A Few of My Favorite Things: Research Tools

As I begin work on the theoretical side of my undergraduate thesis I find myself spending allot of time trying to keep track and organize the reams of sources and notes I’m quickly accumulating. And while I use some pretty specific and archaic tools when it comes to organizing and analyzing my actual data I figured I would share some of the more general tools I use, focusing specifically on open-source and cross-platform tools that could be used to any kind of research.

Browsing: Firefox

Not only is Firefox a superb and innovative browser (while also being both open source and cross-platform) but it’s extensive collection of add-ons make it an excellent platform for researchers and data hoarders. Many of the following tools are add-ons for Firefox and many, many other tools exist.

• Download Firefox: http://www.mozilla.com/en-US/firefox/
• Find Firefox Add-on: https://addons.mozilla.org/en-US/firefox/

Collection and Annotation: Scrapbook

Scrapbook is a Firefox add-on that lets you to save, organize, and annotate snapshots of websites locally. Typically I use scrapbook to save and annotate journal articles that are available in HTML format (i.e. that you can view in your browser) as well as regular web pages, but scrapbook is also useful when I want to archive pages that change frequently or that I want to access off-line.

Annotating a saved page in Scrapbook

• Scrapbook homepage: http://amb.vis.ne.jp/mozilla/scrapbook/
• Download Scrapbook Firefox Add-on: https://addons.mozilla.org/en-US/firefox/addon/427

PDF Annotation: Foxit Reader

While Scrapbook is great when your working with regular web pages, many journals only provide articles as a PDF files and this is when Foxit Reader comes to the rescue. Foxit is a lightweight PDF reader that includes annotation tools that let you markup and take notes directly in PDF files. While Foxit is commercial software, it is so fantastic that it is well worth the cost if your like me and spend allot of time working with PDF files. While it doesn’t come in a native Linux flavor it runs just fine under both Wine and Crossover.

Foxit Reader in Action

• Download Foxit: http://www.foxitsoftware.com/pdf/rd_intro.php

On-line Bibliographic Management: Citeulike and Connotea

Bibliographic management is a real pain and I have yet to find a tool I truly love. Refworks is probably the best on-line citation management tool I have used but I hesitate to lock myself into any tool that I will have to pay for once I am finished university.

Two free alternatives are Citeulike (sponsored by Springer) and Connotea (Sponsored by the Nature Publishing Group) which both offer citation collection and sharing. In my experience, unfortunately, neither service does a flawless job of detecting citation information and so you are frequently forced to manually enter your bibliographic information (oh the horror). Worse, for some inexplicable reason (probably legal) neither service allows references to be exported in finished bibliographic formats like Chicago or APA. Instead, references are exported in different desktop reference management formats (like Endnote or BibTex) which you then presumably use to prepare your finished bibliography.

Still, I think these services have their place, especially if already have desktop bibliographic software and want an easy way to collect and share citations while surfing the internets. Both services allow you to use your universities OpenURL service and make use of DOI links which makes them particularily handy for those with full-text access through their work or school.

Connotea

Citeulike

• Citeulike – http://www.citeulike.org
  • Citeulike FAQ: http://www.citeulike.org/faq/faq.adp
• Connotea – http://www.connotea.org
  • Connotea Guide – http://www.connotea.org/guide

Collection, Annotation, and Bibiliographic Management: Zotero

Zotero is a Firefox add-on that combines data collection and organization (like Scrapbook), with annotation tools (including highlighting and note taking) and bibliographic management (including publication-ready export) in one tool. Zotero lives completely in your browser — so everything is local and accessable whereever you are — while a new version currently in beta-testing will allow syncing and sharing through an on-line portal similar to Connotea and Citeulike.

Zotero in Action

• Learn about and get Zotero: http://www.zotero.org/

Quick Bookmarking: Delicious

Delicious is the one research tool I could not imagine living without. A on-line replacement for in-browser bookmarks, delicious lets you store, share, and search your bookmarks through a web portal. Delicious uses tags instead of folders for organization, which works far more efficiently when you have thousands of bookmarks that do not fall neatly into a single category. Even more impressive, Delicious has resisted the usual feature creep and visual bling that mares so many other web 2.0 services, remaining remarkably simple and stable for years. To see an example check out my Delicious bookmarks here and my tag list here.

Delicious Bookmarks

Bookmakring a website with the official Delicious Firefox Add-on

• Sign up for a Delicious account: http://delicious.com/
• Get the official Delicious Firefox Add-on: https://addons.mozilla.org/en-US/firefox/addon/3615

Backing up your data: Dropbox

While not really a research tool Dropbox is the tool that lets me sleep soundly at night when I finally step away from the computer. While losing your precious data is a nightmare for any confirmed data-hoarder it is a real terror for anyone in the middle of a large, data intensive project.

Regularly backing up your data is one of those chores everyone knows they should do and almost nobody does regularily.  The problem is that while backing up your data in the same location — or even worse, the same drive — as the original is essentially useless, off-site backup requires dragging around an external drive, reducing the likelihood that you do so regularly.

One solution to this problem is on-line backup services which use your Internet connection to transfer data on-line where it is safe and available from anywhere. Many different of these services exist and most offer basic accounts with a limited amount storage space (generally around 2GB) for free. My favorite of these services is Dropbox, which is simple to set-up and runs seamlessly in the background,  incrementally backing up your data as you work.

Dropbox does this by creating a directory inside you home folder and anything that is placed inside this directory gets automatically backed up to Drobox’s servers whenever it changes. In Linux this means that I can simply place a link to my existing research directories inside the Dropbox directory so I do not even need to change the location of any of my files (I know you can do the same with Windows, usually by right-clicking the file in explorer and creating a link, and I am sure OS X has similar functionality).

One caveat is that you should always have more than one backup solution in place, especially with these new on-line services that could potentially go out of business. For me this means a weekly DVD snapshots of my data to supplement my Dropbox account. Consider yourself warned.

• Sign up for Dropbox: http://www.getdropbox.com/
• Dropbox Tour: http://www.getdropbox.com/tour#1