How to use iPad if you are a researcher in conjunction with endnote

[zigidabee]

Endnote, Dropbox and iAnnotate

Jonsims, many thanks for your feedback. I'm going to try Germwise's system if and when I can understand how he makes it all work for him. However, in the meantime, I'd like to try it your way, using Endnote (on my pc), Dropbox, and iAnnotate (on my iPad).

Could you help me with my current situation? Here it is:

1. I've got my pdfs in iAnnotate on my iPad. While on iAnnotate, I uploaded a pdf to Dropbox for fun i.e. as a test. I couldn't 'see' any folders in my Dropbox app on my iPad, so I just clicked on 'upload' and it uploaded. I checked my Dropbox web account, and in my account was a folder called "iAnnotate PDF" (I am guessing iAnnotate created this.) In this folder was my pdf. So, if this is what should happen to 'sync' my iAnnotate pdfs with Dropbox, I'm ok with this (although i thought it was supposed to update my Dropbox pdfs automatically without me doing any uploading, no?).

2. Now, I'd like to try and sync Endnote on my pc with Dropbox so that my Endnote pdfs are automatically updated. However, I can't get my head around how to do this. Currently I don't have any Endnote set up with a library yet, and there are not pdfs linked to Endnote. I just don't know how to do this with Dropbox.

Endnote uses 'Filter', 'Styles' and 'Connection' folders, a library file, and a data folder, from what I've read in the instructions. I don't really know what the 'Filter', 'Styles' and 'Connection' folders are for. But, where should I put them? When installing Endnote, I believe that Endnote automatically puts these folders in My Documents, but shouldn't I put them in somewhere where Dropbox can find them? In other words, where should I put these Endnote folders, and how to let Dropbox know where they are?

3. I THINK Endnote uses the library file for storing reference data for each and every pdf, yes? Then, where do the actual pdfs reside? Where should I store these pdfs, and how to let both Endnote and Dropbox know where they are?

The i) 'Filter', 'Styles' and 'Connection' folders, the ii) Endnote library file, and the iii) actual pdfs: where should all of these be placed? In one main folder I create myself?? If so, where should this main folder be placed?

4. Whatever I do for step 2 and 3 above, what then do I do about the iAnnotate folder in Dropbox that was created by iAnnotate. Should this folder be in the main folder I create above along with the Endnote folders and files?

5. How do I get all my pdfs from iAnnotate to Endnote? (I'm guessing that they should be moved to a folder first, yes? Then, I can use Endnote to create reference data for each pdf, and this data will be stored in the Endnote library file???

Jonsims or any of you other technologically gifted folks out there, if you can in any way help me 'see the light' with all this, it would be much appreciated.

 

[steadysignal]

I used papers for a while and I was not impressed.

I didn't use the ipad for much other than reading papers and maybe some surfing.

how do you justify owing a computer then?

almost everything you can do on a computer in terms of consumption you can do on an ipad. what was it, the cost, the form factor, the buyers remorse?

workflow is workflow.

i have several macs and an ipad. i also have many electronics tools. and i often only use an expensive tool once a month. but it fits the workflow. just as the ipad fits at certain times when the laptop of desktop does not.

its a shame for you to be non-plussed by this device. not knocking you, i just don't get it.

 

[Pennrick]

Workflow- uploading papers to endnote

I use endnote to download my papers, it organizes them in folders if I choose, it keeps the download link, and the pdf file accessible and is fully searchable.

This is a great thread with some really useful ideas. I believe there is a universal struggle to manage all the information we are bombarded wtih.

Like others I have downloaded a number of PDF annotation apps for my ipad. PDFAnnotator is good but I am seriously missing the PDF Annotator program developed by Grahl for Windows. Think I need to play further on the other apps as they are just not feeling very intuitive at the moment.

One question I have is regarding the reference to downloading papers into endnote. I think I am doing this wrong as it is not keeping the download link. Can someone provide further guidance?

Thanks

 

[Piereric]

Extremely useful thread. Thanks for all the info.

My question / contribution to the debate is :
with the recent Endote X5 annotation option, is it still worth it to switch to Sente and/or iAnnotate? I read an Endnote app will be available for ipad eventually, has anyone tried it?

I am considering to purchase an iPad to read and annotate scientific articles but I wonder, is it really more convenient than to do it on your laptop?

Thanks

 

[jojoba]

I'm also a researcher and I use PDF Expert (and to a lesser extent, iAnnotate) to work with journal articles. I sync with Dropbox (not Aji) and this works very well for my purposes - then the latest version is always available both on my work computer and my MBA. I keep a copy of my entire research library in Dropbox.

My university only supports EndNote as a reference manager so I've stuck with that, and like others I'm missing an iPad app that can be synced with my main library. However, it's not really a huge issue for me, as I don't use it as my main file manager and therefore only use it to actually insert references. If I'm not working from the office, I access my EndNote library using remote desktop - in this way I also avoid using two or a travelling library, and my references don't get messed up.

To Piereric, yes I've definitely found it more convenient working with my docs on an iPad than a computer - primarily because of the ease with which I can carry around my entire library, and the opportunity to annotate and make notes using a stylus pen in addition to a keyboard. This was actually my main motivation for getting an iPad, to me it's primarily a tool for work rather than for fun.

I've downloaded Papers but to be honest I'm not quite sure exactly what the added value is. For those who are using it on a regular basis, can you let me know what you use it for?

 

[metanoiac]

Anyway, so I've been tempted by what I've seen/heard about Sente 6. The seamless integration with the iPad, including annotations, looks really cool, but I've read that any annotations made using Sente on the iPad aren't baked in to the actual PDF, meaning that they won't show up when you view the PDF on your Mac using Preview. If so, that's definitely a deal killer for me.

Sente works best I find when combining the iPad and the Mac version. On the Mac, you can print a paper with its annotations, and this would let you "bake in" the annotations. Not ideal, but the idea of Sente and Papers is I believe really to offer an ecosystem for your research.

 

[metanoiac]

I've downloaded Papers but to be honest I'm not quite sure exactly what the added value is. For those who are using it on a regular basis, can you let me know what you use it for?

Jojoba, the added value for me are the database management features of Papers and Sente. Both let you add the same paper to different collections (in slightly different ways), and you can add ratings and notes to the papers. Sente also lets you add tags (this is also the best way to create "smart" collections) to your papers. Papers for iPad does not do this, but its Mac version does (they call it keywords).

In general, the fact that both apps have Mac counterparts is a great deal for me. I use the iPad for reading, and the Mac version for adding / matching papers into my database and to build the reference list in my write-ups.

 

[jojoba]

Jojoba, the added value for me are the database management features of Papers and Sente. Both let you add the same paper to different collections (in slightly different ways), and you can add ratings and notes to the papers. Sente also lets you add tags (this is also the best way to create "smart" collections) to your papers. Papers for iPad does not do this, but its Mac version does (they call it keywords).

In general, the fact that both apps have Mac counterparts is a great deal for me. I use the iPad for reading, and the Mac version for adding / matching papers into my database and to build the reference list in my write-ups.

Thanks, metanoiac!

I'm going to look into this. I'm a bit uncertain what tools to rely on now with my research. At work we have PCs (and specific software programs that we get for free/ are supported if we get any trouble - e.g. EndNote is the only reference manager that is 'officially' supported), so I don't want to give up on that. On the other hand, I'd like to use the potential of apps like Scrivener (which I'm planning to use for my next article, that will be a first) and other stuff to maximise utility. At the moment, I'm only using EndNote for reference purposes and not really for document management. Tags would be a GREAT improvement to my library management. At the moment I'm just using folders, which are synced across my folder structure on my PC, Dropbox, and PDF Expert on my iPad.

I guess I just really need to look a bit more carefully at my options and think through what the best way forward is.

 

[metanoiac]

Jojoba:

I put up the post today. Maybe it helps you in your decision. Good luck!

 

[jojoba]

Thanks for that, it's very helpful to read your blog.

With regard to your table comparing annotation/reference manager apps, iAnnotate now offer tags (which is the main reason why I am switching from predominantly using PDF Expert) - so I think I may have found my main pdf reference manager for now.

 

[metanoiac]

With regard to your table comparing annotation/reference manager apps, iAnnotate now offer tags (which is the main reason why I am switching from predominantly using PDF Expert) - so I think I may have found my main pdf reference manager for now.

Thanks for pointing out the tagging function on iAnnotate. I have missed that.

Do you know if the tags that are assigned to PDFs on Mac OS carry over when accessing the file on iAnnotate via dropbox?

 

[jojoba]

Thanks for pointing out the tagging function on iAnnotate. I have missed that.

Do you know if the tags that are assigned to PDFs on Mac OS carry over when accessing the file on iAnnotate via dropbox?

I think it's been very recently introduced - and no, I haven't tried out 'transferring' tags (I've just recently bought my MBA so all my pdfs originate from my PC which doesn't, at least to my knowledge, tag my pdfs). Let me know if you try it out - it would be extremely useful if it could just be synced.

 

[metanoiac]

I think it's been very recently introduced - and no, I haven't tried out 'transferring' tags (I've just recently bought my MBA so all my pdfs originate from my PC which doesn't, at least to my knowledge, tag my pdfs). Let me know if you try it out - it would be extremely useful if it could just be synced.

Unfortunately, it doesn't.

 

[imMango]

For those of you that use the Endnote-Dropbox-Goodreader combo, do you have issues with the Dropbox sync via Goodreader taking a long time because Endnote stores each individual PDF in its own folder? It seems whenever I press sync on Goodreader, it spends a good minute or two just scanning the folders before any actual data synchronisation occurs. Very annoying.

Of course if there's someway to stop Endnote from doing this that would be good. Or any other workarounds?

 

[Bce1]

I use Sente for just about everything - but I have a copy of endnote to utilize cite as you write. When I'm doing a a paper I export my Sente library and open it into endnote - a bit cumbersome ( only takes 2-3 minutes) but mostly gives me best of both worlds.

 

[jojoba]

I'm trying out some new work flows at the moment. Here's my current set up:

1. As previously, I'm reading and annotating PDFs with iAnnotate. This is synced with my main research library folders on my work pc via DropBox.

2. I'm now doing my writing on my my MBA and work pc in Scrivener, which syncs with SimpleNote on my iPad.

3. I've more or less given up on EndNote, and converted to Papers2. I'm still testing out the latter, but so far it's looking good. I can cite while I write in Scrivener as well as Word, and they are just out with a windows version as well which should make it much easier to work across platforms compared to EndNote.

metanoiac, your recent comparison of Papers2 and Sente was very useful for me!

 

[jojoba]

For the Papers users: how can I add references directly to Papers from library searches and google scholar? This still appears to be much easier with EndNote, or maybe there's a code here I haven't cracked yet?