Welcome to part two of what could become nodalpoint's very own version of TRACKING: sufficiently advanced technology (maybe sufficiently advanced science web technology). All of the following tips are related to Science 2.0 (if you can think of some better term to use please let me know). Read on for the tips...
First off, via YAKAFOKON (excellent blog, with interesting projects related to the semantic web and foaf), is news that an AJAX genome browser is underdevelopment. Apologies if you've seen this, it has been around for a while. You can go try out the current demo version here , although limited in it's current functionality the movable display of the genome (a la google maps) is very impressive. It is my hope that some of web2.0's focus on usability rubs off onto scientific applications. I recall the golden path genome browser was criticised for being a usability nightmare.
Hopefully the development of the AJAX genome browser may change all that. However I must inject a bit of cynicism into the rant so as to not get too optimistic over all this fancy web tech: essentially nothing will change, usability will still suck. Why ? because focus from small labs is always on publications and not application development. Putting a web interface on whatever advanced new algorithm you have developed and turning it into a service is the last thing you do (just before you write documentation. Poor documentation is of course the true mark of cutting edge technology right ?).
While I remain hopeful that bioinformatics applications will become 'user friendly' I don't see the incentive. When you do a piece of science, you do it for you curiosity, then for publication, then for money (i.e. grants), maybe not necessarily in that order. The user of you application comes last. Why ? because they don't give you money, they don't get you published (the reviewers do). So incorporation of modern usability techniques a la AJAX will likely not be realized by academic efforts. Look for this from the commercial world.
On the topic of AJAX here is a golden opportunity for a mashup (via spitshine, btw what's up with quitting science blogging ?) apparently the the major DNA databanks (GenBank, EMBL, DDBJ) include a geographical location feature in their sequence records. They have a map of the world up showing the distribution of sequences by location, however it isn't AJAX enabled. The prize goes to the first person to use the Gmap API to display the same data...
Last but most certainly not least is Alf Eaton's Pimp my Paper (or Structured Markup for Scientific Articles) demo. Alf posted this a while back and shamefully didn't post it on nodalpoint but here is now, with a few notes. What the PMP demo does is take an example of an online publication and mix in microformats, javascript, and other so-called web2.0 features to enhance the usability of the online content (the demo page can be viewed here). Dynamic heading outlines are generated from the structured markup of the paper (e.g. H1, H2, H3), images are resizable, and many other improvements over regular online publications. I'm sure we can think of more featuers ?
So herein ends the first nodalpoint tracking post, please post tips on new 'Science 2.0' developments to the forums or elaborate at lenght on the front page.
Comments
user friendly bioinformatics
I agree: scientists have little incentive to make their programs user friendly. But don't despair! Bioinformatics core facilities help non-programming biologists do bioinformatics without having to become programmers. Folks (like me) in such cores DO have an incentive to making tools easy for their clients to use - namely, they're getting paid to do so. And once you've done the work to go from "usable by geeks only" to "usable by normal people within my organization", it's probably not much more work to make it usable by the world.
-Amir Karger