Integrating Endnote with Ulysses III

As an academic researcher it saves a lot of time to use a bibliography database to automatically output citations in the correct format. Although Pages and Word have direct plug-in capability and is easy to use, often I find myself working in a text editor such as Ulysses III.

Currently I am using Endnote X6, however, it is likely other bibliography databases that have a scan paper function will work as well. To insert citations into Ulysses III so that Endnote will recognize them follow the format guides below.

Steps for generating bibliography with Endnote

  1. Save finished paper as Word .rtf
  2. Open up Endnote, and select Tools > Format Paper. Navigate to the saved file and Endnote will scan the paper and generate a new .rtf file with a bibliography in your chosen Endnote style.

Formatting guide for inserting citations into Ulysses III:

Copy each desired reference within Endnote and then \ Paste reference within Ulysses III.  To avoid using the backslash you can also modify {} as a markup symbol

Ulysses III tips

For author and date:
\{Hurst, 2002 #1796}

Results example:
(Hurst 2002)

For multiple citations:
\{Hurst, 2002 #1796}\{Hurst, 2010 #1636}
\{Hurst, 2010 #1636}\{Johnson, 2011 #739}

Results example:
(Hurst 2002, 2010)
(Hurst 2010; Johnson et al., 2011)

Add prefix to citation:
\{e.g.,\Hurst, 2010 #1636}

Results example:

(e.g., Hurst 2010)

Note:  To get the prefix citation to work you must add the backslash within the RTF document prior to Endnote scanning.  Ulysses removes \ on export to RTF.

Add page numbers:

\{Hurst, 2010 #1636:23-30}

Results example:

(e.g., Hurst, 2010:23-30)

Year only:

Hurst states \{, 2010 #1636} the following

Results example:

Hurst states (2010) the following

iPhone (ios) for use in archaeology: essential apps

Carrying a portable computer and camera in one small package is great for archaeological field work. I have relied upon my iPhone in the field for the past four seasons. Currently, I have the iPhone 5, which had a significant camera upgrade from the iPhone 4. It now has a great macro mode, and I use it to take great shots of artifacts in the lab. Here is an updated list of apps I use in the field.


Topo maps is a relatively inexpensive app for downloading and viewing USGS 7.5 minute quadrangle maps of the United States. The app provides a grid view of the topo quadrangles, and to download a map you simply click on one of the maps (for free). The real value of the app is that it uses your iPhones GPS capabilities to show your location on the topo map. You can set a waypoint, but what I mainly use it for is viewing my location on the topo map so that I can orient myself to the paper topo map that I carry with me in the field. It also uses the iPhones compass function and will also orient the map based on the direction you are facing.


GIS Roam

This is the best GIS app I have found. ESRI has some basic apps out for use on the iPhone, but I found these apps to be limited and too reliant upon their public cloud system. With GIS Roam you can view shapefiles and raster files of your project area right on your iPhone. You can also edit and add new data. Transferring files to the iPhone is a bit cumbersome, you have to do it through iTunes, but I found that it works rather well. It is a 10 dollar data connect fee to transfer the files. The major limitation of this app is that you are limited to the GPS accuracy of the iPhone. So you would not want to rely upon your iPhone for accuracy within a few meters, but within 20 meters the iPhone is accurate enough for site scale plotting and management.


Bento is a database. I use it for storing site information, c14 ages, etc., any information that I might need to have with me in the field. Unfortunately, they have discontinued Bento and is no longer supported. There is a rumor going around that Apple will include a Bento like product in their next iWorks update, which is already a few years over due.


If you have a phone signal than you can use soilweb. It uses your iPhone’s GPS location to determine the soil series that you are standing upon. Now there is no need to carry the County NRCS soils series book with you into the field if you have a connection.



As mentioned earlier, the iPhone camera just keeps getting better and better. Sure you can take better photos with an SLR, but who wants to carry around that bulky thing?

Check out this National Geographic blog on the use of the iPhone 5s camera.

One of Manitou Springs’, CO water fountains



I use the iPhones basic notes app, for record keeping, however, there is a multitude of other writing apps, you can PDF forms as well.

Post-PC or Original Hipster?

I am converting to using an ipad as my main research tool over a laptop or desktop computer.
After all my iPad and iPhone for that matter has a lot more power and ability than my first iMac or iBook computer that had only a 3G hard drive.

Caveat: I still use my MacBook Pro or Windows desktop for statistics, GIS, formatting manuscripts, and backing up data.

Why convert to a Post-PC device?

First off it is really cool being able to work from anywhere, and not to worry about battery power for most of the day. The other critical factor for me is that I think the iPad is the single greatest computer device ever invented. My mother uses an ipad and knows nothing about computers. I like how intimate it is to work on an ipad, it is more like working with a pen and paper at your favorite desk or table. I am also convinced I will read and write more since there are fewer distractions – as long as not too many games are downloaded anyway.

My Favorite Apps

Endnote: excellent reference and PDF manager, this app really makes it possible for me to leave the desktop behind.

Pages: only significant word processor on the market, I do enjoy using this app and having it sync with my desktop version, but I am waiting for the ipad version of Scrievner.

Numbers: only significant spreadsheet app on the market.

Keynote: only significant presentation app on the market; I prefer Keynote over PowerPoint on my desktop, I do not like the changes in format presentations go through converting from the desktop to ipad version.

Goodreader: best pdf reader app; I like the ability to export highlighted sections and notes that I then copy and paste into my notes section within Endnote. I typically open my PDF attached in Endnote into Goodreader due to Endnote’s limited PDF annotation capabilities.

Bento: great and easy to use database. I think it is quicker to enter data on my ipad than on a desktop spreadsheet or database.

Scrievner and Papers a winning combo

This past month I switched from Endnote to the reference manager Papers. Papers unlike Endnote X6 syncs your pdf library with your iPad or iPhone. And Papers is a lot cheaper than endnote. I have also enjoyed the search capabilities of Papers over endnote, and Papers does a better job of importing PDFs and finding the citation information automatically. Papers also allows for in-text citations, and you can insert citations while working within any program.

I have also been using Scrievner for the past year, which is a word processing program built for how you actually write. It is constructed on the philosophy of working on sections of a paper rather than the whole paper. You simply create sections, and then can reorganize the sections at a later date. It is both writing, organizing, and outlining at the same time. It also has a nice project goal feature that monitors the writers’ number of words at each writing session until the project is complete.

Both programs work on a Mac or PC and were created by independent developers. Papers was recently purchased by Springer publishing, and I assume Papers will be an important competitor to Endnote in the future.