I'm really happy to announce that we will be hosting a hack day on Friday for developing scientific applications in google wave. The event was thought up by Cameron Neylon and we at Nature were able to find a room and are able to provide interweb access and coffee. The JISC DevSci project and Google will be providing Pizza. If you have a google wave account you can check out the wave discussing this event.

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.

Posted by Ian Mulvany at 05:56 AM | Permalink | Comments (0) | Postgenomic trackbacks ()

I'm on my way home having just attended the 2009 Microsoft eScience Workshop at Carnegie Mellon University in Pittsburgh, where Tony Hey and his team at Microsoft Research also launched a book called The Fourth Paradigm. It's a collection of essays that provide relatively accessible accounts of the impact and potential of digital science, and has been published in memory of Jim Gray, a pioneer in this area.

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.)

"From Web 2.0 to the Global Database" »

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(Click image to enlarge.)

[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

Posted by Tony Hammond at 11:11 AM | Permalink | Comments (0) | Postgenomic trackbacks ()

(Click image to enlarge.)

[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.)

"nature.com OpenSearch" »

Posted by Tony Hammond at 06:33 AM | Permalink | Comments (0) | Postgenomic trackbacks ()

[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.

"Desktop Widgets: nature.com search" »

Posted by Tony Hammond at 02:38 AM | Permalink | Comments (0) | Postgenomic trackbacks ()