August 24, 2009

I bet you think this blog is about you, don’t you?

Science Online London 2009Last Saturday, The Royal Institution of Great Britain (R.I.) hosted a conference called Science Online London (#solo09) co-organised by mendeley.com and network.nature.com. The event centred around the fantastic Faraday Theatre which according to the R.I. is a “beautiful, historic theatre [which] has deeply raked seating that creates an intimate atmosphere, even when full to capacity”. Absolutely. Just like last year, this event attracted delegates and speakers from a wide range of backgrounds in science, publishing and communication from around the world. This post is an approximately alphabetically ordered link-fest of some of the people involved. People are, after all, the most interesting thing about any conference. If you’re not listed here it’s not because I don’t like you (honest!) it’s because we didn’t speak or I didn’t listen or (unlike many people) you’re not vain enough [1] to have a have a blog (yet) :-)

Now I’m told the presentations mentioned above will be on Nature Precedings in due course, which will be good. Thanks to all the organisers, speakers and participants this year that made Science Online London 2009 well worth attending. Hopefully see some more of you again next year!


  1. Carly Simon (1972) You’re So Vain
  2. Geoffrey Bilder (2006). In Google We Trust? Journal of Electronic Publishing, 9 (1) DOI: 10.3998/3336451.0009.101
  3. Matt Brown (2008). Venerable institute gets a refit Nature, 453 (7195), 568-569 DOI: 10.1038/453568a
  4. Matt Brown (2008). Reimagining the Royal Institution Nature, 453 (7195), 595-595 DOI: 10.1038/453595a
  5. Duncan Hull (2009). Slides from the author identity session: Authenticating Scientists with OpenID
  6. Jennifer Rohn and Richard P. Grant (2009). Pre-conference video: Live Roof Surfing at Mendeley Fringe Frivolous

July 13, 2009

Science Foo Camp 2009: Scifoo Day Two

Theodore Gray (of Wolfram Research) with super-soluble sodium acetateThe fourth International Science Foo Camp (scifoo) 2009 has just concluded. Here are some very brief and incomplete notes and links from some of the sessions on the second day (Saturday), see the scholarly kitchen for a report on the first day. With seven parallel sessions, most people at this event miss most (six sevenths) of the sessions, but here is a summary of the (one seventh) sessions I managed to get to:

  • Larry Page ran a session on Making Artificial Intelligence happen. In brief, Larry argued that not enough people are working on this problem. Marvin Minsky joined in talked about his book The Emotion Machine. I’d write more about this, but Larry asked for what he said to be off-the-record so he could speak more freely.
  • Following on from this Harry Collins and Lee Smolin ran a session titled: The Social Nature of Knowledge, Science and Artificial Intelligence. As David Colquhoun pointed out in the session, you “need to be something of a sado-masochist” to attend a session on the sociology of Science but there was some interesting discussion on the Science (truth?) vs. Belief (religion) debate. Henry Thomspson pointed out: some argue that “Knowledge is true belief” which can make it hard to distinguish between Science and Religion. Jamie Heywood described his simple “truth formula” where truth = cost to make a claim divided by the cost to disprove claim.
  • Next up Douglas Kell did a session on Data-driven Science. This discussed the relationship and balance between hypothesis driven science (hypothetico-deductive) and data driven science (via inductive reasoning and machine learning for example) [1]. Attendees in this session included Tony Tyson (Director of the Large Synoptic Survey Telescope), Craig Rowell (BioRad), George Poste, Julia Lane (NSF), James Wilsdon (Royal Society), David Colquhoun, Nat Torkington, the six-minute-genome guy from Halcyon Molecular whose name I can’t remember and Annalee Newitz. Much of the discussion was about the over-reliance on hypothesis driven science (e.g. 92% of NIH R01 grants have to be hypothesis-driven) which can make the “fishing-trip” or “data-driven” science difficult to do. One conclusion from this presentation was that both types of science are required and complementary.

Then it’s time for lunch, not just any old food, but some yummy Google Food.

  • In the afternoon, I ran a session on The Invisible Scientist: Personal Digital Identity on the Web, Problems and Solutions. After a short set of introductory slides we discussed some solutions to identifying scientists digital contributions, not just electronic journal publications but wiki edits, blog posts, software development, ontology and database curation etc. Participants in this session included Cameron Neylon, Julie Lant (NSF) who will reuse some of my data in a report she is writing (Yay!), Nicola McCarthy (Senior editor of Nature Reviews Cancer), Shirley Wu, Michael Rogan, Mackenzie Cowell and Chris Holmes. The last time I was at Science Foo Camp (back in 2007) I felt slightly phased by the stellar company (nobel prize winners, billionaires, entrepreneurs, silicon valley A-listers, venture capitalists, artists, policy makers, movers and shakers) that I didn’t present anything. I’m very glad I made the effort this year, it forced me to think harder about the problem of digital identity (and solutions), which included a useful chat with Googler Ben Laurie (a cryptography person) who gave me the lowdown on OpenID, PKI and the like. Very useful stuff – thanks Ben and thanks to everyone who turned up at my session.
  • The second session of the afternoon was on Google Wave with Cameron Neylon. I won’t say too much about this, because it will probably be blogged by Cameron and others – but it was an interesting peek into some of the current strengths and weakness of this software – especially from the point of view of scientists.
  • The last two sessions of the day, I stayed in the Lightning Talks organised by Nat Torkington (see blog). These were great, probably my favourite part of scifoo this year. Each speaker got a very strict five minutes, including Natahan Wolfe, Ben Fry on visualisation, George Dyson on Darwin, Christopher Stumm on astronomical metadata, Adam Summers on fish, Linda Stone on unhealthy computing, Ed Lu, Brian Uzzi and Fiorenzo, Shelley Batts, Larry Weiss, Saul Griffith, Chris DiBona on telemedicine, Joshua Bloch on Java puzzlers, Christian Bok on poetry and Gregory Benford.

In the evening there were further demonstrations and talks, including sodium acetate crystals (ChEBI:32594) (with Theodore Gray – see picture above) and a talk by Bob Metcalfe (of Metcalfe law fame) on the “Enernet: Internet Lessons for Solving Energy”. One of the take home messages from this is that the energy industry should be much more decentralised (like the internet is). Bob argued that the huge centralised powerplants we have today are beginning to look as dated and obsolete as mainframe computers.

So in summary, saturday at scifoo was a fantastic action-packed day, started early in the morning and went on late into the night. It’s almost impossible to capture it all in a blog post, so if you’re interested my scifoo 2009 photo set on flickr has more details. My mind has been blown into lots of little pieces again – thanks to all the organisers and participants for another great day.


  1. Kell, D., & Oliver, S. (2004). Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era BioEssays, 26 (1), 99-105 DOI: 10.1002/bies.10385

June 17, 2009

Nettab 2009 Day Two: Wikis ‘n’ Workflows

Alex Bateman on the RNA WikiprojectThis is a  brief report and some links from the second day of Network Applications and Tools in Biology (NETTAB 2009) in Catania, Sicily. There were two keynotes on the RNA WikiProject [1] by Alex Bateman and myExperiment [2] (by me) as as well as presentations by (I think but I wasn’t concentrating enough) Dietlind Gerloff, Guiliano Armano, Frédéric Cadier and Leandro Ciuffo.

Alex Bateman (wikipedia user:Alexbateman) did an entertaining talk on the RNA wikiproject: Community annotation of RNA families where they have taken data from the Rfam database [3], and put it all into regular wikipedia. This project got quite a lot of media attention back in February. In this case, the primary advantages of “letting go of data” by giving it to wikipedia are that it is read by everyone who uses Google (where pages are frequently the top search result) and wikipedia gets lots more traffic than biological databases like rfam.sanger.ac.uk do. Thanks to wikirank which tells you what is popular on wikipedia, it is also possible to quickly compare the popularity of pages, see RNA vs. Ribosomal RNA vs Micro RNA vs SnoRNA for an example. The Rfam project have some interesting stats on who makes the most edits to the Rfam pages, it isn’t always the scientists who make important contributions, but anonymous users and machines (e.g. like Rfambot, Smackbot and Citation bot) who are often doing most of the hard work. There is a very long tail of contributors who make small contributions – which supports the 90% of users in on-line communities are lurkers who never contribute rule and is reminiscent of Citizen Science and Muggles. I wanted to put the slides from this talk on slideshare, but they contain some unpublished data. You can, however, subscribe to the feed of the Rfam and Pfam blog at xfam.wordpress.com, if you’d like to keep up to date on developments in this area.

After the keynote there were presentations by Dietlind Gerloff on Open Knowledge (a new agent-based infrastructure for bioinformatics experimentation – nice pictorial intro using lego here) and Guiliano Armano? on ProDaMa-C – a collaborative web application to generate specialised protein structure datasets.

The next keynote was on myexperiment.org, “Where Experimental Work Flows” – my slides on Who are you, Managing collaborative digital identities in bioinformatics with myexperiment are embedded below.

I followed this presentation with a live 30 minute demonstration and discussion of myexperiment. The most interesting question people asked was Why use OpenID instead of full blown Public Key Infrastructure? (answer: OpenID is currently a lot easier and provides good-enough security). The rest of the day is a bit of a blur, I’m with Tim Bray in enjoying the monster adrenaline high of public speaking, but with all that ChEBI:28918 coursing through my veins it can be difficult to think straight (immediately before, during or after a talk)… so you’ll have to take a look at the proceedings for the full details of what happened in the afternoon – but they included Make Histri (great name!), SBMM: Systems Biology Metabolic Modeling Assistant [4] by Ismael Navas-Delgado and Biomedical Applications of the EELA-2 project.

By the evening time, there was some Opera dei Pupi (traditional sicilian puppet theatre), a trip to Acireale and a delicious italian feast in a ristorante (the name of which I can’t remember) to round off an enjoyable day.


  1. Daub, J., Gardner, P., Tate, J., Ramskold, D., Manske, M., Scott, W., Weinberg, Z., Griffiths-Jones, S., & Bateman, A. (2008). The RNA WikiProject: Community annotation of RNA families RNA, 14 (12), 2462-2464 DOI: 10.1261/rna.1200508
  2. De Roure, D., & Goble, C. (2009). Software Design for Empowering Scientists IEEE Software, 26 (1), 88-95 DOI: 10.1109/MS.2009.22
  3. Gardner, P., Daub, J., Tate, J., Nawrocki, E., Kolbe, D., Lindgreen, S., Wilkinson, A., Finn, R., Griffiths-Jones, S., Eddy, S., & Bateman, A. (2009). Rfam: updates to the RNA families database Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn766
  4. Reyes-Palomares, A., Montanez, R., Real-Chicharro, A., Chniber, O., Kerzazi, A., Navas-Delgado, I., Medina, M., Aldana-Montes, J., & Sanchez-Jimenez, F. (2009). Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling Bioinformatics, 25 (6), 834-835 DOI: 10.1093/bioinformatics/btp061

June 2, 2009

Who Are You? Digital Identity in Science

The Who by The WhoThe organisers of the Science Online London 2009 conference are asking people to propose their own session ideas (see some examples here), so here is a proposal:

Title: Who Are You? Digital Identity in Science

Many important decisions in Science are based on identifying scientists and their contributions. From selecting reviewers for grants and publications, to attributing published data and deciding who is funded, hired or promoted, digital identity is at the heart of Science on the Web.

Despite the importance of digital identity, identifying scientists online is an unsolved problem [1]. Consequently, a significant amount of scientific and scholarly work is not easily cited or credited, especially digital contributions: from blogs and wikis, to source code, databases and traditional peer-reviewed publications on the Web. This (proposed) session will look at current mechanisms for identifying scientists digitally including contributor-id (CrossRef), researcher-id (Thomson), Scopus Author ID (Elsevier), OpenID, Google Scholar [2], Single Sign On, PubMed, Google Scholar [2], FOAF+SSL, LinkedIn, Shared Identifiers (URIs) and the rest. We will introduce and discuss each via a SWOT analysis (Strengths, Weaknesses, Opportunities and Threats). Is digital identity even possible and ethical? Beside the obvious benefits of persistent, reliable and unique identifiers, what are the privacy and security issues with personal digital identity?

If this is a successful proposal, I’ll need some help. Any offers? If you are interested in joining in the fun, more details are at scienceonlinelondon.org


  1. Bourne, P., & Fink, J. (2008). I Am Not a Scientist, I Am a Number PLoS Computational Biology, 4 (12) DOI: 10.1371/journal.pcbi.1000247
  2. Various Publications about unique author identifiers bookmarked in citeulike
  3. Yours Truly (2009) Google thinks I’m Maurice Wilkins
  4. The Who (1978) Who Are You? Who, who, who, who? (Thanks to Jan Aerts for the reference!)

March 16, 2009

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