Showing posts with label Greasemonkey. Show all posts
Showing posts with label Greasemonkey. Show all posts

Monday, 7 January 2008

Enhancing the web for scientists

Egon Willighagen, myself, Harini Gopalakrishnan, Dazhi Jiao, Rajarshi Guha, Christoph Steinbeck and David Wild have just published a paper describing userscripts we have written to enhace and extend web sites for scientists:
Userscripts for the Life Sciences BMC Bioinformatics 2007,8, 487. (Open Access)

Userscripts are Javascript programs that are triggered to run in your web browser when you go to certain web pages. They can alter the content of the web page on-the-fly. For example, one of the userscripts described in the paper looks up all PDB IDs on a web page and adds a link to a webpage showing the structure. For userscripts to work, your browser (e.g. Firefox) needs a special extension (e.g. Greasemonkey).

Our userscripts are divided into two broad categories:
  • Interacting with the scientific literature
    • OSCAR3 running on HTML
    • Add quotes from Chemical blogspace and Postgenomic to DOIs
    • Add to Connotea
  • Linking to chemical and biological data sources
    • Enhancement of PubChem with 3D structures
    • PDB-Jmol userscript
    • Sechemtic
    • Add quotes from Chemical blogspace to molecules
All of these userscripts are available from the Blue Obelisk web site. For other relevant userscripts, search Userscripts.org (the official repository for all userscripts) for userscripts with the tags "Chemistry" or "Biology".

Image credit: Spiders web by Lida Rose (CC BY-ND 2.0)

Friday, 5 October 2007

Bring PDB codes to life on web pages

Wouldn't it be nice if you could click on a PDB code on a web page and you could instantly see the actual structure in 3D? For example, you might be reading the HTML version of a paper which is discussing a particular protein structure.

Some time ago I wrote a Greasemonkey userscript to do just that. You can get it on the Blue Obelisk web site, as well as several other userscripts. Since I haven't previously mentioned it on this blog I thought I might do so now.

To avoid false positives, it only runs on web pages containing the words "protein", "pdb" or "enzyme". For any PDB codes found, it adds the appropriate link to Eric Martz's FirstGlance in Jmol site. For example, the PDB codes on this page are tranformed to:(The yellow Jmol links were added by the script)

Monday, 4 June 2007

Add to Connotea from Journal Pages

If you regularly read journal Table of Contents pages and want an easy way to keep track of papers you find interesting, you may want to try my "Add to Connotea" Greasemonkey script.



To use it, you first need to have a Connotea account. When you navigate to a journal web page for the first time after you have started your browser, you will need to enter your Connotea username and password.

The script adds an "Add to Connotea" link next to every DOI on journal pages. If you click on this, a dialog box appears that allows you to bookmark the paper on Connotea. A useful feature is the ability to quickly select from tags that you have already used. The "Add to Connotea" script also displays a count of the number of people who have already bookmarked a particular paper. If you click on this number, it will bring you to the Connotea page for that paper.

Why use Connotea inside of just bookmarking a paper, or saving it on your computer? Here's why I do: adding to Connotea is 'cheap'. I'm a lazy bookmarker; now that my bookmarks have reached the bottom of the my screen I've given up. Arranging into folders is too much hassle for my busy lifestyle. Now I can tag a paper with "Read me later", or "Journal club", and I will actually be able to find them later. Bookmarks are available from any browser; you can bookmark from home, and read the paper later from work. Your computer may explode (not due to my Greasemonkey script, I hope), but your bookmarks will still exist. Another nice thing is that Connotea is part of Web 2.0 - it provides an API that allows it to be used in mashups; like this Greasemonkey script!

There is also the 'social' side to 'social bookmarking'. I have already mentioned that the "Add to Connotea" script keeps a count of how many people have bookmarked a particular article; this may indicate that a particular article is worth reading. There are people who track all articles posted with particular tags, e.g. "evolution", to keep up to date with the latest articles, but I'm not sure how useful this is in chemistry. Also, you may want to keep up to date with what all the kool kids are reading, in which case you may want to track what articles your friends are bookmarking (note: all bookmarks are generally public, but you can opt to make them private). Connotea allows you to add a description and/or a comment to an article, but while this seems like a neat idea (e.g. for posting a reviews), it does not seem to be used that much and in fact, seems to suffer from link spam (see here).

I should point out that Connotea also provides a bookmarklet that you can click after selecting a DOI. While the bookmarklet is the only option for websites that my Greasemonkey script can't handle, I find my script a handier way to bookmark papers on journal websites, plus you have the added goodness of identifying popular articles.

Thursday, 17 May 2007

Stack It! - Popularity voting for papers

Prompted by a blog post by Ψ*Ψ which referred to a reddit-style voting system for papers, and based on the excellent "Stack It!" feature of Ohloh, I've implemented a Stack It for journal papers using Greasemonkey:


All you need is an account at Connotea. The first time it runs on a journal web page, it asks for your Connotea username and password - this will be remembered until you close the browser. To stack your favourite papers, just click "Stack It!". To unstack, you'll have to log into Connotea. The tag "stackit" is used for all stacked papers.

It should be possible to identify other people with similar stacks to yourself, and see what else they have stacked (Ohloh can do this). Also, you could have an RSS feed to what people are stacking recently, or you could have a list of the most popular JACS articles in the last month.

Tuesday, 1 May 2007

Add quotes from PostGenomic and Chemical Blogspace to journal

Update 18 July 07: Updated address of Blue Obelisk wiki

Greasemonkey is a Firefox extension that allows you to rewrite the HTML of a webpage on-the-fly. Pedro Beltrão was the first to think of adding a link to journal Table of Contents pages whenever a particular paper had been reviewed on PostGenomic.com. I extended Pedro's script to include a clickable pop up of the actual blog post as described by Egon.

I have just released a new version, described on the Blue Obelisk wiki and available from User scripts. This incorporates comments from both Postgenomic and Chemical Blogspace, although you can use the menu to choose just one or the other.

Feedback is welcome. In particular, what journals would people like to see added? Currently, only the following websites are included, although others may work if you add them (please let me know if they do):
  • http://pubs*.acs.org/*
  • http://www.rsc.org/*
  • http://www*.interscience.wiley.com/*
  • http://www.nature.com/*
  • http://*.oxfordjournals.org/* (Added 01/May/07)
  • http://*.plosjournals.org/*
  • http://www.pnas.org/*
Here's the obligatory screenshot showing a recent issue of Nature containing quotes from both Chemical Blogspace and Postgenomic: