WWMM: The World Wide Molecular Matrix

Since I have been asked to talk about the WWMM here’s a bit of background… When the UK e-Science project started (2001) we put in a proposal for a new vision of shared chemistry – the World Wide Molecular Matrix. The term “Matrix” comes from the futuristic computer network and virtual world in William Gibson‘s novels where humans and machines are coupled in cyberspace. Our proposal was for distributed chemistry based on a Napster-like model where chemical objects could be shared in server-browsers just as for music.
It seemed easy. If it worked for music it should be possible for chemistry. Admittedly the content was more variable and the metadata more complex. But nothing that shouldn’t be possible with XML. And when we built the better mousetrap, the chemists would come. Others liked the idea, and there is a n article in Wikipedia (Worldwide molecular matrix).
But it’s taken at least 5 years. The idea seems simple, but there are lots of details. The eScience program helped – we had two postdocs through the Cambridge eScience Centre and the DTI (Molecular Informatics “Molecular Standards for the Grid”). As well as CML ee listed 10 technologies (Java, Jumbo, Apache HTTP Server, Apache Tomcat, Xindice, CDK – Chemistry Development Kit, JMol, JChemPaint, Condor and Condor-G, PHP). We’re not using much PHP, no Xindice and prefer Jetty to Tomcat, but the rest remain core components. We’ve added a lot more – RDF, RSS, Atom, InChI, blogs, wikis, SVN, Eclipse, JUnit, and a good deal more. It’s always more and more technology… OpenBabel, JSpecView, Bioclipse, OSCAR and OSCAR3…
But we needed it. The original vision was correct but impossible in 2002. Now the technology has risen up to meet the expectations. CrystalEye, along with SPECTRa,  is the first example of fully functioning WWMM. It’s free, virtually maintenance-free, and very high quality. We have developed it so it’s portable and we’ll be making the contents and software available wherever they are wanted.
But it also requires content. That’s why we are developing ways of authoring chemical documents and why we are creating mechanisms for sharing. Sharing only comes about when there is mutual benefit, and until the blogosphere arrived there was little public appreciation. We now see the value of trading goods and services and the power of the gift economy. In our case we are adding things like quality and discoverability as added value. We’ve seen the first request for a mashup today.
WWMM requires Open Data, and probably we had to create the definition and management of Openness before we knew how to do it. We’ll start to see more truly Open Data as publishers realise the value and encourage their authors to create Open content as part of the submission process. And funders will encourage the creation and deposition of data as part of the required Open publication process.  Then scientists will see the value of authoring semantic data rather than paying post-publications aggregators to type up up again. At that stage WWMM will truly have arrived