Monthly Archives: May 2009

Google Wave first reactions

I've spent the last 80 minutes a beautiful summer afternoon in the garden - watching the Google Wave video. Nico Adams has enthused about this to me and Cameron has been blown away.:

And my opinion is that this is absolutely game changing - it makes a whole series of problems simply go away, and potentially provides a route to solving many of the problems that I was struggling to see how to manage.

And later from Cameron: I said to someone yesterday, when they write the history of the web, Thursday will be the day that email died. It may be too early to call it the day that the wordprocessor died but I guess well see. I think it will clearly subsume wikis and blogs at least as separate services - there will still need to be some public facing approaches that may be different to what was demoed which was essentially person to person. There was no discussion of subscribing per se. But that is easily do-able.

Its interesting actually - some people just get it and many others dont seem to. All the translation and spell checking and clever embedding is very flash but the key revolution at the core of it seems to me to be the combining of messaging and the collaborative document. Everything else is just nice added functionality.

So why am I not feeling this epiphany the greatest thing since Mosaic? There is no question the demo is impressive and critically important (although there were too many talking heads and not enough demos you could read).

It's because I had the epiphany when Mosaic came out, 15 years ago. At that stage I walked around on air for three days. It changed my world and what I chose to do. The second epiphany was XML, - let's say 1998 - which I was fortunate to have had a small hand in developing. XML is at the heart of Google Wave. It's shared structured information. XML had and has the power necessary to transform the world. It's just taken 10 years to do so.

And I'm now used to the fact that ideas take 10 years to develop, even in the incubator of the Internet and Web. In 1998 I was worried that XML-over-the-Web would be a mad rush between competitive commercial applications. I was worried about ontological warfare. I'd developed Chemical Markup Language (with Henry Rzepa) - XML for chemistry . Adobe et al had developed Scalable Vector Graphics (SVG). I prophesied that SVG would be the killer app for XML-over-the-web. It had everything a good spec, some lovely tools and it hit you between the eyes. So what happened? Microsoft took a different route. Adobe bought Flash and killed SVG. The day the graphics died.

As a reality check - a thoughtful technical piece (It's new but not new) explains GoogleWave-as-infrastructure and mirrors my own views. Nothing is actually new. But everything can be different.

I have seen several false dawns in the last 15 years. And cases where the dawn has been deliberately obliterated. This could be different. But not because of the technology. Because of the organizations and the zeitgeist.

The critical things are:

  • A central approach which is large enough to survive and which potentially can be trusted. (The trust in Google is the single biggest aspect of everything).

  • Open data (and open minds). The success of GW will be based on sharing. Yes, GW has sophisticated security mechanisms but it is based on the idea (unthinkable 10 years ago) that people who have never met will share personal and important information trusted to a third party with whom they have no contract.

  • Standards. GW is built on XML. XML makes the previously impossible just simply hard work. And it makes what used to be hard relatively straightforward. (I imagine they have to do a lot of engineering under the hood, with image formats, etc. )

  • Open Source extensibility. Because GW is Open, people will add to it. And they will. But we shall still have to look to the fine print what is really Open and what is simply exposed? Googlemaps are not Open hence Openstreetmap. I'm more hopeful with Google code because they have created their Open Source site and hence imbibed the culture.

So GW potentially provides everything I have been waiting for for 10 years. An integrated infrastructure, with sufficient tools to make rapid progress. That relieves me from the burden of organising input, parsing, workflow, storage, dissemination. And concentrating on what I really want to do which is to build chemically intelligent systems. Bobby Glen and I put this idea forward 8 years ago as an eScience grant proposal The world wide molecular matrix. It was perhaps naive and optimistic in places and the 2002-zeitgeist would anyway have killed it. (The grant didn't get past the middleware weenies who were looking for Grid stretch - a meaningless term which ensured the funding went to infrastructure based on the rather arrogant idea that academia knew how to build world-beating middleware).

GW has shown that it can build middleware and interactiveware better better better than academia.

So let's turn to what we really should be doing building chemistry based on a universal public information infrastructure. On the pillars of the Blue Obelisk Open Data, Open Source, Open Standards. The Blue Obelisk has got most of the components and we need componentware as well as applications. I haven't looked into GW (though we have been using GWT). I suspect it's not as trivial as it looks to use. GWT took us some time, and Google moves in an industry where developers can be hired in large teams. (I remember at an Xtech (XML) meeting 2 years ago at a session on SVG on mobiles one company developer: We didn't need much resource 10 developers for 3 years was sufficient. I turned bright green.

The key thing is collaboration. The BO has shown that if we work together we get a good mixture of complementarity. GW might be the next impetus I don't know. But I am sure that if we keep developing componentware CDK, Jmol, OpenBabel, JUMBO, OSCAR/OPSIN, etc. we'll end up being ideally suited for the next wave.

And if that is GoogleWave, fine. If not we'll recognize it when it comes.

I'm conscious as I write that we are also working with Microsoft on Open Source chemistry with C# and WPF. How does that fit in? Or doesn't it. I don't know, but as we are thinking of poets Laureates in the UK these days - lines of Tennyson spring to mind:

The old order changeth,
yielding place to new,

And God fulfills himself in many ways,

Lest one good custom should corrupt the world

Come To Science Blogging 2009 in London

I am delighted to hear about this year's Science Blogging conference. Last year was really great a superb introduction by Ben Goldacre destroying yet another hydra head on the pseudoscience monster. Lots of targeted discussions, followed by a panel.

I am really impressed by the quality and impact of the scientific blogosphere. An ou tstanding example was one blogger (I think it was Grll scientist) who was invited but who was in the USA. Her readers clubbed together and found the transatlantic fare I certainly couldn't count on that.

I felt guilty at last year's event because I'd stopped blogging a few months earlier so I felt a sham. I could, however, contribute knowledgeable on the session about not feeling guilty about not blogging! And at the end we knocked together ideas about how we could promote blogging. We suggested a prize for any young scientists who convinced a senior scientist to blog. Timo and colleagues came up with a very generous prize which was a trip to SciFoo. I can't promise that it will happen this year but why don't you go out and do it anyway.

Blogging matters to science and science should take it seriously. One area where it is almost unique is the immediacy and power of any whistleblowing on bad science , bad ethics etc. So when Proteomics (Wiley) published a paper promtoing creationism or when Elsevier published fake journals the blogosphere made sure that people knew all about it in hours.

So come. It's great fun. If you haven't been to the RI it's fantastic worth the trip for the lecture hall alone. I can feel the great scientists, Davy, Faraday looking down.

Building on the success of last years Science Blogging 2009: London conference, wed like to announce that Science Online London 2009 will take place on Saturday August 22, 2009 at the Royal Institution of Great Britain in London. We hope that you can attend.


We decided to change the name of the conference this year to reflect the wide range of science-related activities occurring online today. This years programme will include sessions on blogging and microblogging, online communities, open access, new teaching and research tools, author identifiers, etc.


Registration will soon open on the conference website: You can now sign up to receive email alerts on the site.


There will probably be a registration fee to cover the costs. Exact amount tbc, but likely to be in the range of £10.


Suggest sessions/topics

We need your ideas for sessions and speakers: panel discussions, keynote speakers, demos, etc. Volunteer yourself as a speaker or suggest others youd like to hear from. Please post your ideas to the conferences Nature Network forum, Friendfeed group, or email them to



We need sponsors! If you or your organization would like to be a sponsor, please email You can also suggest organizations you think we should approach.



The event is co-hosted by Nature Network (Nature Publishing Group), Mendeley and the Royal Institution of Great Britain.


Start the networking and spread the word!

Youll find groups for the conference on Nature Network, Twitter (tag: #soloconf_09)

and Friendfeed.


Please also blog/Twitter/etc about the event (if you havent already!) to help us spread the word. Attached is our logo for you to repost on your blogs. And forward this message to your friends and colleagues!


~ The Organizers


Matt Brown / Nature Network, Martin Fenner / Hannover Medical School,
Richard P. Grant / F1000, Victor Henning / Mendeley, Corie Lok / Nature Network and Jan Reichelt / Mendeley

Corie Lok
Senior Editor, Nature Network;

25 First Street, Suite 104
Cambridge, MA   USA    02141

Tel.: 617-475-9220
Website: and

Net Neutrality: Harbour replies (it's the fault of the French)

Pursuing the issue of Net Neutrality I have got a document from Malcolm Harbour through my MEP:

On Wed, May 27, 2009 at 3:30 PM, VAN ORDEN Geoffrey <> wrote:

Dear Mr Murray-Rust,

Thank you for your email about Net Neutrality.  I have taken the liberty of asking my colleague Malcolm Harbour about your query and he has sent me the attached question and answer sheet. 

I do hope this goes some way to answering your question.

Kind regards,

Geoffrey Van Orden MEP

PMR: The document is called Myths Vs Facts and does not appear to have any address or other attribution. I would be grateful for any comments on Mr Harbour's contribution. (Harbour was a rapporteur for (or rather against) the Net Neutrality recommendation).

I have cut out the section relating to the Internet other sections referred to BEREC. If I interpret just the words below it would appear that the EU is not going to impose restrictions but that it isn't going to stop member states doing so. And if you live in France, bad luck.

Myths Vs Facts

 The Telecoms Package and Your Rights on the Internet - the key questions:

1) Does this new Package threaten the freedom of the internet, by allowing big telecoms operators to block or discriminate against content, and my ability to access the services and content I want (net neutrality)?

No.  The ISP provides a commercial service to customers and in principle free to structure that offering as they deem best.  They will of course take customer demand into account.  This means that they can currently for example block access to any site they want, or restrict access to applications, if they deem that to be commercially attractive.  They can also offer different bandwidths, price packages etc.  They can continue doing so also in the future.  The situation is comparable to a bookseller - a bookseller does not have to offer every book available in print. 

The possibility for ISPs to decide what to offer their customers is not changed by the Package.  However, the Package will require ISPs to inform their customers of any such restrictions, so that you can choose whether to use another ISP. 

If an ISP has a dominant position and abuses it, competition rules apply and can be used by the Commission or national authorities to address the situation.   

As between you and your Government, any measures taken by a Member State to limit your access to services and content, for example by forcing ISPs to block access, have to respect your fundamental freedoms.

2) How are my rights as a citizen on the Internet safeguarded? Does this whole package affect my freedom to access and use information?

The fundamental rights of all citizens, whether as internet users or in any other capacity, are protected by the European Convention for the Protection of Human Rights and Fundamental Freedoms.  That Convention for example safeguards freedom of expression, and the right to hold and impart information.  It also provides for judicial remedies.  The Package affirms that these fundamental rights also apply in the field of electronic communications.

3) This proposal has been drafted by the French Government to enable it to impose HADOPI?

No. Amendments that would have facilitated HADOPI were all rejected.  These issues are a matter for national law, and not addressed in the Telecoms Package.  The Package does however restate and reinforce that fundamental rights apply and have to be observed by Member States also in the context of internet usage. 

4) Will I be banned from the Internet if I am caught downloading illegal copyright material from the Internet, such as films and music?

No. The reports that the proposals are going to lead to this are scaremongering. The legislation does not propose this.

5) What has caused all this scaremongering?

France is considering a highly controversial law which will mean that if French citizens are caught downloading illegal content, such as copyright films and music, three times they will be disconnected from the Internet. This is called the "Three Strikes and You're Out" rule. This would mean that Internet Service Providers (ISPs) would have to monitor internet traffic. The telecoms package has been attacked by false statements that it would adopt a similar "Three Strikes and You're Out" approach.

6) So what does the Users´ Rights report proposals say in relation to copyright?

National authorities would, if appropriate, be able to produce generic, standardised information, which would be sent to all customers. This public interest information could cover a range of issues, including copyright, child pornography, viruses, and risks to attacks for personal security. There will be no targeting of individual customers for any particular activity and there will be no identification, spying or surveillance of any specific individuals. There is also a provision enabling national authorities to promote appropriate cooperation between ISPs and rightholders regarding lawful content.

7) What will happen if I illegally download copyright material after this legislation comes into force? Is there any way this legislation could lead to me being banned from the Internet?

There will be no change to the current situation, which means that it is up to Member States to deal with copyright issues according to their national law.

8) I am very interested in copyright and Intellectual Property. Will there be a more detailed dossier covering these issues?

Yes, the upcoming Creative Content Online consultation will explore Intellectual Property Rights in more detail.

 PMR: I need an interpreter...

Revitalisation of the CML Blog

I am now revitalising the CML Blog (see This blog was developed to describe CML but ran into problems with the formatting under WordPress and the particualr settings and tools we had installed. The problems are, I hope, solved.

I will therefore be splitting my posts between chemistry (and especially CML) on the CML Blog and everything else (particular the fight for Openness) on this blog (

I hope these leads to a better approach for readers. The difference between European politics and the number of electrons in ferrocene is considerable and may have deterred some readers. I don't know.

The CML blog will address questions of the design of CML, the user community, and may also act as a way to create material for static web pages. I encourage you to suggest questions as this gives me the excuse and impetus to write on specific topics. In general please use the comment fields although I shall still take queries in email.

For those who wish to follow the CML Blog add into your feed reader. For a week or two I'll probably reference posts from this blog.

Net Neutrality - Web Democracy in Action

I am delighted to have received the following letter from our MEP Andrew Duff on Net Neutrality.

Dear Mr. Murray-Rust,

Thank you for your recent letter on the EU telecoms package. I fully share your concerns about preserving a liberal regime for the internet.

I am pleased to report that it was our Liberal ALDE group in the European Parliament which was decisive in achieving a majority of MEPs for the crucial amendment, which stated that "no restriction may be imposed on the fundamental rights and freedoms of end users, without a prior ruling by the judicial authorities ... save when public security is threatened".

The passage of this amendment meant that the telecoms package was not concluded in this Parliament at second reading. Negotiations will continue in conciliation, once the new Parliament assembles.

If re-elected, you can be sure that I will continue to be involved in these developments.

Yours sincerely,


Andrew Duff


Andrew Duff MEP

Leader, UK Liberal Democrat European Parliamentary Party (LDEPP)

Spokesman, Constitutional Affairs for the Alliance of Liberals and Democrats for Europe (ALDE)

President, Union of European Federalists (UEF)

European Parliament

10 G 346

60, Rue Wiertz

B-1047 Brussels

ICE test 4

I am testing ICE+OO's ability to author XML in a reasonably pretty fashion. Neglect this post unless you are interested in ICE-manship (which I hope many of you are).

This is some text and this is some XML

<module name="metadata" capture="os wday mon day hr min sec year host">
     Date and time (@ss)  : @s3 @s3 @s3 @i2:@i2:@i2 @14
     Host name              : @s                                 

Here is some more XML

<!-- -->
  <owl:DatatypeProperty rdf:about="#hasConcise_att"/>
  <!-- -->
  <owl:DatatypeProperty rdf:about="#hasConvention_att"/>
  <!-- -->
  <owl:DatatypeProperty rdf:about="#hasDictref_att"/>
  <!-- -->
  <owl:DatatypeProperty rdf:about="#hasFormalcharge_att"/>
  <!-- -->

and some more

 <owl:Class rdf:about="">
    <rdfs:subClassOf rdf:resource=""/>
        <owl:onProperty rdf:resource="#hasValue"/>
        <owl:someValuesFrom rdf:resource=""/>
    <rdfs:comment xml:lang="en">def: directives for geometry output</rdfs:comment>
    <rdfs:comment xml:lang="en">desc: needs a description</rdfs:comment>

Repositories: The ICE-man speaketh

Our group has a major commitment in Repositories and we've just had the annual beanfeast OpenRepositories 09 (OR09). Jim Downing went and I have been debriefing (gently) with him but it may need a Trip To The Panton to get a wider picture. Jim, of course, is a Repository star in his own right and at OR09 had plenty to show and tell. One of our projects is ICE-TheOREm which uses Peter Sefton's ICE authoring tool and where we set up a joint project with Peter.

The ICE age is coming.

Embrace it. (This blog is now written with ICE and I am much more productive - at least in writing more words).

So Here are some of Peter's impressions of OR09. There was clearly a major geek-fest going on. I'm sorry I had to miss it.

... Clifford Lynchs 2003 definition of a repository as a set of services:

In my view, a university-based institutional repository is a set of services that a university offers to the members of its community for the management and dissemination of digital materials created by the institution and its community members. .... An institutional repository is not simply a fixed set of software and hardware.

I [PTS] agree. Its not a computer program, its a lifestyle; what Lynch is calling organizational commitment.


I had a little moment in the spotlight when keynote speaker John Willbanks referenced my Scholarly HTML idea. This was reported in Twitter thus:

akosavic Wilbanks at #or09: rename semantic web as scholarly HTML

So there you have it, meet the saviour of the semantic web. Move over Sir Tim.

Actually I wouldnt go that far what I am trying to get at with this Scholarly HTML is that the research article our unit of academic currency should be a web page, not a bit of pretend paper, a PDF. Journals need to be reinvented. Articles should be web pages (yes we need ways to time-stamp and version them). Peer review and editing are both important, but I can think of better ways to get those done than we typically use now. Then theres the idea of embedding machine readable semantics in the form of statements of fact, links to data etc, not to mention machine readable metadata. More on this soon here on the blog I think Ill write a series of papers on this, with appropriate collaborators, in the open then well see if we can get them to count as scholarly literature via peer review. A couple of people told me theyre watching the Scholarly HTML posts so I think Im onto something with this one.

PMR: I like the phrase scholarly HTML. Simple, accurate. (Of course for us geeks it's XHTML, with embedded excitement such as chemistry, but I expect most schoolkids have now heard of HTML).


First up Jim Downing from Cambridge and I showed off the work we did with our teams on the ICE-TheOREM project. Not only were we able to show a thesis going onto the web in HTML as well as the dreaded PDF, it had granular chapter-level embargo, and we were fully buzzword compliant, with ORE and SWORD built in. And for the first time we made our work available as a ready-to run virtual machine, a few copies of which I handed out. Well definitely do more of that, and keep updating our machine with all the software we work with at the moment it runs ICE, ePrints and The Fascinator, but Id love to see DSpace and OJS and Moodle on there as well all integrated.


And there was the poster, which I supplemented with a metaphor a collection of 40mm & 50mm PVC waste pipe and various connectors. David Flanders used it to build a data grid which included a pipe going straight to repository hell a place he has apparently spent a fair bit of time drinking microbrew with too much malt. The idea was to drive the point that we want to make research data plumbing as easy as PCV pipe network engineering. Here I am spruiking the poster with a fistful of PVC.



I attended Microsofts workshop on their growing set of academic tools. Ill reserve judgment on the new Zentity repostiory, but I am very, very pleased to see Microsoft Research working on academic workflows. As part of that, the idea of building HTML conversion into repository deposit tools is getting a serious airing in the repository community and Im very pleased about that. More after my visit to MS Research tomorrow. (I have already spent a little time in Seattle with Pablo Fernicola, wandering in the sculpture garden and talking in general about academic computing).

PMR: I'm pleased that PTS is pleased. I am impressed by MS's commitment to covering the field and their conversion (in MS Research) to Open Source. The major problem is that Microsoft technology can be a barrier. There is an assumption that everyone has implemented the Microsoft technology stack (IIS, SQLServer, SharePoint, Active Directory, Team Foundation Server, .NET, etc.) Not all these are required for Zentity, but some are. And that's a major barrier to uptake. My contacts in MSR are aware of this...

The final thing to mention is the Developer Challenge, run by the unstoppable David Flanders (I was going to say indefatigable but I cant spell that) with Rachael Rodenmayer assisting. This was judged by a team of five based on five minute screencasts. There were some good ideas in there, in a field that spanned entire repository developments that were already done to small prototypes. Read about the winners at the JISC site.



Good conference. Good venue apart from a lack of power points (no lack of PowerPoints unfortunately) in the main venue. I was pleased to be showing off HTML in ePrints at last, and have ICE in production as an eResearch workflow tool. I think the repository world is making a welcome move to (re)embracing the idea of small pieces loosely joined.

PMR: Peter thinks deeply about repositories and disseminates his thoughts on top of working software. Pay great attention.

Openness in the shadow of Wallace

I was one of the first staff at the University of Stirling (Scotland) in 1967 so I'm delighted to see that Stirling continues to forge ahead in Openness:

STORRE, the IR at the University of Stirling, recently passed the 1,000 item milestone. The repository's managers attribute the growth to the university's institutional mandate:

STORRE is a full text only repository that has been up and running at the University of Stirling since 2005. We focussed initially on eTheses, with the submission of eTheses to STORRE becoming mandatory in September 2006. ...

In April 2008 the University's ePrint Mandate was announced - this requires all Journal Articles submitted for publication since January 2007 to be deposited in STORRE immediately on acceptance for publication. ...

Since the ePrint Mandate came into force in September 2008, the rate of submissions of items to STORRE has risen dramatically from less than 20 items per month (sometimes much less!) to around 120 items per month. ...

Scotland has a burning national pride (you didn't need me to tell you that) and one of the results is to act in a united manner. I remember two (three?) years ago at the Open Scholarship meeting in Glasgow the strong feeling that they were united on Openness and were ahead of England in this. I think they still are.

Open access and unacceptable behaviour

It's particularly sad when someone you look up to falls from their pedestal.

Many of us in the Open Access world remember Ian Gibson (UK MP) and his campaign to push for OA through the offices of the Houses of Parliament. See, for example the BMC interview (

Now Ian Gibson is one of the Mps most implicated in the unethical use of expenses ( You can read the sorry story for yourself.

Yes, MPs say, it was within the rules. But I expect Mps to act on ethical as well as legal principles. When Gibson criticised publishers, they were within the rules. But he wanted to change the rules. The lack of ethical principles leaves us stunned and more so for those who we saw being driven by ethical motives.

We are simply bewildered. We all know that politicians can be corrupt, lazy, scheming, etc. But we like (and need) to believe that most are honest and hardworking. We expect them to look out for perils ahead and to alert us. We expect them to indicate when others overstep the bounds of reasonable action. Now we can't.

The only good thing that can come out of this is a radicalisation of democracy. Greater legitimisation of individual action and it's here that the Net is so important. Let's not throw the chance away.