Nascent

I'm nearing the end of an interesting and productive, but also long and tiring, tour of the US East Coast (Atlanta, Baltimore, DC, Boston and NY). It's election time over here, of course, and it looks like it's going to be very interesting this time around. Helpfully, this week's Nature has a News Feature and Commentary on what politics might mean for science, and vice versa.

On Tuesday, among many other things, I paid a visit to the Berkman Center at Harvard Law School. I was catching up with David Weinberger (who was kind enough to give a great talk at our London office last year). David reciprocated by inviting me to give a talk at their Luncheon Series. (Was he kidding? How could I refuse?) My talk was entitled 'What the web means for science' and was about the web revolution in science communication and research.

My slides are too big to post right now, but I'll do that later and put a link in the comments below. In any case, David's notes are probably more comprehensible. It was webcast (and also Second Life-cast), but I don't know if the video is archived somewhere. If anyone has a link, please post it below.

Speaking of Second Life, I mentioned at the end of my talk that Nature now has an island in Second Life, called (inevitably) Second Nature. We've only just begun work, so it's barren right now, but here's a picture:

(Science geeks might like to ponder the significance of the shape.)

We also have an updated version of our M4 (Magical Molecular Model Maker), which builds in-world models of chemical structures by querying the NIH's PubChem database:

(Those who knew the answer to the previous question might like to stretch themselves further by identifying the molecule in this picture.)

We have several more science-related things in the pipeline for Second Nature &mdash watch this space — and we're always on the lookout for other interesting 'virtual science' ideas. If you have one, let us know: either contact Jo Scott (avatar name 'Joanna Wombat') in Second Life, or if you prefer email write to me: t DOT hannay AT nature DOT com.

Posted by Timo Hannay at 09:25 AM | Permalink | Comments (6) | TrackBacks (2)

Having been kindly invited by Jim Gray and Alex Szalay, I spent this weekend at a Microsoft-sponsored eScience Workshop at Johns Hopkins.

I missed the first day on Friday (due to another meeting in Atlanta) but still arrived in time to hear some really excellent talks by (among others) Jim Ostell from the NCBI, Alex Szalay from Johns Hopkins, Paul Ginsparg from Cornell/arXiv.org, and Tony Hey from Microsoft. It was also good to run into some other excellent people I hadn't seen for a while, like Mark Boguski.

Above all, it was wonderful to be among so many people who truly understand how to make the most of information technology in scientific communication, and who are coming up with new ways to exploit its potential. In that sense it was completely unlike any publishing industry conference I've ever been to. (They're still 3-5 years behind the cutting edge, which is both sad and scary.)

For my own part, I gave a talk on 'The Scientific Paper of the Future'. (It covered broadly similar themes to my section in the 2020 Science report, published in March). I'm not sure how much sense they make on their own (or even with my commentary, for that matter), but FWIW here are my slides: 9.2MB PDF.

Posted by Timo Hannay at 09:50 PM | Permalink | Comments (0)

With our fully functional studio up and running, and full time staff working our little socks off, we've recently scaled up our podcasting output to include new sections in the weekly Nature Podcast, as well as several stand-alone shows on Genetics, World Heart Day and Chemistry. Recent highlights have been evolution editor Henry Gee interviewing a leading paleoanthropologist over a curry, journalist Geoff Brumfiel persuading a senior NASA official to pretend to be a space shuttle after another delayed launch and an interview with a leading Iranian cosmologist on what it means to be a scientist and a Muslim in Iran. Look out for next week's show which will feature both Nobel and Ig Nobel prize winners.

Posted by Adam Rutherford at 10:30 AM | Permalink | Comments (0)

The Nature news team, specifically Declan Butler, last night won the Association of Online Publishers award for use of a new digital platform. It was for their stunning avian flu Google Earth mashup.

Congratulations, Declan! I'm sure it will look great on your mantelpiece alongside your Legion D'Honneur Chevalier (Knight) of the National Order of Merit.

We're also chuffed that Tim O'Reilly should say such nice things about NPG during his AOP keynote speech.

Posted by Timo Hannay at 04:48 AM | Permalink | Comments (0) | TrackBacks (1)

Or, put another way, Connotea is for much more than just bibliographic references.

As Jon Udell so ably demonstrated in his recent post (Del.icio.us is a database), the ability to tag items with freely chosen keywords, coupled with the ability to mix-and-match queries on those tags, gives you a powerful database that is good enough for a large range of purposes.

Given that Connotea has these capabilities (and more besides — see below), can Connotea be used as a database too? Absolutely. And happily, Connotea users have already realised this and started applying it to their own specialised needs.

For example, Rod Page wanted to be able to correlate TreeBASE taxon IDs to the original description of the (in this case fossil) species. His solution was elegant and simple — bookmark the original description in Connotea and use the taxon ID as one of the tags. This solution is also highly flexible: by using multiple tags and bookmarks, he could collect together descriptions and databases entries with other relevant items about that taxon to form a kind of browsable mini-database for that species (although I don't think he's explored this yet).

Meanwhile, Robert Muetzelfeldt, an ecological modelling researcher at the University of Edinburgh, is using Connotea as a database in a different way. He's constructing a database of ecology and structural biology models represented in XML by bookmarking links to those XML documents and using tags to label the format and content of the models. This approach allows him to easily collate and query information that would otherwise be highly distributed. Want to find a list of structural biology models involving cyclin? Easy, just have a look at http://www.connotea.org/user/robertm/tag/SBML-XML+cyclin. And using Connotea to create a database of distributed data doesn't stop there — in a lovely piece of self-reference, Robert's even using Connotea to point to stylesheets that let users create custom views on Connotea!

The great thing about Connotea is that the entire database is open to querying and manipulation via the Web API. This means that, in principle at least, many users could collaborate on these databases, and you could run complex queries across the entire collection. So even if you can't do some queries through combining tags (like negative queries, for example), you can still get the answer by writing a quick Perl, Python, Ruby, or any-other-language-you-like program to sift through the data. There's also the raw RDF output, which you can query using SPARQL, as Rod Page has demonstrated elsewhere.

One small, but significant, feature of Connotea that lends itself nicely to all this is the tag note. A tag note lets you explain to other users how you're using a tag, so as well as being able to quickly build an online database by bookmarking and tagging things in Connotea, you can also explain how to use it at the same time.

Posted by at 10:13 AM | Permalink | Comments (0)