We will have a number of our onsite developers taking part, some external people coming in, and quite a few people will be joining in remotely via Wave. It's going to be very interesting to see how a full day of collaboration through wave works out.

The exact number of people coming in has not yet been finalised, but we do have some extra spaces, so if you are a developer with a wave account in the London area or you are a scientist with some great ideas for apps that could work well for scientists then please feel free to drop me a line and we will see if we have space to fit you in. You can email me at i.mulvany@nature.com. You can, of course, pop in via wave and say hi.

The hashtag for the event will be #swlhd (science wave london hack day) if you are into that kind of thing.

I delivered a short talk summarising my essay, which was called "From Web 2.0 to the Global Database". I'm reproducing the text below, together with some of the slides I used to illustrate my talk.

(Update 20/10/09: Added link to book website.)

[Update - 2009.10.05: This post (2. Clients) is one of three. See also: 1. Service, 3. Widgets.]

The previous post described the nature.com OpenSearch service. Prior to that I posted on our new desktop widgets which use one of the XML interfaces - specifically the RSS feed.

Here we wanted to also show what can be done in the browser itself. We've created a small gallery of demo clients which all use the text-based JSON interface (or rather JSONP for cross-site scripting purposes). You can find the demos here:

http://nurture.nature.com/opensearch/apps

[Update - 2009.10.05: This post (1. Service) is one of three. See also: 2. Clients, 3. Widgets.]

Earlier this week we soft-launched a new service: nature.com OpenSearch. Simply put, nature.com OpenSearch provides a structured resource discovery facility for content hosted on nature.com. In effect, this is a sister service to our regular nature.com search service which allows a user to query nature.com and browse the result sets. By contrast, the new service allows applications to query nature.com and to fetch the results back in formats of their choosing. The diagram above attempts to compare the existing user-oriented nature.com search service at a) with the new application-oriented nature.com OpenSearch service at b). Applications from widgets to web pages (and beyond) are the immediate clients of the service. (A companion post here already discussed the new nature.com search search widgets which are one such application.)

In terms of interfacing to the service, machine-readable description documents are available for both OpenSearch and SRU (Search and Retrieval via URL) modes of access. These documents are referenced from autodiscovery links which are beginning to be added to all our nature.com web pages. Each web page thus links not only to our search, but more than that it provides the instructions on 'how to search'.

Query is either by simple search terms or by the query language CQL which is a high-level query language designed to be be human readable and writable, and to be intuitive while maintaining the expressiveness of more complex languages. Result sets can be returned in a variety of media types, both text (HTML and JSON) and XML (SRU, ATOM, RSS). Media types are selectable using HTTP content negotiation or by using the specific parameter 'httpAccept'.

(Click image to enlarge.)

And what does this all mean? Well, it really amounts to the ability to run off-platform search, i.e. I can now run my search over nature.com anywhere I choose to run it. For example, say I want to run it right here in this blog post, I can. Let's jig up a simple interface. What we'll do is to run a full-text keyword search and just list out the raw properties of the first item returned with no real attempt at styling. (The CQL checkbox just allows a CQL query to be input, otherwise the search terms are sent to the server as simple alternates.)

[Update - 2009.10.05: This post (3. Widgets) is one of three. See also: 1. Service, 2. Clients.]

The newly launched nature.com OpenSearch web service (which I'll discuss in a separate post) is an interface that provides distributed access to search on the nature.com platform. Specifically, the interface allows for structured queries from remote clients as well as for structured responses, and implements two compatible industry standards for search: OpenSearch and SRU (Search and Retrieval via URL)

As a practical demonstration of this distributed access we have developed a nature.com search desktop widget which is a small standalone app that runs on a user's desktop and interacts with the nature.com OpenSearch server by sending a simple URL request and receiving in response a regular RSS feed. This URL request closely mirrors the request strings in the OpenSearch URL templates that are now being linked to from a growing number of our web pages.

He is calling for interested people to sign up for a science google wave hack day either in London or somewhere near Didcot. I think some people from NPG might pop along. If you are interested go let Cameron know over on the doodle online poll.

Two new Nature Videos have just gone online.

First up, and my first solo video project, a film about Sci Foo 09. Here it is…



If you enjoyed the film and would like to share it, you can embed it in your own blog by going to Nature Video’s YouTube Channel.

Also just out, the trailer for our latest Lindau film series: Nobel Reactions. Every summer an extraordinary meeting between Nobel Laureates and young scientists takes place on Lindau Island in Germany. In 2009 it was the turn of the chemists and we were there to capture moments of this unique meeting of minds on film. The trailer introduces the Lindau Meetings and offers a taster of the films that follow: five short films on chemistry plus a special film feature on climate change. The films will be released one a week from 27 August. Watch them here, or subscribe to the series in iTunes (just search for ‘Nature Video’ in the iTunes store).

1. Next week's Science Online London meeting (co-produced by Nature Network) has been long sold out, but for those who missed getting a ticket, or who can't travel to London, there will also be live video streaming of the conference into Second Life. Entrance is £10 or $15 and it is open to all. SL attendees will be able to see all the live video and ask questions of the speakers. Jo Scott (avatar name: Joanna Wombat) and colleagues will also be running free orientations sessions for newbies. To avoid missing this one too, register here now.
2. Nature Methods is seeking votes for its 2009 Method of the Year. The previous winners are next-generation sequencing (2007) and super-resolution fluorescence microscopy in (2008). (And if you haven't seen the video on the latter then you should.) Check out the current 2009 nominees and vote tallies here.
3. This isn't exactly new news (hey, it's been busy round here), but for anyone who has seen it yet, Edge has some coverage of outcomes and experiences at Sci Foo '09 (including a contribution from yours truly). We also have a short video from the event coming out soon – watch this space.
4. Meanwhile elsewhere on Edge, check out this report on another wonderful event (though sadly one I didn't attend): a master class from George Church and Craig Venter on the brave new world of synthetic genomics.

Near the end of the (long) thread was this exchange:

"You could try asking them exactly how many downloads their last paper in a 'high impact' journal got... - Peter Binfield

Fair enough, but you know, I really don't think they think about that. They think "what will be in my CV?" and they think any journal that is somewhat competitive [includes other PLoS journals, BMC journals, etc] looks better than one that accepts anything that's methodologically sound. Again, not my view, but perhaps one that is held by many. Do people list # of downloads on their CV for publications? - Shirley Wu

They dont, because they dont have the data. However, people do list if their paper was rated by F1000; or if BMC designated it a 'highly accessed' article. So I think they will start to say "this paper was downloaded 5000 times in the first 3 months which put it in the top x% of all PLoS ONE articles, the top y% of all PLoS articles, and the top z% of ALL articles" (when the rest of the world starts quoting this data) - Peter Binfield"

Do people here think that article downloads stats should be put on academic CVs? (serious question)

It feels wrong to me. IMHO encouraging anybody to take download statistics seriously as a measure of success / quality would be a mistake. Taken on their own they're meaningless, surely - nice to know for the author, but meaningless. For them to be at all useful you'd have to supply a lot of context - as Peter suggests - though I don't think the journal level "top 10% of papers in first three months" context he outlined would be enough either.

(just to be clear I don't think Peter was necessarily saying that people should put only the download count on their CV - am using his comment above simply as a jumping off point for discussion)

A download counter can't tell if the person visiting your paper is a grad student looking for a journal club paper, a researcher interested in your field or... somebody who typed in an obscure porn related search that turned up unconnected words in the abstract. A search bot. Somebody on Google Images looking for free clipart. Got a blog? Check your traffic stats. Journals get those crazy queries too, lots of them. Mainstream search engines are a major source of traffic for journals but not always for the reasons publishers might want.

As a publisher do you account for this and only record 'good' traffic? What if your competition don't?

Institutions and ISPs transparently cache pages. If my lab mate and I both download your paper depending on the publisher's stats package it might register as only one hit (from the university proxy server). Do you compensate for that somehow?

Am I going to be penalized if I host my papers on my homepage? In my institutional repository? Should I add all those counts up for my CV? Do I need to cite my sources?

Should I tell my mum to set my paper as her homepage (and to be sure to delete her cookies each morning)?

If Science spends $50m on SEO next year and hits on their article pages double will the articles in 2010 be twice as good as those in 2009?

As an author should I be repeating keywords in my title to get more Google traffic? Should I try to include a figure of Britney Spears?

If we stick to giving 'top x percentage' context then do we make concessions for smaller disciplines publishing in multidisciplinary journals? More people work and publish in genetics than in quantum physics. Even if every important person in your field downloads your paper they might be outnumbered by grad students from the three dozen groups working on Rab4A effectors that download the genetics paper next to yours in the TOC.

I'm not saying that download stats aren't useful in aggregate or that authors don't have a right to know how many hits their papers received but they're so potentially misleading (& open to misinterpretation) that it doesn't seem to me the type of metric we want to be bandying about as an impact factor replacement.

(Google Wave hasn't been released yet but if you're interested in working with the preview you can request a developer account on the sandbox here)

Google Wave is a new open source project from Google that holds a lot of promise as a platform for scholarly communication. It's a little bit like email but allows for collaborative document editing, versioning and real time conversation within groups - check out Cameron and Martin's archives for more.

Igor is a proof of concept Wave robot that allows Wave users to pull in citations from Pubmed or their libraries on Connotea and CiteULike as they type.

To use it invite helpmeigor@appspot.com to join a wave.

The main changes are:

• a new way of exploring the site - the list view shows you the most popular items within a given time frame. It's sort of like Digg but to vote an item up you need to have commented on it or shared it on a social media site.
• simplified sidebar, visual cues on the grid / timeline view and a help link will hopefully help new users work out what they're seeing
• the aggregation logic now uses Friendfeed's SUP feed and connects directly to Twitter, so messages are picked up much faster.
• trending topics - this is a list of topics that are appearing more frequently than you might expect. Bear in mind that it's generated algorithmically so items are sometimes grouped together in odd (but technically correct ;)) ways...
• clicking on "see details" in the list view or on an item in the grid view brings up a breakdown of comments and tweets which you can use to jump straight into a conversation on, for example, Friendfeed.

There are still lots of little niggles. On smaller timescales (anything under than four hours) there's lots of items that aren't strictly speaking about science, too. Still not sure if that's a bug or a feature.

The next version will focus on people - both the people being followed by Streamosphere and visitors to the site - and grouping items by topic.