The Digital Research Circle Completed

By | Digital Research, The Long Road | No Comments

In April 2010, I began blogging about closing the digital research circle. The iPad had just been released and I had just moved from Endnote to Zotero to take advantage of its ability to share collections and foster collaboration. It was a heady time and I was excited by the possibilities these new technologies offered for a completely digital research cycle.

The hope was to be able to move through the gathering, annotating, note taking, crafting, writing and citing phases of my academic research without printing or interacting with paper.

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Research Cycle Returns to Zotero

By | Digital Research, The Long Road | 6 Comments

Even as I press to finish an article on dogs and wolves in Plato’s Republic for a volume entitled “Plato’s Animals” edited by Michael Naas, it is worth returning for a moment to our ongoing discussion of digitally enhanced research.

When I first wrote about my attempts to close the digital research circle in 2010, I had just relinquished EndNote in favor of Zotero for its superior ability to share and organize references. At the time, Zotero was still a plugin for Firefox and lacked a number of features I needed to facilitate my research – features like the digital reading, annotating and organizing pdf files. Those limitations led me to Mendeley, which I still value for collaborative annotations and research.

However, with three developments in Zotero, I have returned to it with renewed commitment. One reason for this commitment has less to do with features and more with the underlying open source philosophy of the product’s development. Zotero was developed by the Roy Rosenzweig Center for New Media, a leader in digital humanities scholarship and a strong advocate for open collaborative research.

Although I am committed to their values of collaboration and openness, without the functionality I need, I would not have been able to return fully to Zotero. Let me mention the three developments that have made Zotero central again to my digital scholarship.

First, no longer simply a plug-in for Firefox, Zotero is a stand alone product that works across browsers. I rely mostly on Chrome these days, and the stand alone version works beautifully with the Chrome extension.

Second, I have adopted Zotfile to facilitate the simple organization of my pdf files. Zotfile effectively turns Zotero into as powerful a pdf file organizer as Mendeley. It enables you to quickly pull references from online databases and across the web directly into your Zotero collections. (Don’t sync using Dropbox; rather use the native Zotero syncing service to avoid generating duplicates.) Zotfile also facilitates the simple renaming of all files based on the metadata in your reference collections. With Zotfile, Zotero pulls articles from library databases even more easily and efficiently than Sente, which excels in that area.

Third, and most importantly from my perspective, is the development of ZotPad, the iPad application for Zotero. Although it still lacks note taking functionality (under development), it brings all your documents from your collections to your iPad and allows you to use your preferred annotating program to edit, annotate and update the pdf files in your Zotero collections. Because it does not download all your files at once, it works much more efficiently than the Mendeley iPad app, which has languished since its early appearance. I use GoodReader for annotating, and love the ability to annotate files, return them to ZotPad and find them updated in my Zotero library when I return to a computer.

These recent developments have brought me much closer to my goal of closing the digital research circle. They have certainly made my digital research much more efficient; allowing me even to take a moment to write a post about it before returning, as now I must, to my work on wolves and dogs in Plato’s Republic.

Sente, Mendeley, Zotero: Too Many Sharp Tools

By | Digital Research, The Long Road | 14 Comments

As spring rolls into summer, it is time for another appraisal of my digital research ecosystem. For a brief history of my reflections on digital scholarly research, I invite you to take a ride on the Long Road way-back machine circa April 15, 2010, when I first wrote about the elusive quest to close the digital research circle.

Funny how, in that initial post, I thought I was “tantalizingly close” to closing what I called the digital research circle: the ability to gather, curate, annotate, synthesize and cite scholarship without paper using a seamless digital process. More than two years later, I am still close, but now what felt ¬†tantalizing has tilted toward the torturous.

I will not here rehearse my entire research ecosystem which involves Dropbox, Evernote, Scrivener and even Word, although I invite you to read through and comment on my posts on the issue of digital research. Instead, I want to focus again on what should be the very heart of that ecosystem: the reference manager.

Thinking that I might finally close the digital research circle by taking the advice of @Targuman and @history_geek, I decided to give Sente a try. After a bit of fun with Sente, after two weeks I am back to my combined Mendeley/Zotero model. Here is why:

The great strength of Sente is its capacity to gather, which itself is a vital part of the research process. When I experienced the way Sente integrated with the Penn State Library, felt the ease by which I could pull pdf files directly from our huge collection of databases and have Sente parse them quickly according to their bibliographic information and place them at my disposal on my desktop and in a beautiful iPad app, I thought I had died and gone to research heaven. Soon I realized, however, that although it does have a rich and responsive support forum, Sente is missing what both Zotero and Mendeley offer: a robust capacity to share and collaborate with a research community.

Although I am in a humanities discipline, collaboration is becoming an increasingly important part of my academic research. (OK, that came off as a bit too as too cynical – dial the cynicism back a notch or two, but you get the point.) Here is link to a post about how I work with a research assistant to do collaborative research in philosophy – it includes an embedded Prezi as a bonus.

Despite Sente’s excellence at gathering, its limited social capacities, its outmoded ways of integrating with the word processor (using in-text citation tags and the need to initiate scans of the document – as opposed to using Applescripts), its clunky search features, and its brutal lethargy on the iPad app with certain kinds of pdf files led me back to the Mendeley/Zotero model.

In the meantime, I solved a duplicating problem I was having in Mendeley when I stopped having Mendeley sync to a folder in Dropbox and allowed it to sync to a local drive on my various machines. When it comes to organizing pdfs in a social research context, Mendeley is the best. It even allows you, for example, to embed your profile into your blog posts:

Christopher Long is a member of Philosophy on Mendeley.

Mendeley’s capacity to facilitate collaborative research led me to adopt it extensively in my graduate seminar on Aristotle’s De Anima over the spring semester. My graduate students and I shared a collection, and thus were able to refer to the shared highlights, annotations and notes of our various texts together in class. (Above is a picture of me teaching with Mendeley, referring to a document a student had annotated.) Mendeley’s capacities for collaboration enriched our collective research and our seminar discussions throughout the semester.

Mendeley falters, however, at the gathering and the citing phases. They still have not fixed an issue with html code coming into footnotes when using the Chicago Manual of Style Full Note with Bibliography style. Further, the bookmarklet they use to gather document information from the web is … weak: it does not identify bibliographic information on the website and import it directly into Mendeley as Zotero does so beautifully.

Thus, I am forced to continue to use Zotero for the gathering and the citing phases of the process. I really do like Zotero, and especially now that they have a version that stands alone outside of Firefox. But, it does not hold a candle to the pdf managing capacities of Sente or Mendeley.

If, as they say, sometimes you need many sharp tools to get a job done well, still I wish I didn’t need quite so many sharp research tools to close the digital research circle.

Evolving Digital Research Ecosystem

By | Academic, Digital Research, Technology, The Long Road | 8 Comments



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. 

Integrating Mendeley into the Research Circle

By | Academic, Digital Research, Technology, The Long Road | 12 Comments

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.

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