December 22, 2014

2014 vs. 1964: Numbers speak louder than words

It’s that time of year when people look back at over the year that was 2014 (1-5). The place where I work, celebrated it’s 50th anniversary. Colleagues put together a little booklet of facts and figures with an some accompanying web pages to mark the occasion. My personal favourite factoid compares computing in 2014 with 1964. The Atlas Computer represented the state of the art in computing in 1964, and today that crown is held by SpiNNaker – a very different kind of computer.

fifty years of computing

50 years of computing (and pipe-smoking is lesson common around computers)

Sometimes, numbers speak louder than words, so here is a numerical comparison of Atlas (1964) with SpiNNaker (2014):

Feature (see this) Atlas Computer (1964) SpiNNaker (2014)
Size A very large room 19 millimetres square
Transistors 60,000 1,100,000,000
Instructions per second 700,000 3,600,00,000

One way of looking at this data is to say, based on the the instructions per second, SpiNNaker is around ~5000 times faster than Atlas. But what is probably more interesting is that SpiNNaker (which is due for completion in 2015) is expected to be used by neuroscientists and psychologists, as a platform to study problems such as Alzheimer’s disease – something that would have been impossible (and unthinkable) only fifty years ago [6,7]. Wonder where the next 50 years will take us in 2064?


  1. Anon (2014). The most-read Nature news stories of 2014 Nature DOI: 10.1038/nature.2014.16550
  2. Morello, L., Abbott, A., Butler, D., Callaway, E., Cyranoski, D., Reardon, S., Schiermeier, Q., & Witze, A. (2014). 365 days: 2014 in science Nature, 516 (7531), 300-303 DOI: 10.1038/516300a
  3. Anon (2014). 365 days: Nature’s 10, Ten people who mattered this year. Nature, 516 (7531), 311-319 DOI: 10.1038/516311a
  4. Katherine Maher (2014) What did the world make 100 million edits of in 2014? Wikimedia blog
  5. Hand, E. (2014). Comet Breakthrough of the Year + People’s choice Science, 346 (6216), 1442-1443 DOI: 10.1126/science.346.6216.1442
  6. Furber, S., Galluppi, F., Temple, S., & Plana, L. (2014). The SpiNNaker Project Proceedings of the IEEE, 102 (5), 652-665 DOI: 10.1109/JPROC.2014.2304638

May 14, 2013

Measuring scientific coverage of @Wikipedia: Fellows of the Wiki Society index 2013

In 2013, 44% of newly elected Fellows of the Royal Society had biography pages on wikipedia.

Earlier this month confusingly-named “Royal Society” announced their new fellows for 2013. The society is made up of (quote):

“…the most eminent scientists, engineers and technologists from the UK and the Commonwealth. Fellows and Foreign Members are elected for life through a peer review process on the basis of excellence in science.”

A quick-and-dirty measure of the scientific coverage of wikipedia is the percentage of these fellows that have a profile on wikipedia at the time of their election to the prestigious Society.  Let’s call it the Fellows of the Wiki Society index (FWSi),  a good score of 100% indicates that wikipedia has excellent coverage of science while 0% indicates the opposite. Last year, that index was 40% because 21 out of 52 fellows were also Fellows of the Wiki Society.

This year the index is slightly better at 44%, with 24 out of 54 fellows having a wiki-biography, see  [1-54]. So as well as more women this year, there’s more wikipedia too, although the difference isn’t particularly big.

If you’d like to improve the content of wikipedia because there’s plenty of good reasons for doing so, why not take a look at the guidelines for biographies of living persons and create or improve a page for one of the people below?


  1. Harry Anderson
  2. Judith Armitage
  3. Keith Ball
  4. Michael Bevan
  5. Mervyn Bibb
  6. Stephen R Bloom
  7. Gilles Brassard
  8. Michael Burrows
  9. Jon Crowcroft
  10. Ara Darzi
  11. William Earnshaw
  12. Gerard F Gilmore
  13. Nigel Glover
  14. Raymond E Goldstein
  15. Melvyn Goodale
  16. Martin Green
  17. Gillian Griffiths
  18. Joanna Haigh
  19. Phillip Hawkins
  20. Edith Heard
  21. Gideon Henderson
  22. Guy Lloyd-Jones
  23. Stephen P Long
  24. Nicholas Lydon
  25. Anne Mills
  26. Paul O’Brien
  27. William Richardson
  28. Gareth Roberts
  29. Ronald Rowe
  30. John Savill
  31. Christopher Schofield
  32. Paul M Sharp
  33. Stephen Simpson
  34. Terence Speed
  35. Maria Grazia Spillantini
  36. Douglas W Stephan
  37. Brigitta Stockinger
  38. Alan Turnbull
  39. Jean-Paul Vincent
  40. Andrew Wilkie
  41. Sophie Wilson
  42. Terry Wyatt
  43. Julia Yeomans
  44. Robert Young
  45. Margaret Buckingham
  46. Zhu Chen
  47. John Hutchinson
  48. Eric Kandel
  49. Elliott Lieb
  50. Kyriacos Nicolaou
  51. Randy Schekman
  52. Eli Yablonovitch
  53. Andrew The Duke of York (eh?)
  54. Bill Bryson

September 26, 2012

Fellows of the Wiki Society? The Royal Society in London experiments with Wikipedia

wiki wiki

The wiki-wiki (quick) shuttle bus in Hawaii by xordroyd. Creative Commons licensed picture from Flickr.

Regular readers of this blog might remember that back in June of this year, I suggested that the Royal Society should employ a wikipedian in residence. After emailing, blogging and other ranting, Paul Nurse got in touch with me to say that the Society was sympathetic to the idea and would investigate. His email is reproduced below:

From: Paul.Nurse ate royalsociety.org
Subject: Re: An Open Letter to the Royal Society: Please employ a wikipedian in residence
To: hulld ate cs.man.ac.uk
cc: Aosaf.Afzal ate royalsociety.org

Dear Duncan

I floated your idea about Wikipedia in the Society and it is being looked at to see what might be possible. Thanks for your suggestion.

Best wishes.


Time passed and the English summer dripped by in it’s typically rainy fashion. Then, earlier this month, Francis Bacon (not that Francis Bacon, but this Francis Bacon) contacted me, to say the Society is organising an edit-a-thon. With help from Uta Frith, the society is going to investigate the possibilities of wikipedia using Women in Science workshop as a pilot project. See Women of Wikipedia edit planned on BBC News.

This is great news and the event was fully booked in less than a day. It’s good to see a venerable society embracing new and disruptive technology in this way.

Compare and contrast the Royal Society with the Wiki Society

It is informative (and entertaining) to compare and contrast the Royal Society with wikipedia as the two organisiastions share some aims but are very different beasts:

wikipedia.org royalsociety.org
Purpose A place where every single human being can freely share in the sum of all knowledge. To recognise, promote, and support excellence in science and to encourage the development and use of science for the benefit of humanity
Funding The Wikimedia foundation is a non-profit organisation that relies on donations to keep it going A registered charity in the UK, funding comes in the form of gifts and legacies from a range individuals and organisations
How to Join Egalitarian: any idiot one can click on the edit button to become a fellow of the wiki-society (FWS), also known as a wikipedian Elitist: Each year over 700 candidates are proposed by the existing Fellowship. From this pool, 44 Fellows, 8 Foreign Members and up to 1 Honorary Fellow are elected by a rigorous process. You have to do some pretty remarkable science or engineering to become an FRS
Age Only 11 years old in 2012, not even a troublesome teenager (yet). Has wisdom beyond its years. Over 350 years old, some of it’s members invented the modern world and continue to shape it today
Location Virtually the wiki-society is anywhere there is an internet connection. Physically, the head quarters are in San Francisco Based just off The Mall in London, many members cluster in the supposed Golden Triangle of London, Oxford and Cambridge. Other fellows are scattered around the provinces with expats and Foreign Members dispersed around the globe.
Who’s a member 35 million editors, not all of whom are active. About 1500 living fellows including Jocelyn Bell Burnell, Richard Dawkins, Stephen Hawking, Harry Kroto, Tim Berners-Lee, Paul Nurse, David Attenborough and over 80 Nobel prize winners. Thousands more deceased members including Isaac Newton, Charles Darwin, Robert Boyle etc
Profile Ordinary: Most wikipedians are ordinary and reasonable people, but internet trolls, spammers, snake oil sellers, lunatics, bigots, pedants, global village idiots, OCD sufferers other interesting characters are quite common on wikipedia Extraordinary: Most Fellows are extraordinary but reasonable people, some may also be Mad Scientists [citation needed]
Praised for Many things, see praise for the wikipedia and wikimedia projects. Funding excellent scientists and their Science. Engaging the public and young people in science through various events.
Criticised for The worlds biggest database of half-truths and white lies, see criticism of Wikipedia. Patrolled by annoying or partial editors and administrators. It can be frustratingly difficult to verify sources and wikipedia often lacks scientific credibility [1]. Being a nepotistic old boy network with an absence of women and very little in the way of youth. Ouch. Too many members have or currently work in, Oxbridge and London, possible geographic bias.
Origin The name wikipedia comes from the Hawai’in word for quick Wiki, see picture top right. The Royal Society is named after the British Monarchy, set up with help from Charles I. The name is a bit of a misnomer as you don’t need to be a royalist to join – republicans are welcome. In Middle English, the word Royal means s-l-o-w, traditional and painfully conservative [citation needed].

So there you have it, the Wiki Society and the Royal Society are unlike each other in many ways but they share a common goal of spreading knowledge. Perhaps the scientific content of wikipedia will be greatly improved through edit-a-thons and other events like this. Hopefully, the days where wikipedia will tell you everything you ever wanted to know about David Beckham but (at the time of writing) has absolutely nothing to say about leading scientists like John Aggleton, Garret FitzGerald and Margaret Robinson are numbered.

Thanks to Paul Nurse, Francis Bacon, Aosaf Afzal and Uta Frith for making it happen. If you can’t attend the edit-a-thon, watch this wiki-space via the twitter hashtag #WomenSciWP: interesting wiki-things might wiki-happen.


  1. Wodak, S.J., Mietchen, D., Collings, A.M., Russell, R.B. & Bourne, P.E. (2012). Topic Pages: PLoS Computational Biology Meets Wikipedia, PLoS Computational Biology, 8 (3) DOI: 10.1371/journal.pcbi.1002446

June 1, 2012

An Open Letter to the Royal Society: Please employ a wikipedian in residence

Dear Professor Nurse

Fellows of the Wiki Society?

To improve public engagement with Science and Scientists, the Royal Society should employ a wikipedian in residence. Here’s why:

The Royal Society is a National Academy of Science which represents some of the world’s leading scientists. The stated aim of the society is to:

“recognise, promote, and support excellence in science and to encourage the development and use of science for the benefit of humanity.”

Despite the elitist nature of many scientific societies, a significant part of what the Royal Society does is engage with members of the general public of all ages through a wide range of events. The annual Summer Science exhibition, Royal Society Blogs, Policy Centre and Royal Society television channel are just a few examples from amongst many more.

Many Fellows are of interest to the general public and already have extensive biographies in wikipedia which are up to date, well-written, well-referenced and conform to the wikipedia guidelines for the biographies of living persons. Wikipedia biographies often appear top of the list of google search result for a scientists name, for example see:

However, many other scientists do not have pages about them on wikipedia. Unfortunately, alternative sources of information such as academic homepages are often out of date and not particularly engaging. Most scientists are too busy doing Science to spend time updating their home pages, as neatly illustrated by cartoonist Jorge Cham. At the time of writing, less than half of the notable and distinguished Fellows elected in 2012 have biographies on wikipedia, see below of details.

Putting scientific information into wikipedia isn’t as crazy as it sounds. Alex Bateman at the Wellcome Trust Sanger Institute [1], PLoS Computational Biology [2] and many others [3] have already made considerable progress in improving the scientific content of wikipedia. This information is immediately accessible to a huge global audience.

Wikipedia is arguably one of the greatest ever opportunities for public engagement in Science. By employing a wikipedian in residence, the Royal Society could improve and influence the scientific content of wikipedia, while engaging even more with the general public around the world, who are often just as interested in the scientists as the science itself. As the current president of the society I hope you will consider this proposal.

Yours Sincerely

Dr. Duncan Hull
University of Manchester, UK

(this letter has also been sent by email)


  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. Wodak, S., Mietchen, D., Collings, A., Russell, R., & Bourne, P. (2012). Topic Pages: PLoS Computational Biology Meets Wikipedia PLoS Computational Biology, 8 (3) DOI: 10.1371/journal.pcbi.1002446
  3. Xiao, L., & Askin, N. (2012). Wikipedia for Academic Publishing: Advantages and Challenges. Online Information Review, 36(3), 2. Emerald Group Publishing Limited

Appendix: Fellows of the Wiki Society

As of June 2012, only 21 out of the 52 of the Royal Society Fellows elected in 2012 have a biographical page on wikipedia. Where biographies currently exist, they are linked to below

Of course, 2012 is just the tip of the iceberg, there are also the Fellows elected in 20112010 and so on back 350 years to 1660.

May 3, 2012

Need to re-invent the Web (badly)? There’s an App for that!

The Mobile App Trap

The App Trap: Why have just one Web App when you can have hundreds of mobile Apps? A selection of popular Android apps from Google Play, also available for iPad and iPhone from the Apple App Store

I love the convenience of mobile applications but hate the way they re-invent the wheel and are killing the Web. What can be done about it?

I’m in love with the mobile Web

I’ve been smitten with the Web since first venturing out on the information superhighway back in the nineties. This love affair is taken to a new level with the advent of the mobile Web. As an incurable information junkie, having access to news is on the move is great. Using location based services like Google Maps is fantastic, on foot, bike or in the car. I love nerdily scanning barcodes to read Amazon book reviews while browsing the shelves in bookshops, much to Tim Waterstone’s annoyance. And it can be great to have wikipedia in your pocket to settle arguments down the pub.

I hate the mobile Web too

But there’s a big problem with all this appy clappy mobile fun, it’s killing the Web through fragmentation, both for producers and consumers of information. Let me explain.

One of the great things about the Web is that you there is one app to rule them all; a “killer app” called a Web browser. There are several flavours, but they all basically do the same thing using similar technology: they let you surf the Web. One software application (a browser), gives you access to an almost infinite number of Web applications. Wonderfully simple, wonderfully powerful – we’ve got so used to it we sometimes take it for granted.

Now compare this to the mobile Web where each page you visit on a mobile suggests that you download an app to read it. Where there used to be just one application, now there are thousands of glorified “me too” Web browsers apps many of which have re-invented the Web, badly.

Consider the applications in the table below and illustrated on the right. They are all accessible from a Web browser on one of the “four screens ”:  desktop, mobile, tablet and smart-TV:

Native mobile app Purpose Web app
Amazon mobile Online retailer Amazon.com
BBC News mobile News and propaganda news.bbc.co.uk
The Economist mobile More news and propaganda economist.com
eBay mobile online garage sale ebay.com
Flickr mobile photo sharing flickr.com
Guardian mobile Even more news and propaganda guardian.co.uk
Google Reader mobile Feed reader reader.google.com
Google Maps mobile Maps and navigation maps.google.com
MetOffice mobile UK Weather metoffice.gov.uk
PostOffice mobile Postcode / Address finder royalmail.com/postcode-finder
Google Search mobile Search engine google.com
Google Translate mobile Language translator translate.google.com
Twitter mobile Entertaining time-wasting application twitter.com
Wikipedia mobile Encyclopædia en.wikipedia.org/wiki
WordPress mobile Blogging tool wordpress.com
YouTube mobile Videos youtube.com

As you can see, users are encouraged to download, install, understand and maintain sixteen different apps to enjoy this small part of the mobile Web. And this is just the tip of the iceberg, there’s bucket-loads more apps like this in Google Play and the App Store. As a user, you could just use a mobile Web browser on your phone, but you’ll be discouraged from doing so. We’ll return to this later.

Producers and consumers both suffer

As well as being a pain for users who have to manage hundreds of apps on their phones and tablets, the pain is magnified for producers of data too. Instead of designing, building and maintaining one Web application to work across a range of different screens (a challenging but not impossible task), many have chosen to develop lots of different apps. Take twitter for example, in addition to the desktop and Web apps, twitter currently makes no fewer than five different applications just for tablets and phones:

    1. twitter.com/download/ipad (for iPad)
    2. twitter.com/download/blackberry (for Blackberry)
    3. twitter.com/download/wp7 (for Windows phones)
    4. twitter.com/download/android (for Android)
    5. twitter.com/download/iphone (for iPhones)

So a challenging task of delivering content onto a range of different devices has now been transformed into an almost impossible task of building and managing many different apps. It’s not just Twitter, Inc. that chooses to play this game. Potentially any company or organisation putting data on the mobile Web might consider doing this by employing an army of android, blackberry, iPhone and windows developers on top of the existing Web developers already on the payroll. That’s good news for software engineers, but bad news for the organisations that have to pay them. Managing all this complexity isn’t cheap.

Not Appy: How do we get out of this mess?

In the rush to get mobile, many seem to have forgotten why the Web is so successful and turned their back on it. We’ve re-invented the wheel and the Web browser. I’m not the first [1] and certainly not the last [2] to notice this. Jonathan Zittrain even predicted it would happen [3,4] with what he calls “tethered devices”. One solution to this problem, as suggested at last months International World Wide Web conference in Lyon by some bloke called Tim, is to develop mobile Web apps rather than native mobile apps:

There are lots of examples of this. Sites like trains.im provide train times via a simple Web-based interface, no app required. Many Web sites have  two versions, a desktop one and a mobile one. Wikipedia has a mobile site at en.m.wikipedia.org/wiki, Flickr at m.flickr.com, The Economist at m.economist.com, BBC at m.bbc.co.uk/news and so on. But in many cases these sites are poor cousins of the native mobile apps that software developers have focused their efforts on, diluting their work across multiple apps and platforms.

Maybe it’s too late, maybe I’m suffering from the suspicious of change” syndrome described by Douglas Adams like this:

  1. everything that’s already in the world when you’re born is just normal;
  2. anything that gets invented between then and before you turn thirty is incredibly exciting and creative and with any luck you can make a career out of it;
  3. anything that gets invented after you’re thirty is against the natural order of things and the beginning of the end of civilisation as we know it until it’s been around for about ten years when it gradually turns out to be alright really.

The mobile Web makes me suspicous because many apps re-invent the wheel. I’ve argued here that it is against the natural order of the Web, we’ve waved goodbye to the good old Web [5] and its the beginning of the end. I really hope not, it would be a tragedy to carry on killing the Web as it’s given us so much and was designed specifically to solve the problems described above. Let’s hope native mobile apps gradually turn out to be alright really.


  1. Gary Marshall (2011). Could smartphone apps be taking us back to the days of “best viewed with … ”? Net Magazine
  2. Jason Pontin (2012). Why Publishers Don’t Like Apps: The future of media on mobile devices isn’t with Apps but with the Web Technology Review
  3. Jonathan Zittrain (2007). Saving the internet. Harvard Business Review, 85 (6) PMID: 17580647
  4. Jonathan Zittrain (2009). The Future of the Internet: And How to Stop It Penguin, ISBN:014103159X
  5. Hamish MacKenzie (2012) Web 2.0 Is Over, All Hail the Age of Mobile, Pandodaily

August 15, 2011

Wikipedia: I Fought the Lore and the Lore Won

"The age of nations is past. It remains for us now, if we do not wish to perish, to set aside the ancient prejudices and build wikipedia..."Fighting the lore of wikipedia is an increasingly futile battle but there are people who resist using and improving the online encyclopedia. The remarkable thing is that some of this resistance comes from the scientific and academic communities, two groups of people who are supposedly concerned with the dissemination of knowledge.

Wikipedia is the lore

With around 300 million visitors each month, wikipedia is firmly in the top ten of most trafficked websites in the world. But you don’t get 300 million visits without attracting some critics, many of whom object to wikipedia’s inaccuracies and the anonymity of some its contributors. What many critics object to is that wikipedia is the lore. That is not the law, but the lore, as in folklore. Like folklore, wikipedian knowledge often comes handed down by word of mouth, copy-and-paste and other questionable practices. The trouble with lore is, it can sometimes be unreliable, based on hearsay, gossip and urban myths rather than hard facts and knowledge favoured by scientists and academics. To some people, wikipedia is a lore which should be fought in every way possible.

Fighting the lore of wikipedia

Professor Neil Waters is one of many examples of an academic who has fought the lore of wikipedia. Water’s students were infamously told that they can’t cite wikipedia in their work [1]. They are still free to use it, but are forbidden to cite it, because of the lack of academic rigour. Wikipedia, the argument goes,  is a “tertiary source” rather than a primary one and therefore not suitable for serious research.

But people like Patricia Dooley have pointed out that academics fighting the use of wikipedia is hypocritical. In a small study published [2], she found that some university faculty members (the “two-faced professoriate” [2]) depend on Wikipedia in their teaching and published research despite the fact that they often discourage their students from using it. Are critics of wikipedia in the academy hypocrites fighting a losing battle?

Has the lore of wikipedia won?

As with many keywords, if you Google just about any scientific term, wikipedia will be in the first page of results. Here are some examples, taken from by Darren Logan’s why wikipedia is important in science:

At the time of writing, 90% of the search terms above have a wikipedia page as their very first Google hit. So, when it comes to accessibility and visibility, the lore of wikipedia is winning.

Improving the lore of wikipedia: Don’t fight it, edit it

So wikipedia is winning but many articles with scientific content are incomplete, inaccurate or just plain wrong. What should scientists do about it?  Rather than discouraging students to use it, wouldn’t it be better if academics and scientists encouraged their students to correct it? Fusing the lore of wikipedia with the law of science in this way is perhaps, the “greatest ever opportunity for public engagement”.  Ornithologist Alexander Bond is the latest in a long line of scientists arguing exactly this case [3]. Where wikipedia is wrong, he suggests that scientists have a duty to make sure that it is accurate and up to date:

“Regardless of the academy’s views on Wikipedia, it will remain a resource used by students, researchers and the public for the near future. Academics should appropriate Wikipedia as a teaching and outreach tool, resulting in higher quality information, more engaged students and a better-informed public.”

So if you’re a scientist or any other kind of academic, there is plenty of help and advice on hand [4] and many different wiki-projects to get involved in. Don’t fight the lore, edit it.


  1. Neil L. Waters (2007). Why you can’t cite Wikipedia in my class Communications of the ACM, 9, 15-17 DOI: 10.1145/1284621.1284635
  2. Patricia L. Dooley (2010). Wikipedia and the two-faced professoriate WikiSym ’10 Proceedings of the 6th International Symposium on Wikis and Open Collaboration DOI: 10.1145/1832772.1832803
  3. Alexander L. Bond (2011). Why ornithologists should embrace and contribute to Wikipedia Ibis, 153 (3), 640-641 DOI: 10.1111/j.1474-919X.2011.01135.x
  4. Darren Logan, Massimo Sandal, Paul Gardner, Magnus Manske, & Alex Bateman (2010). Ten simple rules for editing Wikipedia. PLoS computational biology, 6 (9) PMID: 20941386
  5. Sonny Curtis et al (1959) I Fought The Law (and the Law Won) as covered by The Clash:

[Acknowledgement: thanks to wikipedian Paul Gardner for posting the Bond paper on the journal picks. Image above via wikipedia.]

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

November 7, 2006

People 2.0: Pioneers of the next generation Web

UK news-rag The Grauniad has a series of interviews with some of the people behind the next generation web, so-called Web 2.0. After reading these interviews, I can’t help wondering, who are the equivalent pioneers in bioinformatics?

The interviews include…

  1. Wikipedian Jimmy Wales
  2. WordPresser Matt Mullenweg
  3. Technorati’s Dave Sifry

…and several others too. Most of the interviews are worth reading, I particularly enjoyed Mullenweg’s which contains a wonderful quote:

Q: What is your big idea?

A: I don’t have big ideas. I sometimes have small ideas, which seem to work out.

So who is currently pioneering the “Web of Science”, Bioinformatics 2.0 if you like? Ensemblian Ewan Birney? Ian Holmes at Berkeley? Or somebody else?

[Image credit: Picture from Steve Jurvetson, this post originally published on nodalpoint with comments]

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