petermr's blog

Some blogs generate lots of comment on every post. Some of the chemistry blogs are like this – Tenderbutton before he had to quit to write his thesis, and Totally Synthetic. There could easily be 50-100 comments, almost by return. This really anticipated Twitter and indeed Twitter and Friendfeed may take over some of this. It clearly suggested that a strong community grew up round these blogs – in this case practising laboratory scientists for the most part. It encouraged chemical gossip – what were things like in other laboratories, etc.

Sometimes, but not always, you can create posts which get reactive comments. These are normally when you air views that are likely to be controversial. (It’s not generally a good idea to invite – say – political discussion just for the sake of it, though obviously some science blogs interact well with current politics. The new enlightenment in the US is crucially important for Open practices.
But sometimes you get quite unusual comments, as Peter Sefton found. He’s a committed cyclist and has a trailer – I think for children. Anyway he mentioned this – or showed a picture – and now his biggest blog karma comes from cyclists (and not from ICE fanatics).

So I was listening to Radio Queensland and it was focusing on Toowoomba where one of the police officers is concerned about bad motoring habits engangering cyclists. So he has installed a camera on his bicycle and uses this to record bad driving, ultimately with a view to prosecution. He’s also said that if any cyclist wishes to do the same, then the police would take such videos seriously.

As a daily cyclist in Cambridge I think this is a great idea. I’ve had a few moderately near misses (I had actual contacts in London which damaged me). I can imagine the idea catching on very rapidly here – the home of web-based government such as FixMyStreet and WhatDoTheyKnow. And, of course, Cambridge is the most comprehensively OpenStreetMapped city anywhere (I think). So just as FixMyStreet encourages people to take photos of potholes, uncleared ice, bad signs, broken railings, etc. what about FixMyDriving?

[I thought I had remembered how to use OO+ICE to post this but it crashed and only posted half the document so I am back to the old methods until the ICE patch].

Oh, and one of the most depressing aspects is that when you do get a comment and think – great! – it’s often some mindlessly depressing linkspam. I have installed Akismet and it’s caught over 100, 000 spams, but some still get through. Make sure you get used to recognising them because otherwise you could ge deindexed by Google. That’s happened to us. Really, really depressing.

Just found The Open Laboratory 2009 blogging competition. An excellent place to see what top-class science blogs are like. Enter yours if you feel like it!

This was a quick post to show how the ICE system at USQ can be used to create blogs. The advantage is that it uses OpenOffice as an authoring tool so the worst excesses of WordPress are removed. The final document is then published into the drafts folder of the blog, where I must log in and republish it.

We are no looking at doing this automatically by using the server at USQ, so the next post may show this.

Currently I have settled on publising directly from OO, using the USQ plugin/toolbar. This has a few minor glitches (you need to retype URLs etc for each post) but they will be fixed. When that is done I shall move to it wholeheartedly. It still goes through wordpress so that the posts are there and can be manged and tweaked, but the bulk of the editing is done offline in a much more congenial environment.

An interesting post from Duncan Hull  The Unreasonable Effectiveness of Google about the challenges of a semantic web of data. Since I am talking on the Chemical Semantic Web at Bio-IT World Conference & Expo 2009 it has a lot to influence me. There is the question of whether to annotate data:

“The first lesson of Web-scale learning is to use available large-scale data rather than hoping for annotated data that isn’t available.”

In general I agree, and believe that it’s possible to use heuristics such as text-mining and ontologies to clear up some of this later (it can never be 100 percent). Data often contain internal checks and consistency relations that show bad values. A typica example is temperature – when you find a small set of values 273 degrees larger than the main set you can be pretty sure someone has muddled celsius and kelvin. But there are many cases where you can’t know an isolated value is wrong.

And so our current approach is painless semantic authoring. For authors to create the same documents as they do now, but checked ontologically and semantically. That’s technically possible – why I am at Toowoomba today. But it needs the tools, and that’s why I am at Toowoomba.

As usual I didn’t know in detail what I would say at Crystal26 – it depends on who is present, what has just been said, how grateful I am to the organizers (10/10). I have an overview page (in HTML) and a menu of a few hundred topics with 10-20 “slides” each. In particular I download chunks of HTML from the web rather than try to emasculate them with powerpoint. This makes it difficult to distribute a “talk” and so I try to blog the major points.

Overview of presentation:

• The Semantic Web is here and ICT companies are investing heavily
• Vision of universal access to knowledge for both humans and machines
• Belief in emergent human/machine phenomena
• SW already well developed in bioscience
• crystallography very well placed in physical science

I do strongly believe in the nascent Sematic Web leading to a new phase of knowledge devlopment and sharing. Some obvious areas will be the continued development of natural language tools and – as others think – a new generation of knowledgebases – beyond Google. Current contenders include Wolfram Alpha and True_Knowledge. Little is known in practice of either – I would guess that WA would have major applicability to physical science, while TK seems to be closer to aSemantic Web approach, but with fuzzy algorithms rather than the formalism of RDF/OWL. We shall see. But at present I’m guessing it’s still worth trying to create semantic documents with controlled ontologies.

Semantic web:

• linked Open Data
• (global) reasoning engine
• social networks

I showed my Tweetdeck as an example of social networks – I have become converted to this as a valuable way of throwing medium-valuable contributions or request to a like-minded community. For example I tweeted my request for support material and was picked up by various members of the direct and informal groups. However I concentrated on Linked Open Data (including the Open) but as always didn’t cover it all – I present material until the time cutoff and then stop. (Whereas a Powerpoint requires you to flip over lots of slides to get to the end).

Expectations:

• global access to data in standardised or interconvertible form
• “natural language” questions linking data
• “giant global brain”

Requirements:

• Open data
• Agreed semantics
• identifier system
• agreed ontologies
• ontology mapping
• authoring tools
• searchable repositories
• validation systems

Crystallography does well implicitly in these areas but it needs for formalising. Data is often not aggressively Open, semantics are not in modern formats, ontologies are implied at best (through CIF dictinaries). Data creattion tools are patchy – the good news is that manufacturers are generally on board, the bad is that there is no semantic editing or authoring. Repositories do not exist except as highly managed, expensive data banks. This has to and will change

Challenges

• getting semantic data
• publishers’ attitudes (not IUCR/Acta)
• creation of ontologies

Tractable approaches

• Open semantic authoring tools
• searchable Open Data (RDF) repositiories

So then some demos. I showed Andrew Walkinshaw’s geo-crystal mashup, CrystalEye, CIF-CML-RDF-OWL in Protege, semantic authoring in Chem4Word and finally a movie of Lensfield molecular repository (Nico, Joe, Jim have made great short movies of what the system looks like).

And, as always, we are keen to collaborate in these areas. My great thanks to Peter Turner for hisx invite and support.

I’ve immersed myself for the last 2 days in the Australia/NZ crystallography meeting – about 100 scientists – some old acquaintances. It’s been wonderful. Some of the imaging and related techniques have been awesome – instrumentation has moved on so much. And, of course, this means that data is more and more critical.

It’s been great to see experiments where theory and experiment are compared (this is almost completely unknown in modern chemoinformatics where there is little theory and virtually no experiment).

I’ll pick just one – quantitative diffuse scattering from Harald Reichert (ESRF). Don’t switch off – as it relates to chemistry. Because as atom moves in a crystal it experiencese the chemical and lattice forces of its neighbours. Since diffuse scattering can now be measured with a dynamic range of (IIRC) 5 orders of magnitude we can see places ikn the crystal where atoms occur rarely and this maps out the anharmonic potential. By working in reciprocal space it’s possible to observe second and third-order interatomic forces.

So what does this have to do with chemistry? Well, for years, according to Harald, the DFT experts have been telling the experimentalists that theory (“first principles”) is so good that experiments are irrelevant.

Well the latest synchrotrons are showing the reverse. That theory is all over the shop compared with experiment. And of course it’s not “first principles” – it’s a folklore of basis sets, functionals and pseudopotentials. So maybe the “correct” DFT parameterisation could be better determined from experiment. [Note this is for alloys at present, but in principle it can be done for ionic solids.]

I miss not doing experiments.

Henry and I have worked together more many years – today he mailed me about the latest entry in his blog. He’s wondering whether blogs are a way of recording scientific ideas – which used to be published in letters. Anyway here’s a link

A molecule with an identity crisis: Aromatic or anti-aromatic?

In 1988, Wilke (DOI: 10.1002/anie.198801851) reported molecule 1

A 24-annulene. Click on image for model.

It was a highly unexpected outcome of a nickel-catalyzed reaction and was described as a 24-annulene with an unusual 3D shape. Little attention has been paid to this molecule since its original report, but the focus has now returned! The reason is that a 24- annulene belongs formally to a class of molecule with 4n (n=6) π-electrons, and which makes it antiaromatic according to the (extended) Hückel rule. This is a select class of molecule, of which the first two members are cyclobutadiene and cyclo-octatetraene. The first of these is exceptionally reactive and unstable and is the archetypal anti-aromatic molecule. The second is not actually unstable, but it is reactive and but conventional wisdom has it that it avoids the antiaromaticity by adopting a highly non-planar tub shape and hence adopts reactive non-aromaticity. Both these examples have localized double bonds, a great contrast with the molecule which sandwiches them, cyclo-hexatriene (i.e. benzene). The reason for the resurgent interest is that a number of crystalline, apparently stable, antiaromatic molecules have recently been discovered, and ostensibly, molecule 1 belongs to this select class! …..

Having moved computers one of the things that got lost was a list of feeds so I am catching up with some of the ones I used to read. I came across Chris Rusbridge’s Digital Curation Blog which is essential reading for anyone interested in the subject. Chris is a clear and thoughtful writer and often uses the blog to explore new ideas. Here is his comment on something I said at #LOTF09:

Libraries of the Future: SourceForge as Repository?

In his talk (which he pre-announced on his resumed blog), Peter Murray-Rust (PMR) suggested (as he has done previously) that we might like to think of SourceForge as an alternative model for a scholarly repository (“Sourceforge. A true repository where I store all my code, versioned, preserved, sharable”). I’ve previously put forward a related suggestion, stimulated by PMR’s earlier remarks, on the JISC-Repositories email list, where it got a bit of consideration. But this time the reaction, especially via the Twitter #lotf09 feed, was quite a bit stronger. Reactions really fell into two groups: firstly something like: SourceForge was setting our sights way too low; it’s ugly, cluttered by adverts, and SLOOOOOWWW (I can’t find the actual quote in my Twitter search; maybe it was on Second Life). Secondly, the use cases are different, eg @lescarr: “Repositories will look like sourceforge when researchers look like developers” (it might be worth noting that PMR is a developer as well as a researcher).

PMR: My demo of Sourceforge was primarily simply to show features of an Open, versioned system – I wanted to show that writers needed versions, needed to share, needed a submit-and-forget system. What I was implying (and it had to be implicit because of the short time) was that we needed similar systems for compound documents. Chris continues:

Journal articles, by contrast, are mostly written using proprietary (sometimes open source) office systems which create and edit highly complex files whose formats are closely linked to the application. Apart from some graphic and tabular elements, an article will usually be one file, and if not, there is no convention on how it might be composed. Workflow for multi-author articles is entirely dependent on the lead author, who will usually work with colleagues to assign sections for authoring, gather these contributions, assemble and edit them into a coherent story, circulating this repeatedly for comments and suggested improvements (sometimes using tracked change features).

PMR: completely so, and I am happy that Chris and others have picked up the baton. We need something of the power of Word or OpenOffice and in an ideal world the repository would allow either tool to access documents in the system. Indeed we should be careful about the word “repository” which implies “repose” and therefore peaceful but dead documents.

Next week I am off to USQ to work with Peter Sefton, guru of the ICE: The Integrated Content Environment. I need to know more detail before I claim it is the answer to Chris’ requirements. A system which manages collaboration, multiple authors, different content types, links, behaviour, styles, versions, platform independence, etc. is not trivial to create and I’ve probably made some facile assumptions about operations.

But if you are a “repository manager” responsible for curating an institution’s published output, you should be actively looking at communal authoring systems. That’s what the researchers really want, and getting the results into a repository should be a manageable task.