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A Simple Academic Workflow

By Jennifer Claro

The amount of lost time and lost productivity resulting from inadequate academic
workflows affects not only individual researchers but their whole field. While there have not
been many studies done on workflows, one survey (University of Minnesota Libraries, 2006)
found that 36% of the social science faculty at the University of Minnesota used reference
managers compared to only 8% in the humanities. If we can assume that even fewer faculty
members are using efficient academic workflows, then the state of research is in need of an
upgrade.
The same study (University of Minnesota Libraries, 2006) found that graduate
students are 50% more likely than faculty to use reference managers. Thus the concept of an
academic apprenticeship (McGowan, 2005) takes on a new meaning, with graduate students
able to teach faculty a lesson.
Howison and Goodrun (2005, p. 3) write that the system for managing academic
papers and is far from standardized and ranges from manual fumbling through to quite
sophisticated if users employ citation managers, such as Endnote or the variety of Bibtex
management systems. Yet even the most sophisticated users experience difficulty in
managing their files. This, they write, is due not only to industry lagging behind in the area
of integrated support for researchers, but due also to the incapacity of PDFs and most other
documents to allow metadata to be included within the document itself. When we download a
paper, we must download the metadata separately, whereas when we download music, the
metadata is included in the music file. This kind of inefficiency, in addition to a lack of

available commercial workflows for researchers, has led many of us to create our own
workflows, with varied results.
This search for a simple yet effective digital academic workflow is not new. Hundreds
of researchers (see e.g. Judson, 2008; Roberts, 2009) have written on the web about their
attempts to set up and use a system that will:
1) Find new articles of interest quickly and download them simply with their metadata
2) Enable them to annotate, mark up, and take notes digitally, with no need for a paper
copy of their documents
3) Keep all their papers and other research documents in one place
4) Provide a way to search through those documents in an efficient way
I currently use a very simple system of Google Scholar, BibDesk, Skim (all free) and
Spotlight (which comes on all Macs) which is a very limited version of a much more
powerful workflow called Researchr (Haklev, n.p.) which was developed by Stian Haklev at
OISE, University of Toronto. One day I hope to be running Researchr (we have experienced
some technical difficulties in running my version of Researchr reliably), but in the meantime
my current very basic workflow does all of the above simply and efficiently. One advantage
of my workflow is that it is so basic that I can run it by myself, with no need for computer
expertise, and so can anyone else. It should be noted here that this workflow will only work
on a Mac as BibDesk, Skim, and Spotlight are applications that work on Macs only, but
similar workflows are possible on any computer OS.
Google Scholar
I chose Google Scholar to do my online searching for articles because it was faster and
more efficient than using the University of Torontos (where I am a graduate student) online
library. Google Scholar probably has the widest coverage of all online library search engines

and provides information on the number of times an article has been cited, which most other
libraries dont (Hull, Pettifer & Kell, 2008). Google Scholar aims to rank documents the way
researchers do, weighing the full text of each document, where it was published, who it was
written by, as well as how often and how recently it has been cited in other scholarly
literature (Scholar.google.com, n.p.). The efficiency of looking up a topic and finding the
most relevant articles ranked top down is currently unmatched by other online library search
engines. However, according to Jasco (2005), a big problem with Google Scholar is that
millions of articles have not yet been indexed, so coverage is far from complete. Despite this,
I find Google Scholar very useful and will likely use it for many years, along with the
University of Toronto online library for backup.
BibDesk
BibDesk is a free and open-source reference manager that is under active development
by a small group of volunteers (SourceForge.net, n.d.). With BibDesk, your collection of
PDFs and other documents is organized by author name, document title, date of publication,
etc. so that finding documents is easy. BibDesk automatically imports keywords when it
imports the citation data, but you can add your own keywords as well, which is something
that I have started to do with painstaking commitment. By adding my own keywords, I can
find information I am looking for much faster (please see attached video for a demonstration).
BibDesk can search titles but cannot search the PDFs themselves, which would be a
very useful feature, but this is easily done on a Mac using Spotlight, Apples powerful search
tool. BibDesk also allows automatic generation of references for Latex users, and there are
programs (BibDeskToWord, BibFuse) that are supposed to allow for BibDesk to Word full
reference generation as well.

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I am relatively happy with BibDesk as finally all my articles are in one place and

bedlam has been defeated (Judson, 2008). But I could get neither the BibDeskToWord
program nor BibFuse to work. So at present my workflow cannot generate instant references
like a program like EndNote (over $100 for the student edition) can. As well, Zotero (free)
seems very interesting and useful, so I will check out Zotero and may possibly switch from
BibDesk to Zotero in the near future. This workflow is an evolving workflow which is as it
should be. There will always be new and more efficient programs appearing on the market,
and Im keeping my options open.
Image 1. BibDesk Screenshot

Skim
Skim is a PDF reader that allows highlighting and annotation. The most useful Skim
tool for me is the Note tool, which allows me to write your own notes within the document. In
the screenshot below, I have highlighted text referring to a topic I am very interested in
mutual aid and I have made mutual aid the title of the note. By tagging text in this way,
when I do a search using Spotlight, this reference to mutual aid will turn up (even though the

words mutual aid do not appear in the text) and thus I can find this and other important
references to mutual aid quickly and easily. This feature of Skim has ended a problem Id had
for years with not being able to tag text and search those tags.
Image 2. Skim Screenshot

Spotlight is an incredibly powerful search tool that comes installed on all Macs and allows for
very efficient searching of documents, webpages, and more. The handy combination of
Google Scholar, BibDesk, Skim, and Spotlight has been a huge relief for me, as my workflow
used to be terribly disorganized and now it is streamlined, smooth, and highly functional, if
basic. I will be developing this workflow in the coming years and I hope that it will
continually be getting more efficient and powerful. Please see the attached video for a
demonstration of this workflow in action.
In closing, I have not yet mentioned anything about Web 2.0 and its capacity for
enabling collaboration between researchers. Blogs, wikis, social bookmarking, and other Web
2.0 tools are changing the way we interact, and making international collaboration possible.

Once we get our own personal workflows in order, the time saved and the efficiency gained
will lead to better and more productive personal research, and international networking with
researchers in our fields is leading us to Research 2.0 networked, collaborative research on a
global scale.
The future is looking good for researchers! And the first step is finding a great
academic workflow.

References
Haklev, S. (2011). Researchr. Available at http://reganmian.net/wiki/researchr:start
Hull, D., Pettifer, S. & Kell, D. (2008). Defrosting the Digital Library: Bibliographic
Tools for the Next Generation Web. PLoS Comput Biol 4(10): e1000204.
doi:10.1371/journal.pcbi.1000204
Judson, O. (2008). Defeating bedlam. The New York Times [online version], December
16, 2008. Available at
http://opinionator.blogs.nytimes.com/2008/12/16/defeating-bedlam/
Muldrow, J. & Yoder, S. (2009). Out of Cite! How Reference Managers Are Taking
Research to the Next Level. PS: Political Science and Politics 42(1), pp. 167-172.
Roberts, B. (2009). Get started handling academic citations like a pro. Available at
http://www.soulphysics.org/2009/12/get-started-handling-academic-citations.html
Scholar.google.com (2011). About Google Scholar. Available at
http://scholar.google.com/intl/en/scholar/about.html
University of Minnesota Libraries (2006). A Multi-Dimensional Framework for
Academic Support. University of Minnesota. Available at
http://www.lib.umn.edu/about/mellon/docs.phtml