The setup on my laptop:
- Zotero (https://www.zotero.org/) A software that allows you to easily keep references to academic papers right from your browser. Available as standalone app with multiple browser extension, or directly integrated into firefox. When you are on a paper's webpage, clicking on the button extracts its information, its PDF (if available) and do a capture of the webpage and store everything structured. You can then copy citation directly from zotero, generate a bibtex file, or use libreoffice extension. It also allow to sync between computer up to 300M, and extending the storage is quite cheap.
- Zotfile (https://github.com/jlegewie/zotfile) An Zotero extension that monitor the download folder to let you attach downloaded PDF to existing entries. It also rename PDFs with the pattern you want. And the killer feature: It is able to extract what you electronically annotated on the PDF (Highlights, comments)!!
- Okular (https://okular.kde.org/) For reading and annotating PDF. Straightforward use, nice annotations tools (F6 to open, double click items to make them permanent). Ctrl-S to save the annotation to file (otherwise stored somewhere in the user home file).
All these are open source software and are available on Linux!
I posted instructions on the Zotero forums a while back: https://forums.zotero.org/discussion/50191/syncing-zotero-wi...
«I thought about doing so with owncloud, then I decided that paying when I reach the syncing limit would be a nice way to encourage the project.»
I use Zotero in conjunction with Papership (http://www.papershipapp.com) on an iPad. Papership syncs with WebDAV storage, which means that, after syncing, downloaded PDFs are available on your iPad for reading offline. Any annotations are pushed back and available in the Zotero client. It's a great client and really stable. In conjunction with the Apple Pencil, it's a really nice system.
I'd advise an iPad Pro 12.9" if you do a lot of reading. The extra size means that you spend less time zooming in and out, and an app like Liquid Text (http://liquidtext.net) comes into its own for bringing text and figures into the same region of the screen and reduce the amount of time you spend flipping between the two.
Papership and LiquidText looks really nice, I would love to see such applications for Android. But I presume Apple is a more interesting platform as many researchers are on MacBooks. I suppose this is because researchers have really few spare free time and they don't want to use it fighting against the (linux) machines.
Similarly, I made the switch to a Macbook Pro after a bad day in 2011 in which I was first unable to connect my (Linux) laptop to a projector when visiting an institute to give a talk, and then unable to Skype in to a conference call. It was a bad morning, away from base, so I went to the Apple shop at lunchtime. I value the Linux box I use at work, and enjoy working with its tools, but easy collaboration is also important to me.
Need to get some system in place as my hard-drive is becoming littered with cryptically named PDF files.
The open-source side is important for me because the data accumulated in these software is really valuable. If one day the company has to close, you may be stuck without access to your data. With open-source software I'm at least sure to be able to continue running the latest software version on my own, and a community can start to take over and maintain it. Also the way data are stored in the computer can be deduced/found in the code, allowing to make exportation/importation to other software easier. I don't mind to pay for a good software – like I'll probably do with zotero for storage when I'll hit the memory limit – but it has to be open-source.
Except this the concept looks quite interesting and the UI seems nice. The only additional feature (in regard to my setup) that I can see on the homepage is the recommendation system, that can be quite interesting though.
What I need is an e-ink device that lets me take notes on it and is large and fast and shows the images in color. Zooming would make it superior to paper. It's just not there yet. I tried to read articles in NCBI's ebook format on my kindle but you can't hop back and forward easily on a Kindle and note taking is of course not an option.
Sounds interesting, but for $420 I doubt it would pay off compared to printing (black&white anyway).
If the stylus is as real-time as they claim (input latency of 55 ms) - it's basically my holy grail device - e-ink that is just like real paper.
Device is shown with drawing on it at 0:41.
I've been in communication with the guys behind it (via email), and they seem confident of hitting their timeframe. Obviously the proof is in the pudding =).
Oh, and for storing my pdfs and epubs I use Calibre. Also a great app.
I find tablets and e-readers very convenient for reading things from front to back and for full-text search, but find myself resorting to paper copies for anything else.
It's not a waste of paper if paper is the most efficient way to get my work done. Paper has a large viewport and unlimited battery life, while only weighing a fraction of most electronic alternatives.
The only thing that a computer does better is searching, but this problem can be easily solved by having a PDF open on some other device as well. You don't have to choose one or the other.
Related question: doing the above had some pain points so I wrote an app to give me the ability to give files and directories human readable names. Read, annotate, and bookmark the pdf within the app. Then be able to search across the whole library on annotations and keywords which would open the pdf to the page and paragraph the annotation referenced. The big thing it does is answer the question: I have read something that I need right now, but where in this huge pile of paper (or directory) is it?
I have gotten the app to the MVP stage, is there any other functionality that would be useful, and would anyone else find this useful?
Ideally, it would be nice if the app could do a search across a drive (or NAS, or whatever) for PDFs, pull out a summary and title, and then use that for naming/search/etc. Maybe your app already does this?
To be honest - what I wish I had was a personal Google Search appliance spidering all of my data on my NAS, which was also linked to normal Google, with priority of search results given to local information.
Maybe something like that already exists - I've found open-source solutions that come close, but all for the search/spidering typically required a machine waaaay better than my desktop...
I am experimenting with a lightweight solution, but am working out which compromises are reasonable to take so that it is worthwhile but not overwhelming of the machine it runs on. Still have to give it a real test with a large number of files as well.
For the hardware, I figure I could potentially use some old stuff I have (thinking like a Core2 Quad with 16gb RAM and a large hard drive would be fine). I could probably stuff it into an old half-depth 1u server case. The problem now is finding the time to build it...
One criterion I had for a lightweight solution was to not require Java. No problem with Java, just that it is a big dependency and my perception is that it is not a common install on the laptop or desktop of people reading pdfs, at least out side of the STEM stream.
For storage I use Papers (http://papersapp.com/). Highly recommended if a little pricey.
(If you know f.lux, it's an open source version of that)
One day its battery is going to die, and I have no idea what I'll do then.
It really is perfect for PDFs. I'm sad they never made an updated version. I've stopped using mine as much after grad school, but I do miss it quite often.
What device do you use to read academic papers?
What device do you read academic papers with?
Non-native speaker here, so my nitpicking might actually be useless.
What you're nitpicking is a common and frequently-taught misconception. You can end a sentence with a preposition. Some elitists in the 17th century tried to make English conform to the rules of Latin and those rules have stuck around even though they weren't necessary in the first place, unlike in Latin where a sentence doesn't make sense if you don't follow the rules.
This article gives a few examples of when it's more natural to end a sentence with a preposition (and mentions the history): http://blog.oxforddictionaries.com/2011/11/grammar-myths-pre...
"What device do you read academic papers with?" - fine
"What device do you use to read academic papers?" - fine
"What device do you use to read academic papers with?" - ungrammatical
Yes - either "use to read" or "read with" is fine. "use to read with" is just awkward. I'd guess it was an incomplete edit.
Zotero + Zotfile + Dropbox keeps my papers synced across all devices. PDF X-change is such a good PDF editor/viewer that I happily pay for it.
As as aside: Why do journals permit authors to submit plots and other line art as raster images. Have they no shame?
I’m currently using Mendeley. Previously, I used Papers. Unfortunately, the latest version of Papers (3.x) is terrible compared to how slick the old version (2.x) was. I’ve tried ReadCube, but somehow I find Mendeley easier to work with. I used EndNote before I discovered Papers, and wouldn’t recommend it. I keep all my .pdf files in Dropbox.
Discussions/recommendations for papers:
In-person, well run, reading groups still seem to work best. Although I’ve seen good discussions on /r/maths and /r/physics on Reddit. ResearchGate is useful for finding recent papers, while Mendeley is good for more historical connections.
I’ve tried a Kindle, but having to convert with Calibre adds too much friction to the process, and the result still isn’t that easy to work with. Reading for long periods of time on a laptop or desktop monitor is painful. An iPad with a Retina display comes close, but old school paper printout still wins the day. You can carry paper anywhere and scribble annotations on it with ease. I also find being able to have multiple pages “in view” at the same time is sometimes helpful for understanding. Not easily (cheaply) done with iPads or laptops.
Personally, I very much prefer Zotero but here's a great comparison of both software http://www.library.yorku.ca/web/research-learn/citations/zot...
I only wish it had pen support (surface). If I could markup papers as I go with my pen it would be the ultimate tool.
Apps don't support its completely obsolete iOS version any more, but the device itself works perfectly well.
I only use it to read academic papers, but it's still fine for that task.
My software setup currently includes:
- Zotero -- reference management
- Zotfile -- pulls annotations out of the PDF for saving in Evernote, among other things
- Evernote -- The workhorse of my setup. I use this for both organizing my research projects, task lists, etc and also for notetaking while reading a PDF. This includes pulling annotations out of the PDF with Zotfile and storing them in an Evernote note.
- Google Drive -- for storing my PDFs. Each PDF has an Evernote note linked to it. This allows Evernote to full text search all my PDFs that are stored in Google Drive with OCR, so it will even detect any handwritten notes in a PDF.
- XODO -- I've tried many Android PDF annotation tools and currently XODO has been the best as far as UX while reading/annotating and also stability and integration with Evernote via Google Drive. Ideally I would use the built in annotation tool in Evernote but it is frustratingly slow on my Android device and the UX is suboptimal.
I've had a few issues with the Samsung Tab
- It is only 8" so it involves a lot of zooming and panning while reading.
- It has a split screen mode so I can have my notetaking app in one pane and my pdf annotator in the second screen. This works well except that, again, there is limited screen space
- I've struggled with finding an acceptable PDF annotation tool on Android.
I stare at a screen for way too long otherwise, so my eyes need a break.
The convenience of just taking the phone out of my pocket and start reading more than compensates for not having a whole page in view.
Storing: filesystem (notes include where I stored it).
I started with Pocketbook 622 (a 6", 800x600 display). Worked very well. Can open many formats _natively_ (doc, rtf, djvu etc, check specs for full list). One of the first docs was anatomy atlas from 19century via archive. Rendered only decently, required huge magnification/landscape mode/margin cutting to be of any use. I had varying experience with other pdf/djvu documents - depending how they were created. Some djvus rendered excellently on 6", despite being meant for bigger (close to a4) page size. No problem with rtf/epub and other such formats. Magazines in pdf (a4) very hard to read, not worth it really. Arxiv's pdfs looked good/very good, sometimes they could be reflowed or put into column view, which helped a lot but with reflow I learned math not always shows up properly. Old computer manuals (my hobby, they are just scaned typewritten books) - not good enough.
Next model was Inkpad 840 (a 8", 1600x1200 display). What looks good on Pb622, looks good too on Ip840. Magazines look better, but they require a good light for really comfortably reading. Otherwise, I can go with dim night light. This model has backlight, but I don't like the idea of shining into my eyes.
Huge plus: sd card slot. I go on for months airgapped.
Huge minus: maybe it is just me, but reading html docs almost always sucks one way or another.
What to look for: external hard case so I don't have to be oh so wary. It was a PITA trying to find case for Ip840 thanks to its nonstandard dimensions. I settled down with some oversized tablet case.
Ip840 feels a bit slow and awkward (compared to Pb622) but I got used to it. If I had to buy again, I would have had a closer look on Kobo models too. Kindle does not cut it for me - requires too big commitment.
All of this just MHO, of course.
This upcoming one looks interesting - 10.3" E-Ink tablet, with a stylus - and they claim they've got input latency down to 55 ms:
The YouTube video above shows them drawing with the device at 0:40 - I asked, and apparently that's the actual device in use.
I'd say for a large 13-inch ebook reader, a 167ppi grayscale display (for anti-aliasing) is pretty good.
Until very recently all ebook readers were around 167ppi (most of them 6 inches diagonally) and most people were OK with it.
The high prices are due to the eInk panels, they must have a very low yield at large sizes making them very expensive.
I really like the idea and hope that it takes off when they release it, hopefully scale could make them cheaper.
1. The screen size is too small for a readable, fit-to-screen experience
2. Scrolling is too sluggish to even try, you don't want to scroll horizontally and vertically on a PDF which is zoomed a few levels
Currently, laptop works much better I'd say.
Seeing two pages side by side, like a book, even on small screens makes a huge difference for me. Also the ability to switch between documents easily (ctrl+tab and ctrl+shift+tab) is really handy, when I am researching a topic.
I haven't figured out the annotation and highlighting part yet. I just copy and paste important parts into an Emacs org-mode document and summarize the article I read.
It's also easier to remember, what I tought when I read the article at the time, if I take extensive notes.
(I see Mendeley mentioned for example; there's some overlap here)
- Bibdesk (http://bibdesk.sourceforge.net): archiving papers (automatic rename / custom citekey generation), Google Scholar bibtex extraction, and bibtex interface w/ TeXShop
- Google Drive: storing archive ... it's not a great archive solution because of google's special system of renaming files, however stuck with it because of work
- Goodreader: fast PDF renderer
I wish there was a bibdesk app for the ipad linking to goodreader.
I had some doubts myself before buying my first e-ink based device. It helped a lot to watch movies on y-t where guys were test driving them.
Not all e-ink displays are of equal quality. The newer ones should be ok, those claiming 16 levels of grey. However the definitive test should be made by your very own eyes.
Edit: I don't have a Kindle.
For papers though, not so much. The screen is too small for a layout format like PDF to work. The document has to be able to reflow for the screen like a proper e-book to work really well, and PDFs don't. I've heard the Kindle DX was great but those haven't been made in a while, otherwise there's a few big ones Sony made which are apparently awesome but expensive.
their stupid idea to make it just small enough to not fit a page from a pdf, and the completely broken scrolling killed it. even tried the larger one. same problem.
they may have prevented the two people that would have read a pirated pdf of a novel instead of buying it from amazon. but it cost them the entire academia market.
Would the reason be economical, information density (more real state on a modern laptop/desktop) or something else?
When you read a physical book, you can flip through pages instantly and scan the contents with zero wait time. A laptop is much closer to this ideal than a tablet.
Sometimes iPad Pro
More rarely, on a desktop or laptop
I've been thinking about upgrading to a 12.9" iPad Pro myself, but the additional benefits (larger screen, Apple Pencil support, better colour fidelity) aren't worth it for my use cases.
So, I'm waiting for a refresh and then I'll decide whether I can justify having two iPads.
Because it's too large to carry around all the time, or because it's not comfortable to use when lying down, or something else?
I don't remember whether there were other problems because it took all of 15 minutes to realize I couldn't sell my smaller iPad to help pay for it and still have an iPad to use most of the time.
mupdf is pretty lightweight for skimming.
I much prefer the e-reader over a laptop (14" Thinkpad), but there are some downsides. Taking notes on the e-reader is clunky (so I don't do that), and the battery life is less than that of the earlier models (still workable, though).
The color-adjustable backlight is quite nice. The only e-reader I've seen that's better for this kind of thing is the Sony DPTS1, but then you are talking about a completely different price class.
I use a laptop mostly, but yeh paper is best because freeform annotations.
Reams of paper saved and I can read anywhere... but I can't do scratch-work on my cell phone!
Really a game changer.