Academics with iPad Pro: How do you keep track of your texts?

[va1984]

Possibly some of the best designed Pro apps for the App Store come from Readdle. Documents is outstanding for professionally managing your files and PDFs. Check it out: Documents by Readdle by Readdle Inc. https://itunes.apple.com/us/app/documents-by-readdle/id364901807?mt=8

There is a difference between storing a few dozen pdfs for fun and an academic research collection extending over thousands of PDFs. Academic reference managers can filter and sort by date, authors, subjects, journals, keywords, they can automatically fetch new articles from academic search engines, they handle citations in some word processors via plug ins... Documents by Readdle is a lovely little app but it's not the same thing as an academic professional tool. It's like comparing a home espresso machine with the customizable beasts they have in real coffee shops.

Out if interest: why do you consider some of these apps evil? And why is one the ethical choice?

Because of the companies that acquired them. Mendeley used to be a neat bunch of folks. Same for Papers, they were PhD students in the Netherlands who hated Endnote for its general crappiness and high price. Then they were bought up, all of them, by big publishing giants. Except for Sente, which went bust (or anyway died off) and Zotero, which remains independent to this day.
Mendeley in particular had the misfortune of being acquired by Elsevier, which out of all the giant publishers had the reputation of being the most evil. Among the dirtiest tricks they used to play, is creating a bunch of "fake" (ie. filled with junk, non-peer reviewed) journals, and then forcing university libraries to purchase access to the real, reputable journals only via an expensive bundle with many of those fake journals... (like saying: you need a toothbrush (price: $5), but you can only buy it in a bundle with toothbrushes for cats, dogs and every animal species (price: $5 each) for a total bundle price of $500). Something like that. I am in the mood for wild similes today.
Anyway, this was just one of the reason university libraries used to hate Elsevier's guts. Do a quick google search and you'll find the whole history. Including how disappointed people were when they bought the good old Mendeley.
As a start:
https://www.theguardian.com/science/2012/feb/02/academics-boycott-publisher-elsevier
https://www.theguardian.com/higher-...r/10/elsevier-buys-mendeley-academic-reaction

 

[ericwn]

There is a difference between storing a few dozen pdfs for fun and an academic research collection extending over thousands of PDFs. Academic reference managers can filter and sort by date, authors, subjects, journals, keywords, they can automatically fetch new articles from academic search engines, they handle citations in some word processors via plug ins... Documents by Readdle is a lovely little app but it's not the same thing as an academic professional tool. It's like comparing a home espresso machine with the customizable beasts they have in real coffee shops.



Because of the companies that acquired them. Mendeley used to be a neat bunch of folks. Same for Papers, they were PhD students in the Netherlands who hated Endnote for its general crappiness and high price. Then they were bought up, all of them, by big publishing giants. Except for Sente, which went bust (or anyway died off) and Zotero, which remains independent to this day.
Mendeley in particular had the misfortune of being acquired by Elsevier, which out of all the giant publishers had the reputation of being the most evil. Among the dirtiest tricks they used to play, is creating a bunch of "fake" (ie. filled with junk, non-peer reviewed) journals, and then forcing university libraries to purchase access to the real, reputable journals only via an expensive bundle with many of those fake journals... (like saying: you need a toothbrush (price: $5), but you can only buy it in a bundle with toothbrushes for cats, dogs and every animal species (price: $5 each) for a total bundle price of $500). Something like that. I am in the mood for wild similes today.
Anyway, this was just one of the reason university libraries used to hate Elsevier's guts. Do a quick google search and you'll find the whole history. Including how disappointed people were when they bought the good old Mendeley.
As a start:
https://www.theguardian.com/science/2012/feb/02/academics-boycott-publisher-elsevier
https://www.theguardian.com/higher-...r/10/elsevier-buys-mendeley-academic-reaction

Thanks much for taking the time and elaborating - much appreciated.

 

[fortepianissimo]

Zotero on my Mac. I use the PaperShip app on iOS. I do pay $120 a year for unlimited space because I sync everything. So my highlighted docs are on every device. I highly highly recommend: so much so, that, as a broke graduate student, I am more than willing to pay the $120 per year.

I love PaperShip, especially the annotation functionality. But sadly it seems to have been abandoned (last update was in 2016), and with the latest iOS 12.1 beta the annotation icon seems no longer work.

Is there any new and regularly updated app? For me it has to have the ability to search/import papers from multiple sources (ArXiv, Google Scholars are the two main ones), and a good set of annotation tools, including handwriting (for math it’s absolutely needed).

 

[ahostmadsen]

There is a difference between storing a few dozen pdfs for fun and an academic research collection extending over thousands of PDFs. Academic reference managers can filter and sort by date, authors, subjects, journals, keywords, they can automatically fetch new articles from academic search engines, they handle citations in some word processors via plug ins... Documents by Readdle is a lovely little app but it's not the same thing as an academic professional tool. It's like comparing a home espresso machine with the customizable beasts they have in real coffee shops.

I store all my pdfs in Dropbox, and sync them to PDF Expert. That works very well (I am an academic).

I have all my references in Bibtex, but that of course only works if you write in Latex -- which is mostly the case in the sciences.

 

[va1984]

I love PaperShip, especially the annotation functionality. But sadly it seems to have been abandoned (last update was in 2016), and with the latest iOS 12.1 beta the annotation icon seems no longer work.

Is there any new and regularly updated app? For me it has to have the ability to search/import papers from multiple sources (ArXiv, Google Scholars are the two main ones), and a good set of annotation tools, including handwriting (for math it’s absolutely needed).

Papership has been abandoned, the devs have long been bought out.
Bookends is the only serious one left at the moment.
Readcube Papers has become a disaster...
Zotero still has no iOS companion app...
Mendeley still has no annotation support...

 

[MFDoom]

I am a big fan of DEVONthink 2 GO and LiquidText.

 

[ctg7w6]

I love PaperShip, especially the annotation functionality. But sadly it seems to have been abandoned (last update was in 2016), and with the latest iOS 12.1 beta the annotation icon seems no longer work.

Is there any new and regularly updated app? For me it has to have the ability to search/import papers from multiple sources (ArXiv, Google Scholars are the two main ones), and a good set of annotation tools, including handwriting (for math it’s absolutely needed).

I have since moved on to bookends.

 

[Bobdriving]

Current disgruntled Papers v3 user. Has anyone found anything better since the last post?

 

[va1984]

Current disgruntled Papers v3 user. Has anyone found anything better since the last post?

I have since moved on to Bookends too. Once you learn to ignore the rather ugly interface, it does everything it’s supposed to.

 

[xraydoc]

I use GoodNotes 5 to keep reference PDFs handy and for markup, and EndNote for iPad & Windows/Word to organize, store and format bibliographies.

I’m iOS for mobile, but at the moment prefer Windows 10 for the desktop. Fortunately, EndNote for iPad will cloud sync to EndNote for Windows (presumably for macOS as well, but I’ve not used it on the Mac in over a decade).

 

[Bobdriving]

I have since moved on to Bookends too. Once you learn to ignore the rather ugly interface, it does everything it’s supposed to.

Ah, interesting - see what you mean about the interface. Does the mac to iPad sync (and back again) work ok?Thats my major motivation for leaving Papers, sad to see what’s it become as it was great in v1 days.

 

[kristalsoldier]

I store all my pdfs in Dropbox, and sync them to PDF Expert. That works very well (I am an academic).

I have all my references in Bibtex, but that of course only works if you write in Latex -- which is mostly the case in the sciences.

I do something similar, but I use OnrDrive since I have an O365 sub.

 

[Kostas3000]

I do a lot of work in this field and I have tried almost all options.
I realized that couple of things mattered a lot to me:
1 the PDFs should not be locked in any app, but should be available in Files app. That makes it much more versatile, allows the use of a Shortcuts, future proof etc
2 iOS only workflows. I hate having to rely on my Mac to complete my work
3 workflow as simple as possible

The above led me to just organize the articles in iCloud with careful choice of tags, Folder names, file names (each person would likely need to come up with his own naming system, tailored to his needs)
When I need to cite an article in a manuscript, I use endnote. Endnote allows you to create temporary citation and the by using Endnote web, you can create the final bibliography


Do not lock your PDFs and your precious notes in any note that might stop be supported, that might decide to charge you with a subscription etc etc

 

[Yodalogger]

Bookends is really fantastic with a responsive development team. I think the Bookends pdf annotation ability is really pretty good, PDF expert is still a little better in my opinion. Being able to set up recurrent searches is also a useful feature. Very stable with my 5k+ Document library. Has ability to iCloud sync with an iOS app. Overall just a great app

 

[fortepianissimo]

Bookends is really fantastic with a responsive development team. I think the Bookends pdf annotation ability is really pretty good, PDF expert is still a little better in my opinion. Being able to set up recurrent searches is also a useful feature. Very stable with my 5k+ Document library. Has ability to iCloud sync with an iOS app. Overall just a great app

Overall agreed, but with a few wishes

* The UI really can use some polish (not the annotation UI - that part is wonderful).

* The search is hit-or-miss. Many times I typed a title verbatim but couldn’t find any result. Only when I reduced my query to one or two words did it work.

* If it can be used with Mendeley (where I stashed my papers) then that’s even better!

 

[canesalato]

There is a difference between storing a few dozen pdfs for fun and an academic research collection extending over thousands of PDFs. Academic reference managers can filter and sort by date, authors, subjects, journals, keywords, they can automatically fetch new articles from academic search engines, they handle citations in some word processors via plug ins... Documents by Readdle is a lovely little app but it's not the same thing as an academic professional tool. It's like comparing a home espresso machine with the customizable beasts they have in real coffee shops.



Because of the companies that acquired them. Mendeley used to be a neat bunch of folks. Same for Papers, they were PhD students in the Netherlands who hated Endnote for its general crappiness and high price. Then they were bought up, all of them, by big publishing giants. Except for Sente, which went bust (or anyway died off) and Zotero, which remains independent to this day.
Mendeley in particular had the misfortune of being acquired by Elsevier, which out of all the giant publishers had the reputation of being the most evil. Among the dirtiest tricks they used to play, is creating a bunch of "fake" (ie. filled with junk, non-peer reviewed) journals, and then forcing university libraries to purchase access to the real, reputable journals only via an expensive bundle with many of those fake journals... (like saying: you need a toothbrush (price: $5), but you can only buy it in a bundle with toothbrushes for cats, dogs and every animal species (price: $5 each) for a total bundle price of $500). Something like that. I am in the mood for wild similes today.
Anyway, this was just one of the reason university libraries used to hate Elsevier's guts. Do a quick google search and you'll find the whole history. Including how disappointed people were when they bought the good old Mendeley.
As a start:
https://www.theguardian.com/science/2012/feb/02/academics-boycott-publisher-elsevier
https://www.theguardian.com/higher-...r/10/elsevier-buys-mendeley-academic-reaction

great post

 

[ProteinePlus]

Are we talking of your own texts or PDFs?

Wow, almost a different option per post. Let me add to the chaos: Microsoft OneNote. It’s free, available for Mac and iOS, it interacts wonderfully with Windows and it’s well maintained.

 

[rhyzome]

I do a lot of work in this field and I have tried almost all options.
I realized that couple of things mattered a lot to me:
1 the PDFs should not be locked in any app, but should be available in Files app. That makes it much more versatile, allows the use of a Shortcuts, future proof etc
2 iOS only workflows. I hate having to rely on my Mac to complete my work
3 workflow as simple as possible

The above led me to just organize the articles in iCloud with careful choice of tags, Folder names, file names (each person would likely need to come up with his own naming system, tailored to his needs)
When I need to cite an article in a manuscript, I use endnote. Endnote allows you to create temporary citation and the by using Endnote web, you can create the final bibliography


Do not lock your PDFs and your precious notes in any note that might stop be supported, that might decide to charge you with a subscription etc etc

So what app do you use to actually open, read and annotate the files?

 

[Kostas3000]

So what app do you use to actually open, read and annotate the files?

pdf viewer

I have tried them all

pdf expert used to be my favorite but the poor integration with Files, the lack of any new updates, the loss of focus on developing good products of the parent company, the new absurd subscription model of $50/year made me move away

the important point is: do NOT get locked in any app

 

[Cruz3LT]

For books, my school uses VitalSource Bookshelf, there is an app for it as well as the website. It keeps everything all nice and organized.

 

[Bbloke]

For managing large numbers (e.g. thousands) of research papers, presentations, theses, and other documents, I've used specialist reference management software. Other tools which were not designed for this purpose might be workable, but I suspect they will not perform as well when it comes to organization and management of bibliographies. Years ago, I used EndNote on OS X. I stuck with a few updates, but I kept finding the software would "break" when there was an OS update, an update to Word, or the like and then the developers would offer a workaround rather than a fix, with the full fix coming in a paid upgrade... This happened a few times, so I did some searching and jumped ship!

The tool that I switched to was Sente. I primarily used this on OS X, but they also created an iOS version, so I began using both. Sente was excellent, both in terms of its GUI and its capabilities. In my view, this was the best reference management software I worked with and other companies were later adding capabilities similar to Sente's. Unfortunately, the developers began scaling back their support on the forums and then, one day, stopped responding and the server, using to sync between different devices, was taken offline. The developers seemingly gave their customers no official warning, disappeared, and left their customers hanging (and discussing amongst themselves to work out what was going on), something which I still think was disgraceful.

This forced me to jump ship once again. I looked at EndNote again, Mendeley, Zotero, Papers, ReadCube, and others. In the end, I opted for Bookends, which has both macOS and iOS versions. Bookends has been around for many years (longer than Sente and others) and I wanted something that would hopefully remain in business, as much as we can try to predict the future! Also, I was looking to make sure any app I invested in would also let me jump ship again if I needed to, so the ability to export libraries in common formats was important for me too. Bookends has some very capable features and the developers are extremely responsive. The GUI and some of the other features are still not as good as Sente was, but Bookends is probably more powerful than Sente (a simplistic comparison would be power user vs. "slick"), and their current iOS version is much better than Sente's iOS version was.

I'm happy with Bookends and I'd find life a lot more difficult if I was managing large numbers of documents myself and manually creating bibliographies!

 

[Kostas3000]

bookends is a legit option. However I found it’s UI too annoying to work with. Additionally the search function is unreliable (it doesn’t give the same results when searching pubmed in the native website vs from within bookends).
I have been burnt too many times in the past by getting locked in apps, that I cannot rely on creating my databases within any proprietary app system. Extracting the database from any reference management app loses information (like groups, subgroups etc).

My current workflow is as simple as possible. I keep my pdfs in the icloud, using the full power of Files app (folders, tags etc), syncing without any issues and knowing that I can move my library to any other operating system any time I want.

I still use readcube rarely by syncing some folders with Mac OS version of readcube. Readcube has a nice “recommended” function, it shows you the articles that citate the paper of interest etc

I also use rarely Endnote. I import the articles I want to cite, I copy temporary citations on Endnote iOS and I create the final bibliography with Endnote Web, allowing for a workflow that is 100% on iOS


Overall, my academic workflow is:

20% qxmed, browzine, Safari to search and download articles

75% pdf viewer to study-annotate the material and simultaneously write on Word and Apple notes

2% readcube to search for additional articles

2% Endnote to create the citations

1% Files app to organize folders

 

[iDron]

Interesting topic, I ordered an iPad for reading and annotating academic papers.
Seems like BookEnds is the way to go, in terms of a "EndNote-like" experience that also has a useable iPad App.

Anybody been writing papers in Latex with a Bookends bibliography (on Mac or iPad)?

 

[Easttime]

I’ve been publishing since before personal computers and into computers since the IBM 8088 processor PC. I’ve tried all kinds of software solutions for managing my huge electronic library and citing references in papers. I grew tired of fancy programs that sold out or were abandoned. I simply use the basic file folder system to store documents by topic, Word documents for summary notes and Endnote for citations and abstracts (university provides it). I’ve tried to use iPads for academic work, but always end up using a desktop mac with two big screens, and a MacBook for mobility. iPad is fine for lighter academic work, I find. Keeping it simple.

 

[T'hain Esh Kelch]

Interesting topic, I ordered an iPad for reading and annotating academic papers.
Seems like BookEnds is the way to go, in terms of a "EndNote-like" experience that also has a useable iPad App.

I've been using Papers2 to write several manuscripts, and been very happy with it. It was hands down the best bibliography and smat citation experience you can have for manuscript writing. Unfortunately it is pretty bug ridden, and stability has been going down as we got newer macOS releases. I never jumped to Papers3, because it was even more bug ridden. They then got bought up by Readcube, who gutted the application for features, and released a bare boned application on a subscription service no less. At least it is modern, and likely to get more features, and the smart cite feature and bibliography is still king of the crop IMHO. Give it a go, they have a free trial. Unsure if the smart cite feature works on iPad though.