Disappointed with Popfly

Popfly is the mashup editor that Microsoft released last year. The idea is good. The 3D graphics are good. Silverlight is a bit buggy in Firefox (sidebars don't always redraw properly) but that's OK.

If you're going to create a web 2.0 mashups builder, though, don't you think it's be a good idea to provide some Atom support?

Meta-analysis

The journal platform team here at NPG just rolled out machine readable metadata for the papers we publish in Dublin Core, PRISM (good PRISM, not to be confused with evil PRISM) and Google metadata formats.

No more scraping to automatically get the citation for a paper, it's all in the HEAD:

<meta name="citation_journal_title" content="Nature" />
<meta name="citation_publisher" content="Nature Publishing Group" />
<meta name="citation_authors" content="Paul Schenk, Isamu Matsuyama, Francis Nimmo" />
<meta name="citation_title" content="True polar wander on Europa from global-scale small-circle depressions" />
<meta name="citation_volume" content="453" />
<meta name="citation_issue" content="7193" />
<meta name="citation_firstpage" content="368" />
<meta name="citation_doi" content="doi:10.1038/nature06911" />

Useful for apps like Zotero and Connotea (which before now downloaded two files each time you bookmarked a Nature paper: the page itself and then the linked EndNote file to parse).

The metadata will be there for all papers going forward and back through some of the archives.

For fulltext indexing of papers behind the paywall you can use the linekd OTMI file (I only just saw Twease, which does just that) although there's only OTMI for Nature papers at the moment, I think.

Lastly at some point in the future we're aiming to put XMP metadata in our PDFs, which should make it much easier for scripts and applications (like Papers) to look at PDF files on your filesystem and work out what they represent.

Nice work Pedro!

Noticed while leafing through today's Nature that Pedro has a paper out (Isalan et al., Evolvability and hierarchy in rewired bacterial gene networks).

There's more on this over at Public Rambling.

Ian owes me a pint

(update: Gavin Bell at Nature gave up one of his app spots so that I could put this live, which I did: only to discover that Google App Engine is even more unforgiving of timeouts than Facebook. Currently trying to work out how to make the bookmarking process, for now it doesn't work very well. Also the search is broken, though that's Google's fault and not mine.)

I bet Ian earlier that I could rewrite Connotea on App Engine in six hours. I can't remember why. Probably ego (mine, I mean). He didn't actually bet me a pint but he should have done...



... because the original estimate was a tad optimistic (ahem). After twelve hours I've produced pycite, though, which is pretty good going I think. I'll admit it: Python is actually very cool.

pycite is three hundred lines of logic and a set of html templates that implements a (very simple) social bookmarking service. Sadly I don't actually have an App Engine account so it's not live on the web anywhere (I'll buy whoever does have an account and puts it up first a pint - let's spread the love), you'll have to download it and run it locally to see it in action.

What you can do with it:

• run it without owning a server of your own


• log in with your Google account


• add new bookmarks (the citation will be collected automagically)


• view everybody's bookmarks


• filter bookmarks by user:

  http://path.to.pycite/users/bob.smith



• and by tag:

  http://path.to.pycite/tags/diabetes



• and by user and tag:

  http://path.to.pycite/users/bob.smith/tags/diabetes



• and by keyword (the full text of each bookmarked page is searchable):

  http://path.to.pycite/users/bob.smith?q=t2d



• get atom feeds for all of the above

What you can't do with it (yet):

• edit or delete bookmarks


• anything else

I've put it all up on Google Code. It's fairly straightforward stuff so if you've got any brilliant social bookmarking ideas then go for it. Send me an email and I'll give you write access to the subversion repository.

Gaggle

I hadn't heard of Gaggle before but both Deepak and Sutee Dee (who needs a homepage.. ;)) from the ISB mentioned it last week so I figured it was worth a look. It's a system built by Paul Shannon at the ISB in Seattle to share data between different bioinformatics applications on the fly. It has been around for a while, I think - there was a BMC Bioinformatics paper describing the system in March 2006.

A small server program (the ´Gaggle Boss´) provides communication among analysis and display programs (the ´geese´) which are modest and minimal adaptations of existing (or novel) bioinformatics and computational biology programs, and web resources. The Boss and the geese all run as separate programs on the user´s desktop computer, communicating with each other, at the user´s behest, by passing simple messages.

(from the ISB's 'about Gaggle' page)

I ran through a tutorial showing data sharing between (modified versions of) Cytoscape (also developed by ISB), R and a data matrix viewer no problem. Quite cool.

You can't share data from an arbitrary application (I don't think?), they need to be modified to send messages to the Boss goose. Having said that there's a Firefox extension called Firegoose which lets you pass messages to and from web apps, Entrez etc. I couldn't get it working properly but suspect that's something to do with my install rather than the extension itself.

Anyway, it's good to see stuff like this. Truth be told it's not the slickest thing ever, but it's still pretty cool - and it works. I wonder if you could turn it into a simple lab notebook - could you write a brief description of what you're going to try and do for the Boss app every time you send data to another app or something?

Why you should try online dating

(you can jump to the short answer here, if you're feeling impatient)

Onto the psychology of social media. Kristin Stecher of the University of Washington and Dave Evans of Psychster LLC both gave interesting talks about profile pages.

Psychster is a consulting company dedicated to "the social science of social networking". Recently they've been looking at interpersonal perception (how does person A perceive person B? How close is that to B's self perception?). Most research into this uses 'fake' people - i.e. A is given a detailed written description of B and works off of that, rather than meeting anybody face to face.

To try and get a large 'real people' dataset Psychster created a Facebook application (and later a website) where users could fill out a questionnaire that rated their personality on a variant of the big five personality inventory (the big five being openness, conscientiousness, extraversion, agreeableness, and neuroticism). They then had the option of rating the personalities of other people (not just their friends), the idea being to collect how users saw themselves, how others saw them and the correlation between the two.

On the standalone website users created profiles to reflect their personalities. Profiles could contain any number of elements (name, location, gender, favourite movie, most embarrassing moment...) chosen from a large list.

The results in general:

• people do 'get' each other (where to 'get' a person means to guess a personality close to their actual, self-rated personality).
  
• people on Facebook get each other better (this kind of figures - you'd want to go rate your real life friends).
  
• women are better guessers than men - but only when guessing random strangers.
  
• women are easier to get.
  

Psychster looked at different profile elements on the standalone website to see if the presence or any in particular were correlated with higher rates of accuracy.

Profile elements that make somebody easier to get:

• A link to a funny video (the number one predictor of personality)
  
• What makes me glad to be alive?
  
• Most embarassing thing I ever did:
  
• Proudest thing I ever did:
  
• My spirituality:
  
• A great person:
  
• I believe this:
  

Profile elements that make you harder to get:

• Profile picture (but only if it is of a non-person)
  
• An awful website:
  
• An awful person:
  
• A great book:
  

That last one (naming a great book making it harder to guess your personality) is pretty interesting. Dave did say that he hadn't yet done any proper analysis of why it might be. I wonder if there's any research into how much (or little) reading habits have to do with your personality? Here's a tangent (why do some people get interested in science fiction?) if you're interested. Here's another (people who read lots of fiction aren't socially awkward, in fact the tendency to get absorbed in a story correlates with empathy scores).

OK, anyway...

Why were women easier to read? Because they tended to fill out the profile elements that were good predictors ("my most embarrassing moment").

At this point you might be wondering (well, I wondered) who cares how well an online profile reflects your true personality. One answer is the online dating industry who have a vested interest in not setting you up with anybody plainly unsuitable. If profiles were set up the right way then maybe you could tell in advance if the guy or girl messaging you is worth seeing in the real world.

Sticking with the online dating theme,  it turns out that the levels of agreement (between actual and guessed personalities) you get by looking at Facebook profiles approach those you see in long term acquaintances. They're certainly better than what you get after a short face to face meeting (like a date). In fact, short f2f meetings are particularly bad at helping you gauge levels of agreeableness and neuroticism - not good. I think this means that stalking potential partners online actually makes good, practical sense and should be encouraged.

In case you needed any reassurance.