My Papers to Sente Workflow

In a previous post I discussed two great programs, Third Street Software’s Sente & Mekentosj’s Papers, for managing your bibliographic data on Mac computers. Papers, in my view, is much better at finding references and PDFs but Sente is great at getting those references into your documents. I love having both, but if you can only buy one program I would recommend Sente. It has the added functionality of document citation and allows you to find references too, I just don’t think it’s as enjoyable to use as Papers. The setup below allows me to use the best features of each program and really enhances my personal research.

Since I have three Macs that I use regularly (my primary computer is a MacBook Pro, but I also borrow my wife’s iMac on occasion and have a Mac Mini at work) it’s important that I not only keep Sente and Papers in sync with each other, but also keep those two programs in sync on three different computers. Thankfully this isn’t all that hard to do.

The setup below assumes that you prefer using Papers as a reference finder basically just want to use Sente to cite those references. If that’s not the case, then there is probably an easier way to sync the two.

Step One: Sign up for a Dropbox Account

[If you already have a Dropbox account, skip to Step Two. If you only have one computer this is optional, though still highly recommended since you’ll essentially have an off-site backup of all your references.]

After you sign up for an account you’ll download the Dropbox application. This will install a folder on your computer and anything you put in that folder will be seamlessly synced to any other computers where you do the same. It’s quite amazing how well this program works. It’s also free for up to 2GB of data (if you use this link we’ll both get an extra 250MB worth of space).

Dropbox will create a new folder called “Dropbox.” You get to choose where you want that folder to be located so I’d pick a place that’s easy to navigate to. Regardless where you put it, just remember the location.

Step Two: Move your Papers Folder to the Dropbox Folder

All the files that Papers uses are conveniently located in one single folder called “Papers” (unless you changed it to something else when you installed the program). Move that folder into the newly created Dropbox folder. The next time you run Papers it won’t be able to find the files that it needs, but it’s relatively straight forward to select the new location within the Dropbox folder. Once you’ve done that you can continue to use Papers just like you did before. Repeat this process on any other computers you use and you’ll always have the exact same reference library on each machine.

If you have the basic (i.e. free) Dropbox account you only get 2GB worth of data to sync. Some may be worried that having your entire reference library will take up too much space. That may be true for some people, but to give you an idea of what to expect I have over 400 references from my Papers library, all my dissertation files, and four years worth of class files and I’ve only used just over 30% of that 2GB. (That will continue to grow, but Dropbox has a generous referall program – see link above – that allows for up to 10GB for free. If you need more than 10GB of data then you can buy additional space at a fair price.)

There is one more thing you’ll need to do before we move on. In Papers create a “Smart Collection” with some specific rules. All you need to do is select ‘File’ then ‘New Smart Collection’. From the popup window select “Date of Import” for the first dropdown menu, “After” for the second menu, and then type today’s date in the third box. Any references you find on or after that date will automatically be added to that smart collection (we’ll change that date later on, but today’s date is fine for now).

Step Three: Set up Sente to Work with Your Papers References

What I want between the two programs is for each to always have the exact same references on all three computers. If you’ve been using Sente and Papers together already, then you’ll need to figure out a way to merge the two into one. I didn’t want to mess with that hassle and just created a brand new library within Sente. That may not be an option for you if you have two significantly different sets of references. Merging the two goes beyond this guide so once you get that figured out, come back and see how to keep them in sync.

One of the advantages of Sente over Papers is that it has built in syncing for your files and references. So if all you are using is Sente you don’t even have to bother with Dropbox because the program itself will automatically stay in sync with your other computers. The downside to using the built in syncing with this setup is that you’ll end up with two copies of each PDF. If that’s something you want to avoid then you can tell Sente to only link to PDF files and not copy or move. That’s what I’ve done.

To set it up just open Sente, go to the preferences pane, and select ‘Attachments’. Choose to ‘Link to the file where it is’ and then close the preferences pane. When it’s time to get the Papers data over to the Sente program all the bibliographic data from Papers will be copied over, but the PDFs will stay where they are.

To keep that bibliographic data in sync across multiple computers you’ll also need to turn Syncing on within Sente. This can be done in the preference pane, but for more detailed instructions I suggest visiting their website. (It is very easy to do.)

Step Four: Finding New References

Now is the fun part. Open Papers and find new references and PDFs. When you’re ready to start citing them in your word processor (or just want to have these new references in Sente) select the smart collection you created in Step Two (I called mine ‘Transfer’ just to make it easy to find) and then go to ‘File’, ‘Export’, ‘EndNote XML Library’. A popup window will appear. In the first dropdown menu select “Selected Group” and in the second “Endnote 8 or higher.” Give the export a name and save the file to a place easy to find.

Next, right click on the smart collection from Step Two and change the date to the current date (this will prevent you from getting duplicate references in Sente). For example, if you’ve been adding references to Papers for two weeks, then the smart collection will only pick out the references you added within those two weeks. After you export them to Sente you don’t want to export them a second time so just change the date in the smart collection rule to the current (or next) day. The next time your export your references you won’t have any duplicates.

Step Five: Importing Your Files

Open the Sente library you created in Step Three and select ‘File’, ‘Import’. Navigate to the file you saved in Step Four and click ‘Open’. Now all the references you had in Papers are now in Sente along with links to the associated PDFs. Sente will take care of syncing each computer’s references on its own and the Papers references are kept in sync via Dropbox. Additionally, because Sente is only linking to the files in your Dropbox folder you’re not getting two of every PDF file.

A Caveat

All things are not perfect and neither is this. If you have more than one computer and the Home Folder does not have the same name on each computer then Sente will not be able to locate the “linked to” files on the additional computers you set up. You have two options: change the name of your Home Folders to match or copy the PDF files instead of linking to them. Doing the first is cumbersome, but not difficult if you follow these detailed instructions. (Please do a quick Google search about changing the name of your Home Folder before engaging in this task. I’ve had no problems with this, but would feel bad if you did and I didn’t warn you.) The second avoids this process but you do end up with either multiple copies of each PDF (if Sente copies the files) or no PDFs for Papers (if Sente moves the files). Since I like to read my PDFs in Papers because of its outstanding PDF reader, I decided to just make my Home Folders match and haven’t had any issues with it at all. (Occasionally you may have to update where a program thinks it’s files are since it’ll look for them under the old Home Folder name. It takes 2 seconds to navigate to the new folder so that wasn’t a big deal for me.)

Conclusions

I hope that this makes your academic research easier. It’s only a small amount of work to set up, but once you have it will truly revolutionize your work flow. I simply love being able to sit down at any computer I own and know that I have all my references and PDFs and any new ones I find at that computer will be accessible at all my others.

Overview

This may seem like a complicated process, but most of the above are one-time-only tasks. Once everything is set up, here’s what the workflow looks like.

1. Browse for new references and PDFs using Papers.

2. As needed, export the Smart Collection within Papers as an ‘EndNote 8 or higher’ file.

3. Import that file into Sente.

4. Use Sente to cite those references in your masterpiece!

5. Publish said masterpiece and get tenure!

Dropbox ensures that all my computers always have the exact same Papers library. Exporting the smart collection gets all that information to Sente which is responsible for syncing the information to Sente on all of the other computers.

So, what do you think? Is there any easier way to accomplish the same thing? If so, please let me know in the comments.

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Leave a comment

15 Comments

  1. Andre

     /  June 23, 2010

    Thanks for sharing! I’ll be looking close to it.
    Best,
    André

    Reply
  2. Reese

     /  July 1, 2010

    Thanks, this is nice. A couple things to add.

    1)Let’s say you have a laptop and desktop with all of the above configured. To keep the libraries synced correctly, only run papers on one of them at a time. That is, quit one before you start the other. Also make sure dropbox has time to update files. For more information see: comment #7.

    2)If you suffer from the caveat above where your home directories have different names and you wish to use the /home/username/Dropbox/Papers route, you can do this by making /home accessible again. Here is a step by step explanation of how to do this. I chose to change the name of the automount folder to “auto_home” and this has not caused any problems after a week of use. (Note the point of the thread is not related to papers/dropbox, but it does provide a solution for using the /home folder on OSX 10.5.) Give yourself read/write permissions, then simply create a folder /home/username and place your /Dropbox/Papers folder in it.

    3)To my knowledge sente 5 does not have built in syncing, which is especially relevant if you run OSX 10.4. There are many workarounds for this. I have been creating a file analogous to the one created in step 4 in my dropbox and importing into sente when necessary.

    Enjoy.

    Reply
  3. Reese

     /  July 1, 2010

    Oops – it would be great if someone could properly close my ‘s for me.

    Thanks.

    Reply
    • Reese,

      Thanks for those tips. I guess I’ve lucked out regarding having two copies open at once, but I’ll be sure to keep this in mind in the future.

      Reply
  4. Reese

     /  July 2, 2010

    Thanks again for the guide and also for cleaning up my post.

    Reply
  5. sam

     /  October 1, 2010

    thanks for all the info! i have been trying to come up with a way to keep all this information updated. with multiple computers and worksites. it has been driving me crazy. looks like i can use sente and papers and not keep two sets of information for both programs. This will really be useful. I will make sure you use your link.

    sam

    Reply
    • I’m glad you found this helpful. I’ve been kicking a few ideas around about how to make the flow a bit more streamlined in the other direction (Sente’s PDF browsing keeps getting better and sometimes it’s more reliable with my institution’s library than Papers). If I come up with something I’ll update the post.

      Thanks for using the link too, growing PDF libraries need more and more Dropbox space!

      Best, Paul

      Reply
  6. John

     /  November 30, 2010

    Thanks a lot for this… I’ve been running your exact Papers/Dropbox setup for a while now and just love Papers for finding/reading the published literature in my field as well as the certainty that I have equal access from home or office. I need to integrate reference management and the automatic citation generation into my workflow, and you may well have given it to me. I’d entertained the idea of Sente already but there is just so much overlap with Papers. I do want that “automagical” citation generation in my word-processing (Pages) document though.

    Thanks again!

    Reply
    • Thanks for feedback, I’m still fiddling around with the workflow but keep coming back to the one I’ve already got . So are you still considering Sente or have you already bought in? If you do start using the two together, feel free to let us know if you come up with a smoother/more robust workflow. My goal is still to figure out how to get a true two-way sync (I’ve got to do ‘something’ besides actually finish the dissertation!).

      Best,

      Reply
  7. David

     /  December 4, 2010

    Thanks for this great idea. I use EndNote X3 and Papers and think that the logic of your workflow will apply in this case too. We’ll see! Would be interested to know if any of your readers have tried this.

    Reply
  8. Yue

     /  March 21, 2011

    Great post. But do I have to search or enter the paper info for each pdf again when I’m importing pdf from papers to sente? If so, it’s kind of annoying.

    Reply
    • That’s a good question. In my experience using the method above keeps all the metadata as it was in Papers. There are a few differences, but they’re more due to Papers limitations than the export process. For example, Papers doesn’t have categories for book chapter or book reviews so those would have to be modified in Sente.

      Now that Papers2 is out I’m hoping to do another evaluation to see if Papers-to-Sente is any easier. (Hopefully Papers2 will get citation features for Mellel, if so then I may not need Sente anymore.)

      Thanks for stopping by!

      Paul

      Reply
  9. KDowns

     /  November 15, 2011

    Any ideas for how you could integrate a PC into a Papers/Sente or Sente workflow? Say with Refworks or Mendeley? I enjoy using Papers on my Mac but have been considering moving to Sente for many of the aforementioned reasons. However my department also provides me with a PC laptop and I’d like to be able to have some interfacing between the two.

    This may be too much to ask but I’d love to be able to take advantage of Papers and/or Sente without purchasing other software (Endnote) and still be able to use both computers (Mac and PC), even if I can do more on my Mac than my PC.

    I’d appreciate any ideas. Thanks!

    Reply
  10. Kaishu

     /  October 20, 2012

    Hi Paul,
    Will you have a chance to write an up to date review, especially because they both have their own iPad apps an all?
    Best,
    Kaishu

    Reply
  11. Great post! We are linking to this great article on
    our website. Keep up the great writing.

    Reply

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