Scholarly Research and Writing 101

Submitted by khellekson on Mon, 08/16/2010 - 21:45

This 101 feature originally appeared as Karen Hellekson, "Scholarly Research and Writing 101," SFRA Review 292 (Spring 2010): 4–8. A PDF of this issue is available here.

Introduction

Long gone are the days of laboriously handwriting outlines and crafting index cards with bibliographic information, to literally cut and paste, shuffle, and rearrange while drafting and writing. Certainly such strategies, formerly taught in high school, may still be of value for researchers who require tactile and visual cues for organization. Many researchers, myself included, enjoy handling books, choosing colors to code data, shaking White-Out correction pens, and writing on high-quality paper with carefully selected inks. Yet when it comes time to create a document, particularly a meticulously documented scholarly essay, mastering some of the new online tools may make work quicker and more accurate.

Most research and writing now begins and ends on a computer, just as, to teachers' dismay, most forays into research topics begin (but, one hopes, do not end) with Wikipedia. These tools' abilities to capture data are remarkable: imaging and filing cited Web pages can now be done with the press of a button. Most of these tools are platform independent: for the tools I outline below, unless specified otherwise, both Macs and PCs are supported. In addition, I highlight only tools that are free. Some require payment if you want extra functionality or if you want to store lots of information. Depending on your setup, data may be stored in the cloud (that is, information is stored on remote servers owned by a service, not by you, so it can be accessed from anywhere), which is convenient—but may also be a security risk.

The array of programs possible for seeing a writing project through, from brainstorming to research to writing to submission for publication, is truly dizzying. Paid programs not discussed here vie for attention among open source collaborative projects. In general, I recommend open source projects before proprietary, closed software, but because many universities provide expensive paid tools to instructors and students, it may not be practical, or even possible, to port information embedded in these proprietary programs to a more open format. If you are ready to begin a large research project—for example, you are writing your dissertation or a book—instead of using the closed tools your university might offer, consider free alternatives so you aren't forced into a proprietary format that might lock up your information and perhaps later become a financial burden.

Before I delve into the best applications for scholarly research done on computers, a caveat: experimenting with online tools may result in initial frustration and even data loss. It's best to run a small-scale test before porting over important data. If you are syncing data across computers, run a test sync before committing valuable data.

Note: All URLs have been checked and were active as of May 1, 2010.

Mind Mapping

Mind mapping is directed brainstorming. Mind maps are like outlines, except they need not be linear. They show connections between nodes of information. Mind mapping is used in businesses to organize complicated projects with constantly changing objectives. In addition to the free applications listed here, well-regarded paid mind mapping tools include MindManager (http://www.mindjet.com/products/overview) and OmniOutliner (for Mac; http://www.omnigroup.com/products/omnioutliner/).

Personal Information Management

  • EverNote (http://www.evernote.com/)—Online dumping ground for any kind of information you can upload: photos, screen shots, text notes or Word documents. The premium version buys extra storage space, better security, and PDF searching. Use your browser, iPhone, or iPod touch to access your EverNote account; items are stored remotely.
  • KeepNote (http://rasm.ods.org/keepnote/)—Note-taking software geared to students. Permits outlining, drafting, full-text search. Download the program; items are stored on your computer.

Paid programs with personal information management functionality include Microsoft's OneNote (http://office.microsoft.com/en-us/onenote/default.aspx), which you can purchase as part of the Office suite, and UltraRecall (http://www.kinook.com/UltraRecall/).

Personal information management is a way to aggregate vast amounts of information and then make that information searchable. It is valuable during the early phase of research. Rather than spending time getting bogged down in proper citation and obtaining full text, information can just be captured and tossed into a giant bin for later sorting. Tagging the items in EverNote as you go may permit you to find connections between items of information that may prove fruitful. Instead of transcribing the outline that you sketched on a cocktail napkin, you can snap a picture of it and upload it to EverNote, add a few tags, and then access it later.

Data Syncing and Storage

  • Dropbox (https://www.dropbox.com/)—Remote backup and syncing across computers (2GB provided free; premium version buys much more space). Download the program; items stored on your computer are synced across computers and also stored remotely. iPhone/iPod touch app available.
  • Windows Live Sync (https://sync.live.com/)—Associated with your Windows Live ID (the same as your Hotmail account); permits automatic syncing across computers. Download the program and set it up.
  • Xmarks (formerly Foxmarks) (http://www.xmarks.com/)—Syncs Web browser bookmarks across computers and, optionally, across browsers on the same computer. Works with Internet Explorer, Firefox (best), Chrome, and Safari. Download as a plug-in for your browser. Stores bookmark info remotely.

Most people have access to more than one computer: a desktop at home, a laptop at the office, a netbook to carry to the coffee shop. Keeping data organized across computers is a full-time job in itself. Enter these tools, which back up and update information across multiple computers according to criteria you specify. Carbonite (http://www.carbonite.com/) and Mozy (http://mozy.com/) are two well-regarded platform-nonspecific paid autobackup programs with a Web component that let you access your data from any browser. Apple users may want to use Time Machine (http://www.apple.com/macosx/what-is-macosx/time-machine.html), perhaps with Time Capsule (http://www.apple.com/timecapsule/).

Dropbox and Windows Live Sync will automatically sync one computer with another while keeping a copy on a remote site. Xmarks will sync bookmarks across computers running the same browser; just install the Xmarks plug-in into each browser on each computer that you want synced.

Dropbox and Windows SkyDrive may be used, perhaps in conjunction with Zotero, to store and share research information because your online account can be set so that others can access it. With Dropbox and Windows Live Sync, you could set your Zotero library to back up automatically. Or you could dump project-specific PDFs and your paper draft in a special subdirectory that is automatically backed up. One big strength of Dropbox in particular: it's possible to undelete and to revert to earlier versions of data.

Simple Data Storage

  • Gladinet (http://www.gladinet.com/)—Downloadable Windows-only program that maps a remote Web site as a drive right on your computer, so you can easily drag and drop to copy files to an off-site location. Paid version has extra functionality and backup capabilities. Integrates remote storage at SkyDrive (free), Box.net (paid), Google Docs (free), Picasa (free), and more with your desktop.
  • Google Groups (http://groups.google.com/)—Provides 100MB of free storage in the Files section, so you can upload and store files and documents. Web-based interface works on any computer platform.
  • SDExplorer (formerly SkyDrive Explorer) (http://www.cloudstorageexplorer.com/)—Windows-only program that maps your Windows SkyDrive as a drive right on your computer. Paid version has extra functionality.
  • Windows SkyDrive (http://skydrive.live.com/)—Associated with your Windows Live ID (the same as your Hotmail account); WebDAV; permits manual backup and remote storage of up to 25GB of information. File size limit is 50MB. Web-based interface works on any computer platform, not just Windows.

If you need a scheme for free off-site storage of important documents, like your research notes or your dissertation draft, for occasional backup or for access while traveling, these tools may do the trick.

One classic method of backing up important documents is simply e-mailing them to yourself. Similarly, signing yourself up for your own personal Google Group, without any other members, and then uploading documents to its Files section is a quick and easy way to gain some data storage without sucking down your e-mail's space allotment. It's an easy storage option if you like the Google integrated suite of features. You may also find that you can use the Google Group's functionality to organize research information: notes, sources, links, and so on.

Windows SkyDrive has an astounding amount of free space, but you have to upload files laboriously by hand, file by file. It won't transfer anything automatically. Still, it may be worth it to spend some time uploading particularly valuable documents. If you're uploading by hand on a regular schedule, you may as well also upload backups by date in case you need to revert to a previous version.

If you want to get fancy, it is possible to turn SkyDrive into a space you can access like an extra hard drive right from your Windows computer (this won't work for Mac users). You can either do this via a hack (http://www.makeuseof.com/tag/upload-sync-files-skydrive-windows-explorer/), or you can do it via SDExplorer or Gladinet, both of which make your SkyDrive appear on your list of hard-drive options. But it won't automatically anything back up; you will have to drag and drop the files to copy them.

Unless you want to make neatly organized, named files available to others, as for a collaborative project, simple hand-uploaded data storage is best done with zipped versions of the files. Just ensure that the file size of the compressed file meets any limits set by the remote site—50MB for SkyDrive, for example.

The sheer hassle of remembering to back up manually, not to mention the inevitable infrequency and incompleteness of the task, may make the $60 a year for automatic backups via Carbonite or Mozy look affordable. Particularly for researchers with big databases of bibliographic information, including lots of annotated PDFs, or for people who need to back up lots of images or clips, a "set it and forget it" method of backing up combined with storage may be an elegant solution.

Bibliographic Tracking

Both Delicious and CiteULike let you create tags, and both have a social networking/sharing aspect. They work well if all you want to do is keep track of pages or capture citation information while you surf, without obtaining the full text. Delicious is the less scholarly of the two tools: it permits tagging and organizing any kind of information, and it generates nice summary Web pages for your review.

CiteULike, sponsored by powerhouse multinational publisher Springer, is dedicated to the scientific academic market. Like Delicious, it permits tagging; unlike Delicious, it stores information in a bibliographic form that can be output to a reference manager like EndNote. It also lets you store and search PDFs. Although CiteULike supports only scientific journals, not journals in the humanities, it may be used for any bibliographic information. It won't autofill data for unsupported journals, so the information must be keyed in by hand. CiteULike integrates with several other bibliographic tools, such as BibMe and Mendeley.

Bibliographic Entry Generator

  • BibMe (http://www.bibme.org/)—Books, magazines, newspapers, Web sites, journals, films. Input partial information and fill in required fields as cued. Outputs in MLA, APA, Chicago, or Turabian style. Databases include Amazon.com, FindArticles, Yahoo! News, and CiteULike.
  • OttoBib (http://www.ottobib.com/)—Books only. Input the ISBN, choose a style output, and cut and paste the delivered properly formatted reference into your paper. Outputs in MLA, APA, or Chicago/Turabian style; and as cut-and-paste code for BibTeX and Wikipedia. Database is ISBN numbers.

These tools generate a properly styled bibliographic entry from partial information that is meant to be cut and pasted from your browser into your paper.

Academic Bibliographies and Paper Composition

  • Bibus (http://sourceforge.net/projects/bibus-biblio/)—Downloadable open source desktop program that uses a MySQL database to store references.
  • Mendeley (http://www.mendeley.com/)—Downloadable desktop and Web program. Imports citations from academic databases, including Google Scholar. Syncs with Zotero and CiteULike.
  • Synapsen (http://www.verzetteln.de/synapsen/synapsen_e.html)—Downloadable Java hypertextual card catalog that permits connections to be drawn between individual bibliographic entries, so it helps the writer find unexpected connections between ideas. Uses the card catalog metaphor; may be a good fit for old-school researchers who like index cards.
  • Zotero (http://www.zotero.org/)—Firefox extension that automatically captures on-screen bibliographic information. Works with library aggregating tools like JSTOR. Permits linked storage and annotation of Web pages and PDFs. Supports creation of notes. Syncs to a Web account for backup and sharing.

These programs serve a variety of useful functions: they permit organization of bibliographic material; they organize data storage, as of PDFs, Web pages, images, and films/clips; and they plug into Word or Open Office to automatically insert citations and then generate the matching bibliography. The databases created are fully searchable, and some of these programs permit grouping the items into smaller sublibraries.

Many programs in this class are geared more to the sciences. However, automatically importing a PDF via a PubMed ID, for instance, is rarely needed in the humanities, nor are scholars in the humanities likely to use LaTeX-based writing and bibliographic tools, like the paid Mac program BiblioTeX (http://www.novajo.ca/bibliotex/).

Paid programs (with free demos) include EndNote (http://www.endnote.com/), which is the granddaddy of citation management, Reference Manager (http://www.risinc.com/), and ProCite (http://www.procite.com/); all these programs are owned by Thomson Reuters and are criticized as being generally unwieldy, annoyingly proprietary, and feature poor. However, many universities purchase these programs, so lots of people end up using them. Biblioscape (http://www.biblioscape.com/) is another paid program with some attractive features, including integrated writing capabilities, but like EndNote, the hefty price tag means it is out of reach for individual users. The Open Office folks have a free standards-compliant bibliographic project in the works called Bibliographic (http://bibliographic.openoffice.org/), but it's not yet live.

Many of these programs, both paid and unpaid, have a social networking aspect: their Web component permits sharing items or entire libraries with colleagues. Usually only the bibliographic data and associated notes and comments are shared, not, for example, PDFs of the items themselves, for copyright reasons. For the Web sharing functionality, storage may become an issue: storing many PDFs will quickly gobble up the minimal free storage, and extra space must be purchased. So when thinking about backups, you ought to consider whether you want to back up an entire library, including PDFs, to the Web and pay storage fees, or whether you want to just back up the metadata to the Web site and back up the PDFs in some other manner.

Zotero is unique in that it runs as a Firefox extension, integrated into the Web browser. It permits capture of data on the screen, be it Web page, PDF, or image. Depending on the metadata provided by the item's creator, it may autofill much of the bibliographic information. Or you can create an entry within the Zotero environment and type in all the publication information by hand, as for books you own in hard copy. A stand-alone (desktop) version of Zotero is in the works.

Mendeley has much the same functionality as Zotero, except it already has a desktop component that is downloaded to your computer. Like Zotero, Mendeley has an online tool that backs up data and permits collaboration and sharing of information with colleagues. It syncs with Zotero and CiteULike.

One important caveat for these bibliography managers: the data generated are only as good as the data input. Choosing the wrong sort of source—journal article instead of chapter in a book, for instance—will result in output errors. This is definitely a case of garbage in, garbage out. Papers with in-text and end citations generated with these bibliographical managers will inevitably contain errors and will need to be corrected before submission.

Word Processors

Full-featured desktop-based office suites

Web-based office suites with document-sharing functionality

Word and Open Office are the only go-to programs for integration with bibliographic software. Word (Microsoft Office) and Writer (Open Office) are full-featured word processors. Although you could use Google Docs as a word processor, it is more useful as a collaboration tool: you can import a word-processed document, then enable other users to view and edit it. Google Docs and Office Live may not be used with the bibliographic programs I discuss above, and if your connection is slow, writing is painful. Google Docs has a brand-name edge; Office Live has the benefit of familiar functionality based on the Microsoft Office suite.

Users of Word 2007 may choose to use the software's Reference ribbon to input bibliographic data and then insert in-text citations that will automatically be used to generate a bibliography (http://office.microsoft.com/en-us/word/HA100674921033.aspx). Many styles are supported, including MLA. This method may work well for shorter projects, and a big benefit is that it is integrated directly into the Word environment. However, all the data must be entered by hand, and it's not possible to tag entries, attach notes, or manipulate the database. You also can't attach or view PDFs or other files.

Recommendations

For the most flexible and portable research/writing system, I recommend running Zotero, embedded within Firefox, off a portable drive that you carry around with you on your key chain.

First purchase a high-memory (32GB minimum) USB flash drive/memory stick. Then download and install portable versions of Firefox and Open Office to this small external drive. A one-stop shop for applications optimized to run off memory sticks is the Portable Apps Suite (http://portableapps.com/). Run the portable app version of Firefox and install the Zotero extension. All your data, including Web pages and PDFs, will be saved to this small external hard drive. You can use Open Office Writer, again running it off the USB device, to write your document and embed the bibliographic information.

If you prefer not to use a small, easily lost, sometimes slow USB port but instead use your primary computer, then I suggest you use Zotero in conjunction with Dropbox or Windows Live Sync to automatically back up a Zotero database subdirectory. (I personally use Windows Live Sync, which backs up my data files from my primary desktop computer to the cloud and then to my laptop.) Be sure to follow Zotero's backup instructions to the letter (http://www.zotero.org/support/zotero_data) as you set up your sync. Otherwise you may lose data. Be sure to do a test backup and sync before you commit to this scheme.

For your account at Zotero.org, I recommend you set it up so it syncs metadata only—not the documents themselves. Your PDFs will quickly max out the 2GB of free remote storage.

For backups, I recommend purchasing Carbonite or Mozy. The fee is worth it for the peace of mind and everywhere access. If you must go free, then use Windows Live Sync to sync to the cloud, and if possible, to another computer in a remote location.

Conclusion

Online tools do not replicate the experience of writing by hand. They provide a whole new way of thinking about and manipulating information that may not be intuitive or workable for everyone. Visual thinkers may still need to scribble on a whiteboard—but now they can snap a photo of their work with their iPhone, type in a few tags, and immediately upload it to EverNote. Further, while organizing information, creating categories and tags may help you find connections between nodes of information that you had not considered, which can be helpful when brainstorming.

One big concern is the safety of data in the cloud. It's generally true that the servers that store your remote backups are less likely to fail than your computer's hard drive, but some people find it impossible to fundamentally trust the security of online data and will refuse to upload data to a remote site. That's fine—but be sure to back up your data faithfully to a hard drive or laptop that is kept in a different physical space. Most people will use the strategy of having a copy on a local hard drive plus a remote backup, instead of storing all information in the cloud. If you're worried about security of online access, generating hard-to-crack passwords via a password manager like KeePass (http://keepass.info/) or LastPass (http://lastpass.com/) may provide some peace of mind.

Many of the tools I describe above have an online component geared to social networking: you can log in and access the information via your account, plus share your information with others. It's important to carefully examine default privacy settings. It's usually possible to lock down your information so that only you can see it, but usually profiles are available to be viewed, even if the info you submit is minimal. Scholars particularly concerned about their privacy may want to choose online usernames that don't evoke their real-life names.

However, unless you are working on a project that might result in harassment, or unless your employer has concerns about national security or privacy of proprietary projects, I advocate transparency. Create a consistent online persona and maintain it carefully so you, and not a Google bot, control your presentation. Queries will then hit properly and will accurately reflect your interests. I don't think that's a bad thing—in fact, I think that's the point of discourse within a scholarly community.

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