Science Online London 2009! – The Prequel

I have just returned from the “prequel” of the Science Online ’09 Conference here in London, which was jointly organised by Nature Network, Mendeley and the Royal Institution. The word “prequel” really is a bit of a euphemism for having an amazing time here: the day was ably organised and very charmingly led by Matt Brown, Matt is both a scientist and a “Londonista” extraordinaire, who took us on a tour of scientific London.

We started the day off by a visit to the offices of Nature Publishing Group (NPG) and got a glimpse of how Nature was produced: how do the editors make decisions over acceptance and rejections, what happens to a manuscript once it has been accepted and what does the postproduction look like? The offices themselves are in a converted brewery building and located right next to some canals which were used to move stuff round London in the old days.

It was interesting to see just how confident the editors were in their ability to predict high impact papers before they even send them out for review (approximately 70% of all manuscripts submitted to Nature get rejected outright before even undergoing peer review). I suppose that it is true that they see an awful lot of cutting edge science, attend a lot of conferences and travel a lot – nevertheless the amount of confidence did surprise me somewhat.

John Hunter by John jackson (obtained from Wikipedia under a Wikimedia Licence)

Once were were done at Nature, our next stop was the Hunterian Museum at the Royal College of Surgeons. The collection of the museum was developed by John Hunter – one of the most prolific surgeons and anatomists of his time. Of Scottish origin, Hunter came to London at the age of 20 and started work in the anatomy school of his older brother William. He soon eclipsed his brother in the skillful preparation of anatomical samples as well as in anatomical knowledge. As is often the case, this led to sibling rivalry and the two eventually fell out. This left John unemployed for a while and, after stints in the army (he used his army time productively to study gun shot wounds and their treatment) and as a dentist, he managed to establish himself in London as an anatomist and surgeon of considerable standing. Eventually he became a Fellow of the Royal Society and Surgeon Extraordinary to King George III (the mad one). During his time in London he established a public anatomy school and a museum which was free and open to the public. The work of his many students and apprentices furnished the collection of his museum, which was ultimately bought by the state. Two-thirds of the very large collection of anatomical samples of both human and animal origin were destroyed during the German bombing of London during the second world war. The surviving collection is still extensive and gives an impression of the size and diversity of the original.

Afer so much anatomy a break was in order and, in good British fashion, we ate our lunch in a London Park in the rain – all part of the experience. From there, on to the Wellcome Collection, which, at the moment hosts a special exhibition of anatomical wax models and curiosities – the “Exquisite Bodies” exhibition. Most of the models were produced between thr 17th and 20th century. Certainly the Victorians loved them….anatomy shows mixed the eductional with entertainment and displays of “freaks” juxtaposed with detailed anatomical models and models illustrating the symptoms of common ailments of the time were commonplace. it was a stark contrast from the cool scientific objectiveness of Hunter’s collection.

The last order of the day involved the sampling of many of London’s finest beers together with conversations about blogging, barcamps, novel forms of scientific communication etc. What was striking was the diversity of backgrounds (we had practising scientists, doctors, publishers, journalism students, astronomers etc..) and their enthusiasm for new forms of science communication. It makes me entirely optimistic that the future of science is bright and that many of the crusty old modes of scientific communication, assessment and measures of productivity will simply get blown away and obliterated. Sure, a lot of them are finishing their PhDs or their undergraduate studies right now, some are post-docs. It’ll take us a while to change things, but change they will – it is inevitable. Some of the people in our group won’t wait and have already started causing change now: we had the first organiser of a science barcamp in our midst and her idea is now spreading and carried by other people internationally. I take my hat off to them and wish that, as a student, I had listened less to all my advisors preaching about impact factors, publications and papers, papers, papers. There is something new and fresh afoot and young scientists without formal academic position are now able to organise themselves and form powerful networks like never before. It’s exhilarating. I am probably gushing somewhat now and maybe am not too coherent in my writing….I’ll put it down to the lateness of the hour and to the sheer excitement I feel for the first time in a long while. It’s an excitement, which can so easily get lost or crushed by current science managers and professors.

So a wonderful day. Again, thanks to Matt and all the others who had a hand in arranging it and to the great people attending.

Screencasts for scientists.

So you have just installed a new piece of software you need to go about your work. You fire the thing up for the first time. Getting that sinking feeling already? Is the software in keeping with the fine traditions of academic software which only a minimalist or non-existent user interface? Software that has been written with the “user-friendliness is for wimps” mantra and is as usable as a blended iPod? Gromacs keeping you up at night? And the only way to cope with it all, is to work through large heaps of documentation (if existent?).

Well, there may be a solution on the horizon: Bioscreencast. Screencast is a a free video-tutorial library specifically for science-related software tools. The number of tutorials is small so far (the site is in beta), but it contains all sorts of useful things from how to use BLAST and sequence alignment tools to PyMol tips and tricks and ideas for the “paperless PhD”:

Much to my delight I have also discovered a screencast on how to model physical objects in OWL:

and there are further tutorials on how to use Reference Managers, Connotea etc. Users can also request tutorials (one request is for an R tutorial (much needed I think), other users can vote for the request and someone can pick up the baton and produce a tute.

Furthermore, the site provides all the necesary functionality to capture a screencast: no software downloads etc….it’s a little bit like Seesmic. It seems like a great way to show off (new) software and tools, to demonstrate how to use them and to make a contribution to the community.

I will certainly have a think what we can contribute…and I would urge you to check out the site.

The Semantic Web of Data

Peter has already blogged that Paul Miller visited us yesterday and gave an excellent talk on evolving the Web from a Web of Documents to a semantic web of data. He does so without any jargon and using beautiful slides and his talk is a wonderful explanation of the philosophy we have taken in polymer informatics.

In short, it is stuff that everyone should know about and certainly scientists – it will change the way in which we report, analyze and distribute data and scientific information forever. Paul has kindly allowed us to video his talk and to upload it to Google. Treat yourself and watch Paul’s talk here:

Aesthetic Data

I have a confession to make: I am a sucker for bright ideas and bright people – particularly when those ideas resonate with my academic work, or when they strike a particular aesthetic cord with me. And there are a number of places on the web, where both can usually be found abundantly. One of these places is a podcast, “Entrepreneurial Thought Leaders” produced by the Stanford Department of Management Science and Engineering. Another one is the homepage of the TED (Technology, Entertainment, Design) conference and in particular their videocasts.

When browsing their website, I came across a short presentation by Jonathan Harris, who has done work, which not only resonated with our own, but is just simply beautiful. Jonathan is both a computer scientist and an artist, who is trying to understand the world and us human beings by analyzing the content and artefacts they are contributing on the web. He does this by collecting huge amounts of data, which he then visualizes in incredibly beautiful displays. One of his most impressive projects is the “We feel fine” project.

In “We feel fine” he scours the world’s blogs and extracts all those sentences from blog entries which contain the phrases “I feel” and “I am feeling”. If a sentence like this is found, it is scraped and transferred into a database. Using language processing it is then scanned to determine whether it contains a set of “pre-defined” feelings. If the blog post contains a picture, that is scraped too and associated with the sentence. Using statistics and a lot of visualization, Jonathan can draw an amazing amount of conclusions about “how the world feels” at the moment. I did a search just now, asking, how both men and women in the UK feel, when the weather is sunny between 2005 and 2007. The results speak volumes: the top 10 emotions in descending order are: ill, old, free, tired, weired, sorry, down, guilty, sad and happy.
Conceptually, there is so much in this that is analogous to the work some of my colleagues are doing here in the Centre (data gathering and analysis in Crystal Eye for example…..I am sure that if we were allowed to gather a bit more metadata than we are, we could tell so much about what’s occupying science at the moment, follow scientific progress etc…..just by looking at the molecules people are working on), and so much that we will have to learn about yet (e.g. analysis and visualization of large data sets, useful representations of data for chemistry).
But enough of me, best let Jonathan do the talking and the presentation. And I urge you to spend some time with the “We feel fine” website….it is fascinating.

Web 2.0 for Scientists

I have used the Word web 2.0 on a number of occasions. Now most scientists tend to be relatively internet-savy. Talking to people, I find, however, that most have not heard of “web 2.0” and certainly have no notion what it entails. My colleague, Dr. Andrew Walkingshaw recently gave an excellent talk to the Department of Earth Sciences here in Cambridge. We have video’ed his talk and it is up on YouTube. Alternatively watch it straight on here!

Wikis have hit IUPAC!

Just saw an announcement on the frontpage of the IUPAC website, that they have finally discovered wikis. Kermit Murray and his colleague have used them as a collaborative tool to develop standard definitions of terms relating to mass spectroscopy. You can look at the project wiki here and the link to the paper is here.

For those of you who don’t know what wikis are: the name comes from the Hawaiian word ‘wiki-wiki’, which apparently means “quick.” Wikis combine the processes of editing and viewing a website. Website content is stored in a database on a webserver and the actual webpage is generated (using PHP) on the fly as the page is requested, using content in the database. Changes are also stored in the database, which means they can be tracked and undone, if necessary.

Because of their eas of use, wikis are an interesting an efficient collaborative tools, and can be used for communal paper writing to lab-journaling and, of course, knowledge sharing (see Wikipedia itself). I know of at least one VERY VERY (hint) large chemical company that is using wikis for this purpose in house.