Tools for Academia

Every day I use web-based tools in my research. Some are specifically designed for scientific research, but some are just general purpose tools. It continually surprises me when researchers have not heard of the many different ways the web can help research. This list is not meant to be exhaustive so please let me know if there are any tools you use that deserve a mention. This list originally started as a blog post but I am now trying to keep it up-to-date in this format.

Paper hunting:

• The arXiv - You aren't going to get far in physics without having heard of the arXiv, but it deserves a mention for getting rid of trips to the library.
• SPIRES - For article searches in particle physics/astrophysics, SPIRES is the last word. The search syntax is a little more involved than a Google search ("find a authorname and j journalname" etc.) but the information available for each article is worth the effort. Particularly valuable is the BibTeX entry for each article, and links to both arXiv preprints and e-journals.
• Google Scholar - Not specific to physics, this is Google's take on academic search. It catalogues the main journal indexes, and has some useful features like the "Related Articles" search, which does a good job of finding other articles with similar subjects.

In the old days, researchers had piles of papers on their desks, under their desks, and generally all over the place. But if required they could pick a required paper out of this filing disaster quite easily with a good memory and a little luck. Today most of the papers you read might remain out there on the network with only a select few qualifying for ink and paper. How do you remember which papers you’ve read, where they are and what you thought of them?

• Citeulike - This site allows you to add papers to a personal list, add tags to describe the papers, and provides automatic links to the electronic versions. When looking at an abstract on the arxiv for example, you simply click a bookmarklet and the title, journal etc are automatically added. You are also able to rate papers, and export a BibTeX list of all your papers.
• Connotea - This is the Nature Publishing Company's effort at an online reference manager. As with Citeulike a bookmarklet is used to add papers to your collection. The export functions also allow you to also use a desktop based reference manager such as Endnote.
• The Academic Reader - This is a very new site that hopes to offer a portal to many different sources of scientific articles. Unlike Citeulike or Connotea you read the abstracts on the site itself and don't have to deal with bookmarklets. It also provides a "Library" where you can store references to papers you have read.
• Del.icio.us - This is not a science specific tool, but rather a handy social bookmarking system. You give webpages tags, can view other users' saved items (while also being able to hide selected items) and use "Live bookmarks" of the RSS feed of tags to access your bookmarks in your browser. Now with the new Firefox extension, this functionality is integrated seamlessly into the browsing experience. A lot of people tag abstract pages so they can go back to get the file any time, many using the arXiv tag.

A large part of doing research is becoming part of the research community, communicating with your peers about your work and networking to form possibly collaborative relationships.

• CosmoCoffee - For cosmologists, this site provides a forum for discussions of recent papers and general queries. There is some integration with the arXiv, allowing search and BibTeX retrieval (handy as this is not provided by the arXiv itself) but also keyword based filtering of the latest papers. This allows you to concentrate on papers relevant to your work, especially from large sections like astro-ph, which is getting so large it's easy lose your way.
• Nature Network London - This is the Nature Publishing Group's attempt at a social network for scientists. It only started recently, so there is not that much activity yet, but it does seem to have a few people writing and networking. [Update] PZ Myers points to a good discussion of the benefits of social networking for scientists and the Nature Network in particular.

Additional CosmoCoffee features: There are some additional features on CosmoCoffee which make it something of a research hub.

• Firstly the bibtex page accesses arXiv and ADS and retrieves a bibtex entry for the chosen paper. I don't know how useful this might be, as I tend to use the integrated search bar in Firefox to directly search SPIRES and the arXiv.
• There is also a bookmarking system, linked to the arXiv listings. While not as fully featured as either Citeulike or Connotea, this is a very intuitive system and can be easily integrated into your workflow if you already use Cosmocoffee to access new arXiv papers.
• The final tool is a complimentary function of the bookmarking system, allowing multiple users to share lists of bookmarks in a "Journal Club" system. There is a rudimentary management system, with the ability to add users and other managers, and move papers into "old" and "ignored" categories. There is also an anonymous list of all the papers that have been bookmarked so far, which provides an interesting insight into the reading habits of Cosmocoffee users.

To use the bookmarking system you will need to register at the Cosmocoffee site. Since last year registration has been restricted to people affiliated with academic institutions.

This is not an exhaustive list, but hopefully there are a few useful resources there. As I said above, if there are any other sites you would recommend please let me know in the comments section.