automatically embed the annotations in the document, so when I view them on Kindle, they are not there. Of course if you have lots of already annotated documents, this is not very helpful.
Helena