Merry Christmas Everyone

German painting, 1457
Image via Wikipedia

Another year is coming to a close and it has been nothing short of eventful. There has been the end of one direction of research, the beginning of my existence as a service provider at the EBI and several new strands of research. Not to speak of moving house and a number of other things.

I have learned a lot about people this year and sometimes more than I wanted to. In particular, I have learned that “trust” is the only way that allows anyone to manage anything – both in business and academia. Destroying trust between people or people and organisations, causes untold harm in the medium and long term, no matter how expedient it seems at the time.

However, it is christmas now and the world rests for a few days. Time to reflect on 2009 and to look forward to the new year with all its possibilities and challenges.

A very merry christmas and a happy new year to you all, thank you for reading the blog and see you in 2010!

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Notes from Science Online – What is a Scientific Paper?

Session to discuss how technology, blogging, the internet etc. has changed the nature of scientific communication.

The Panel was kicked off by an illustration of science communication through the ages

Katherine Barnes (Launch Editor, Nature Protocols)

  • Papers: Traditional peer reviews and edited Nature Protocols
  • Not papers: Network protocols uploaded by the community
  • Movies – visualised experiments – should be part of experimental descriptions
  • Nature Preceedings: preprint server
  • Nature Chemistry: 3D models, downloadable ChemDraw files etc.
  • Which improvements does the community desire? Data downloading, layour wenhancements etc.
  • The Bottom Line: basic unit of a publshed paper is peer reviewed and edited – BUT keen to enhance the basic unit with movies, data etc.

Theodora Bloom (PLoS Biology)

  • Does paper work in the online age? – NO. How can we radically overhaul the paper?
  • Unique author identifiers
  • Methods ought to be date-stamped per experiment in a central database
  • For large datasets: need to link paper to a snapshot of a large database containing the data
  • Showing examples of multimedia sources illustrating author claims in papers e.g. a claim that two protein structures are similar is linked to a movie showing an overlay of the two structures
  • References: real-time citation analysis

Enrico Balli – Media Lab Sissa…

  • Publishes Journal of High Energy Physics, Proceedings of Science
  • Sissa publishes papers, preceedings, posters – how do you peer review posters, presentations, software manuals for scientific software and educational material?
  • Bottom Line: many types of scientific content that needs to be scited and linked to – but we have no means for publishing or citing it.
  • Do we need to think about a “Journal of Stuff?”

General Discussion:

How do you pay for the increased cost for the creation of this enhanced multimedia content.

  • Funders should..
  • Authors should supply data – it’s easy right?
  • Editors should provide editing capability for multimedia
  • Preservation of digital artefacts is a huge problem…

Audiance DIsagreement

Providing data is incredibly hard – at least providing it in such a form that others can understand it…general agreement from the audience: data publication is extremely expensive if the data is to be reusable..…

Biology has bifurcation of publishing: papers on the one hand and real knowledge in the form of do we reconcile the two?

Audience: There has been no innovation in the scientific paper….Research Assesment Exercise is distorting: computer scientists publishing in biology journals get evaluated in computern science units…which leads to low evaluations….but high ones if evaluated in Biology units

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Notes From Science Online – Cat Herding

Image representing ResearchGate as depicted in...
Image via CrunchBase

The challenges and rewards of managing online communities

Arikia Millikan – Science Blogs

Arikia’s Hierarchy of Blogger Needs: Tier 1: CMS and Tech support, Tier 2: Acknowledgement, Accessibility and Analytics, Tier 3; individuatlity and Tier 4 Community

All tiers need to be there otherwise communities can fall apart,…but even if they do use the internet principle of rapid iteration: learn from mistakes and rebuild.

Corie-Lok – Nature Network

Nature Network started as Network for scientists covering lot of stuff….life in the community, protocols etc…

To be a successful cat herder you need to be there…communities do not build themselves…important to have a community of several interested parties to drive this

some funding agencies are starting networks

Ilja d Madisch – ResearchGate

offerings on an individual user lever (groups, rapid response, q&A, journal finder) and institutional offerings (community tools, communication platforms for institutional communities)

much community building so far – but challenge; catering for the diversity of scintists….solution: open platform, make api available and crowdsource app development. 140000 members now but only 30% activity measured as users logging in at least once a month.

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Notes from Science Online – Real time statistics and new impact metrics in science

Virginia Barbour – PLoS

How can we assess the impact of any piece of research?

  • Usage
  • Media Coverage
  • Blog Coverage
  • Discussion Thread Activity
  • Social Bookmarking Activity
  • Expert Ratings
  • Effect on Public Policy
  • Where the Research was done
  • Who is citing it
  • Who is reading it

In general: articles have broken free of journals and can be assessed on their own merits. Some examples of paper statistics in New England Journal of Medicine and one other.

PLOs Steps for new article metrics: phase 1: acquire raw data which is open and non-proprietary…and can be independently verified

Phase Two…linkking,,.showing a PLoS paper with links to blog entries and papers citing this article. Also attaching Article usage in terms of viewing statistics – in the future add in more data sources.

Richard Grant – F1000

Showing real-time solo09 twitter feed.

We all want to make an impact – how do we do this? Who cares about impact?

  • Science Publishers
  • People who want to know where to read research
  • Funding agencies

What can and can’t metrics do?

For this meeting, for example, twitter is an immediate real time metric. Later then blogging and re-blogging. But no quality metric. In science we use the impact factor…it’s slow and takes time before it reflects any real interest. Can be gamed and does not tell you how good research is.

Now plugging f1000 –

Victor Henning – Mendeley

Usage metrics for individual researchers – analogy to LastFM. Why not build a similar system to Last FM for science.

1. Build a system to measure article pervasiveness…how many people have the article in their library

2. Track article reading time in PDF viewers as a measure of interest

3. Track user tags and ratings

BUT preserve privacy – scientists may not wish to have information about their paper reading and interest behaviour displayed.

Now the system is Mendeley…cross platform…aggregates reading material, tag it, read it….etc….Ultimate goal is to aggregate these statistics for analysis….data segmantation with increasing pervasiveness..what are profs reading vs undergraduates, usage by geography etc…

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Science In the Open 2009 London – Blogging for Impact

Several of the attendees in this panel are participating via Second Life

What can blogging do for science in the media (Mark Henderson, Science Editor of the Times).

Blogging allows to communicate with a different voice and different material.

Can use blogs as background research for journalistic research – blogging as a substitute for going to the primary literature? Science bloggers can use blogging as a way to promote their work to journalists and the general public….journalists are watching science blogs…..

Dave Mearkus speaking now via Second Life

  • Blogging allows to tell a longer story than in a lecture or a paper
  • Blogging allows control over message and online personality
  • Case Study: Cognitive Daily (Husband Wife Blog)
  • Different motives: becoming rich and famous vs telling the world about science… – small success has come to both…one is writing a regular column now, the other has had a lot of institutional support from university
  • Talking about – it’s an aggregator and a filter of scientitic blog posts…also some form of overlay journal – editors pick which blog posts they consider the best in a week and aggregate them on a separate page.
  • Even casual bloggers can make a differenct through aggregation services…

Daniel MacArthur (Genetic Future) is now responding (works at Sanger Institute):

The challenges of academc blogging are:

  • Time spent blogging – time spent not experimenting, coding, writing papers
  • Easier to blog if blog is close to area of research expertise
  • Microblogging – second channel for providing information but it is quick…dangers: information stream becomes more superficial…
  • Criticism has consequences: controversy sells, BUT inaccurate criticism can damage careers….need to balance intreresting and open reviews with career protection
  • Uneasy interaction with the commercial world: litigation risks, consultancy and product offers…insight vs. staying objective.
  • Sustaining multiple identities… divergence of online persona from professional identity
  • Talking openly about science vs. reporting on science

Floor open for discussion now…

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)

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.

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Just a quick note from the International Conference on Biomedical Ontology

I am normally pretty noisy these days when it comes to blogging or tweeting conferences….but haven’t produced anything for ICBO so far. This has mainly to do with the fact that I am far too busy learning, thinking and absorbing people’s ideas and yet again realising just how far ahead biology/biomedicine is in thinking how to deal with data properly. In any case, all I wanted to say was that ICBO has its own friendfeed group where Robert Hoehndorf and others are doing a sterling job documenting the conference and discussing what is said during the tutorial sessions that are currently going on. The friendfeed page is here:

So do read along if you want to follow what is going on from afar!