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Summer Research in Digital

By Christopher P. Long on May 19, 2011 10:12 PM  |

Desktop Literacies
Originally uploaded by cplong11
This summer John Dolan, Director of Digital Media and Pedagogy, and I are heading up a summer digital research project in the College of the Liberal Arts. 

For a description of the project, check out John's post on our Digital Research in the Liberal Arts blog about the iPad Summer Research Project.

The iPad project is part of a larger initiative designed to put technologies in the hands of faculty to empower them to do scholarly research. What excites me most about this project specifically and the Digital Research Initiative more generally, is that it is driven by the idea that if we put technologies in the hands of faculty to pursue scholarly research, they will not only produce excellent new scholarship, but also they will learn the affordances and limitations of the technologies as they think about how to integrate them into their teaching.

By inviting faculty to use the technology for research they are already doing and asking them to reflect a bit in writing on a public blog, we hope to cultivate a community of digitally literate scholars who are doing excellent academic work.  The measure of success from my perspective as a scholar and an Associate Dean will not be the number of posts we write or the various aspects of the technologies we uncover, but the quality of the research we do, the articles and book chapters written, submitted and published, the manuscript and dissertation reviews we write, and the conference papers we submit.  


I hope you all will follow the Digital Research in the Liberal Arts blog and contribute when you are so moved.

Evolving Digital Research Ecosystem

By Christopher P. Long on December 27, 2010 10:00 AM  |

Final Edits
Originally uploaded by cplong11
In the months since my last posts on using Mendeley, Zotero and the iPad for academic research, my experience has been more fully informed by practice. This fall I was able to research, develop and write an essay on Plato's Apology for a talk and seminar I will be giving in Bogata, Columbia at the Universidad de los Andes.

The practice of doing research under extreme time constraints as I taught a 400-level course on Critical Theory and served as Associate Dean brought a number of important affordances and limitations of digital research into sharper relief for me.

For those who are uninterested in the details, my general experience is that while the iPad, Mendeley and Zotero continue to evolve in the right direction, there remains as yet no simple solution that will close the research circle of which I spoke last spring. And yet, the evolution of these tools - particularly improvements to the iPad's ability to handle pdf files stored in Dropbox and Mendeley's strong move toward mobile computing - has brought me closer to that vision.

For those of you who would like to hear some of the details about how I am using digital media to do academic research more efficiently and effectively, here they are:


Desktop Literacies
Originally uploaded by cplong11
First, sharing reference collections on both Mendeley and Zotero has become integral to my work. My research assistant, Sabrina Aggelton, is able to locate, identify and organize articles and books related to my work into our shared collection where the texts themselves are immediately accessible to me. This allows me to make the most effective use of the often very limited research time I have. When I do have time blocked off, I can focus immediately on the texts most relevant to my project. Because Mendeley organizes pdf files so well into files on Dropbox for me, I have used the shared collections on Mendeley rather than Zotero for this purpose.

Second, integration of pdf files with the iPad is much improved over the past few months.  Although Mendeley itself has an iPad/iPhone app, the application remains rather limited with respect to annotation, file transfer and even reading files on the iPad. I prefer to use Mendeley to organize my pdf files onto Dropbox, and then GoodReader with Dropbox integration to annotate and Evernote to take notes on the text. I often find myself reading via GoodReader on the iPad and taking notes on my laptop via Evernote.  I have even been known to use Evernote on the iPhone when reading articles on the iPad, if I am on the go. This is not an integrated solution, but I find that having all my notes accessible and searchable in Evernote works fairly well.

Third, Mendeley is unable yet to compete with Zotero in terms of its integration with Word processors for citation styles. Mendeley does not yet support footnote citations in the Chicago Manual Style (my preferred method), so I return to Zotero when writing. This means that I need to continue to make sure that references added to Mendeley are entered in Zotero.  Mendeley is able to read Zotero databases and display and organize pdf files from Zotero, but Zotero does not yet play with Mendeley in the opposite direction. Happily, it is extremely easy to add references to Zotero from the web, but still, this is an extra step when entering references. 

I would like to consolidate all my references into a single program if possible. A few months ago, I thought that program would be Mendeley, but the announcement of Zotero Everywhere makes me think that Zotero might yet win that battle. Mendeley is ahead of Zotero in iPhone/iPad development and pdf file organization, Zotero ahead in terms of citation integration with Word processing. The future of Zotero depends upon its development of a stand alone desktop app and integration into web browsers beyond Firefox. It will also need to develop a software solution for mobile devices. I am not sure, however, that it sees itself as a pdf organizing program, so in this regard Mendeley may have the advantage.

As I reflect upon the state of my digital research ecosystem, I am encouraged by the increasing ease by which scholarship can be accessed and organized online. Not only do I have access to a huge number of digital resources through Penn State's excellent library, I also use Google Books and Amazon.com to access and gather references from hundreds of thousands of books. Happily, as I move further into my own administrative work, the resources that facilitate the academic research that remains of central importance to me continue to improve. They have, however, yet to mature to their full potential. 


Mendeley on the iPhone

By Christopher P. Long on July 20, 2010 11:38 PM  |

Mendeley on the iPhone
Originally uploaded by cplong11
I am happy to report that Mendeley has developed an iPhone app that brings us a step closer to the digital research model I hope to implement in the months to come.

Before I mention a few of the limitations of the application, I want to celebrate its very appearance. This is a huge step forward in mobile bibliographic and reference computing.

About three years ago, I had a phone conversation with a person in the sales department at Thomson Reuters, the company that makes Endnote. The purpose of my call was to see if they were developing a version of Endnote for the recently released iPhone. They told me that they did have plans, once Apple released the Software Development Kit, to develop a mobile version of Endnote. Already at that point, I could see the value of having my references so easily accessible.

Although that application has yet to materialize, I shifted, in the meantime, to Zotero because it facilitated the sort of collaborative research I hoped to put into practice with my students. As I mentioned in my previous posts on digital research more generally and on the way I use of Zotero in particular, a significant limitation to all the bibliographic software was the inability to use anything other than the web browser to interface with my reference libraries when using my iPhone and iPad.

I turned to Mendeley in the hope that I would find an application that would have all the collaborative functionality I required even as it allowed me to organize, read and annotate pdf files in a way that would integrate with my word processing software. I am very happy with Mendeley when I am sitting in front of a desktop computer. However, it is critical to the model of digital research I am trying to establish that all my references be accessible to me on all my devices wherever I am.

This is where the new iPhone application, even if it is tantalizingly labeled 'Lite', adds substantive value to my research workflow. The application syncs with my Mendeley libraries beautifully and allows me to read any of the pdf files I have posted to it. In the photo on the right, you can see the collections exactly as they appear in the Mendeley Desktop application and on the web.

If you have pdf files included in those collections, you can access them via the mobile device, assuming you are connected to the internet, by downloading them individually. This allows you to effectively carry your entire reference library in your pocket, putting thousands of pages of scholarship at your fingertips wherever you are.

For all of this, however, the application's features remain rudimentary. You cannot annotate pdf files via the application nor can you edit any of the tags or bibliographic information associated with the references. The first iteration of the application is clearly designed to establish Mendeley in the mobile space - a place it basically has all to itself at the moment. But is also gives us a taste of possibilities to come.


PDF via Mendeley on the iPhone
Originally uploaded by cplong11
As for some of those possibilities, I would hope that this is the first stage in a series of upgrades on the road to a single integrated iPhone/iPad application. 

Porting such an application to the iPad has enormous potential for scholarship. If it allows for annotation, we will have a powerful new research tool on which to actively read texts related to our scholarly work. Building on solid web and desktop applications, Mendeley for the iPhone and iPad would offer us an integrated way to do serious productive research wherever we find ourselves. This will allow us to move more quickly from the research gathering to the productive writing phase of the process.

In the end, I am very happy to see the first iteration of this mobile reference resource. I look forward to the updates and to the "Pro" version, if indeed, that is the direction toward which the label "Lite" is gesturing. 

Despite some reticence at first, the appearance of the iPhone app tips the balance for me and I am now moving all of my references over the Mendeley in anticipation of upgrades to come.

Integrating Mendeley into the Research Circle

By Christopher P. Long on June 3, 2010 9:26 PM  |

Mendeley
Originally uploaded by AJC1
It seems that my quest to close the digital research circle has been joined by a few fellow researchers. 

The idea is compelling and would not only save both time and paper, but would offer new opportunities for collaborative research.  

In my post, Closing the Digital Research Circle, I outlined the basic structure by which we could download PDF files into a reference management system that would handle bibliographic data and manage the PDF files themselves. These libraries of files and data would be sharable with others, or made private. Notes could be take digitally, the files could be annotated and remained synced in the cloud so they are accessible across multiple devices. Finally, the bibliographical information would interface seamlessly with word processing programs so that the transition from gathering to integrating to processing research and, ultimately, to creating new work could be done dynamically and digitally.

In the weeks since I wrote the post on Closing the Digital Research Circle, and the follow-up post, Zotero, the iPad and Summer Research, I have started to play with Mendeley. 

Mendeley is being designed and developed by the people who made Last.fm, and the idea is to do for research what Last.fm did for music. What they have done for me, though, is offer an easy way to organize all my pdf files with their bibliographical information. They have also given me an easy way to create a digital vita with links to pdf files of my work accessible to those who visit my Mendeley Profile.

Mendeley has both a web interface and a client. Applications for the iPad, iPhone and Droid are being developed, at least according to William Gunn, who has been very helpful in introducing Mendeley to me. Having played a bit with Papers, Mendeley has much of the same file managing functionality and the same iTunes-like ease of use, but adds the dimension of bibliographic information and the ability to share libraries on the web.

The benefit of Mendeley over Zotero is that Mendeley also gives you the ability to annotate PDF files right in the program itself. The social side of it is also more dynamic than Zotero. The strength of Zotero over Mendeley is its ability to simply bring bibliographical information from the web via the Firefox web plug-in into your library.  Zotero does this beautifully. Happily, Mendeley integrates well with Zotero and you can have your Zotero library sync with Mendeley.

So, we are now getting closer to the ultimate vision (although I am still thinking about how best to integrate ebooks into the process, but one thing at a time). Here is what I do now:

  1. Download bibliographic information and pdf files into my Zotero library using the Zotero Firefox plug-in.
  2. Sync with Mendeley to bring the Zotero information and the files into Mendeley.
  3. Have Mendeley organize my pdf files to a folder on Dropbox.
  4. Using the iPad Dropbox application, connect to the folder into which Mendeley has organized my files.
  5. Pull up the paper, read it in Dropbox without annotation, OR
  6. Using the Open In button at the top right, open the file in iAnnotate for the iPad and do annotations right there.
  7. Sadly, to return the document to Dropbox, you will need to email it back to yourself and overwrite the file in Dropbox - this is the weak link at the moment.

So, we are getting closer here. I am very hopeful that a Mendeley iPad application will have adequate annotating capabilities and file managing abilities, but until then, this just might work for me. 

Zotero, the iPad and Summer Research

By Christopher P. Long on May 21, 2010 9:51 PM  |

Zotero Icon
Originally uploaded by lorda
Last month in a post about closing the digital research circle, I wrote about using the iPad to read, take notes on pdf files and integrate those files into a bibliography program. We are still some distance from the vision of the closed research circle, however, there are some positive new developments.

First, I upgraded my Zotero account by buying 1GB of storage. This allowed me to transfer all my citations along with their pdf files to the Zotero servers. This was a decisive step because now, when I access my Zotero libraries through the web, I can read the pdf files directly from the Zotero servers.

This is important because now through Safari on the iPad, I can access those files directly and read them right there on the iPad or iPhone, for that matter.

My research assistant, Josh Testa, and I have begun using a closed but shared group library to collect articles. He is gathering them together in the shared group, leaving me notes as to what he thinks is relevant in the article to the book project on which I am working, and I can view both the pdf files and his notes online.

I am still missing an integrated way to annotate the pdf files, but we are moving in the right direction here. The iAnnotate program on the iPad is improving, but the manner in which files are transfered remains unwieldy. What I really need is a way to pull the pdf files from the Zotero server onto the iPad, annotate them, and have them sync back up with the Zotero database. If the Zotero database functioned more like Dropbox does on the iPad, and if Dropbox had the functionality of iAnnotate built into it, then we would be very close.

As it stands, I am nevertheless excited to see how the group library Josh and I are working on will grow and, in particular, how this sort of collaboration will shape my work in unanticipated ways.

Closing the Digital Research Circle

By Christopher P. Long on April 15, 2010 8:07 AM  |
I have been looking for a way to close the circle of my digital academic research. The idea is to do rigorous philosophical research without paper, taking full advantage of cloud computing, the syncing of notes, articles, bibliographic information, and the ultimate production of academic work in a completely digital environment. 

I took a decisive step in this direction when I adopted Zotero as my main bibliographic tool. Still, Zotero is bibliography software, and it does not facilitate the reading, note taking and organization of articles and books digitally on mobile devices. 

Now, however, with the iPad, I am tantalizingly close to a process that closes the research circle. The problem is that there is no Zotero or Endnote for the iPad...yet. Even so, such bibliographic programs would need to add the functionality of PDF file and ebook reading and organization. 

If they did, the research circle I envision might look like this: Online library research would be directly downloaded as PDF files or ebooks into my bibliography database. It would sync with an app on the iPad and iPhone where I would easily read the text, annotate it, take notes, etc., all of which would stay with the digital article/book and it's bibliographic information. When I begin to synthesize my research, I would be able to search all my notes, which should be organizable via tagging. As I write, I should be able to pull the bibliographic information into my word processor, refer easily to my notes, pull up articles and books, and continue the circle of research and writing.
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