O'Really?

August 17, 2012

What is the collective noun for a group of Systems Biologists?

From helix to hairball

According to Arthur Lander, “hairball” networks like the one of human proteins above, are the new icon of biology, taking over from the famous double-helix. Image originally published in BMC Biology [1].

What happened was, I was looking for a creatively commons licensed picture of Pedro Mendes to upload to commons.wikimedia.org. Not the footballing Pedro Mendes who played for Rangers, Spurs, Pompey and Porto but the systems biologist Pedro Mendes who plays for Virginia Tech and Manchester. Thankfully, another systems biologist, Michael Hucka kindly pointed to his impressive collection of pictures, taken at various events over the years which include some shots of Pedro. Looking at these pictures made me idly wonder: What is the collective noun for a group of systems biologists?

Systems biology is the study networks of various kinds [2,3] so it’s ripe for a collective noun, and there were several suggested on twitter. Since twitter has recently developed a nasty habit of disappearing tweets, here is a collection gathered and preserved for posterity from the twitterome*:

A jamboree of systems biologists?

Tom Williamson and Mike Hucka initially plumped for a Jamboree of systems biologists:

http://twitter.com/mhucka/status/235157197632462849

A loop or an ome of systems biologists?

Mike Hucka and Nathan Pearson voted for a Loop or an Ome of systems biologists:

http://twitter.com/mhucka/status/235158395181735936

A cluster of systems biologists?

Then again, maybe it should be a cluster of biologists?

http://twitter.com/mhucka/status/235159013371830273

A network of systems biologists?

Douglas Kell reckoned on a network of systems biologists:

http://twitter.com/skepticCanary/status/235150998614728704

A system of systems biologists?

Ewan Birney thought it had be be a system:

So there you have it, according to the twitterome, the collective noun for a group of systems biologists is a system, network, cluster, ome, jamboree or loop (delete as appropriate). No doubt there are many more, that’s what twitter hashtags are for, #SysBiologists.

References

  1. Arthur D. Lander (2010). The edges of understanding, BMC Biology, 8 (1) DOI: 10.1186/1741-7007-8-40
  2. Hiroaki Kitano (2002). Systems Biology: A Brief Overview, Science, 295 (5560) 1664. DOI: 10.1126/science.1069492
  3. Trey Ideker, Timothy Galitski & Leroy Hood (2001). Systems Biology: A new approach to decoding life, Annual Review of Genomics and Human Genetics, 2 (1) 372. DOI: 10.1146/annurev.genom.2.1.343

* That’s another #badomics award for Jonathan Eisen’s growing collection…don’t blame me, blame Leonid Kruglyak

August 15, 2012

Fancy becoming a Software Fellow?

Filed under: engineering,Science — Duncan Hull @ 3:48 pm
Tags: , , , ,
Airplane by  By Kuster & Wildhaber Photography

Airplane by By Kuster & Wildhaber Photography

The Software Sustainability Institute www.software.ac.uk has launched a Fellowship programme that recognises outstanding UK-based researchers who use software. The Fellowships come with £3000 funding which can be used for travel, collaboration and running events.

Fellows advise the Institute on important software, evangelise software practices and champion the adoption of best-of-breed software. Fellows will contribute to the software blog, and are supported in advertising their own research.

You can apply to become a Fellow online. Keep an eye on the software.ac.uk blog and Twitter account @SoftwareSaved for further information.

Launch event

A Fellowship Launch event will be held at the Digital Research 2012 in Oxford on 10th September 2012. Attendees at the launch event will receive free entry to the conference on 10 September and, if they choose to stay on, a 50% reduced fee for the rest of the conference. Applicants to the Fellowship Programme put themselves in an advantageous position if they have attended the workshop.

Who should apply

The SSI is seeking fifteen outstanding researchers at different  stages in their career, from PhDs to Professors, and from a wide range of research disciplines in science, technology and engineering. Successful Fellows will have a demonstrable knowledge and visibility in their community and have excellent communication skills.

Funding

The £3000 funding is flexible and can be used for travel to conferences, setting up and running workshops, starting new collaborations or hosting/teaching at Software Carpentry training events.

Application details

The Software Sustainability Institute is a national facility that helps researchers and developers to build and use better research software.

The closing date for applications is Thursday 20 September 2012 at 5pm.

Fellowships last eighteen months and are available from the 1st of January 2012 through the 30th of June 2014.

Successful recipients of the Software Sustainability Institute’s Fellowships will be announced in November 2012.

Questions?

If you have any questions, please contact the Institute: info@software.ac.uk.

August 3, 2012

July 27, 2012

Olympic Science: The Long Jump to Conclusions

Snohomish Long Jumper by Philo Nordlund

Long jumper for Snohomish. Creative Commons licensed picture by by Philo Nordlund on Flickr

If Science were an Olympic sport, which events would scientists excel at?

During the Beijing Olympics in 2008, I wondered what Olympic activities scientists would be good at, with a list of events. This satirical post was kindly re-published [1] by the learned American Physical Society (thanks guys!) in their newsletter, though some of the proposed events look a little dated now.

Doesn’t time fly? Here we are four years later and London 2012 is already upon us. The Boris Johnson Olympic Stadium is finally complete. Oscar winner Danny Boyle has the eagerly anticipated opening ceremony all planned out. Sculptor Anish Kapoor’s spectacular Orbit Olympic observation tower looks out over the Olympic Park. Teams of athletes from all over the world have gathered in the capital to see how years of training will pay off.

Meanwhile Team Science [2] also play their part in supporting the Olympics, through sports science, drug testing and other services. Some are sparring for their bouts of impact factor boxing but may need a soothing ego massage afterwards to recover from the particularly painful peer-reviewed punches. Others are limbering up for the long jump to conclusions an event at which some scientists (and many policitians) are strong medal contenders. There are lots of other events proposed for the future too, some of them quite controversial [3,4,5], they might need genetically enhanced security guards, with superhuman abilities (sponsored by G4S)?

Readers of this blog will probably have much better ideas than the rather ropey suggestions I cobbled together. If that’s you, please post them below in the comments section or tweet them with the hashtag #OlympicScience.

Scientists and athletes have much in common, many are naturally obsessed [6] with their eyes firmly fixed on the prize and will often bend the rules to win Gold [7]. So wherever you are, whichever prizes you admire, enjoy the superb sporting spectacle that is the London 2012 Summer Olympics.

References

  1. Yours Truly (2008). If Science Were an Olympic Sport Zero Gravity: The Lighter Side of Science, American Physical Society (APS) Physics
  2. Daniel Cressey & Ewen Callaway (2012). Science at the Olympics: Team Science, Nature, 487 (7407) 292. DOI: 10.1038/487290a
  3. Helen Thompson (2012). Performance enhancement: Superhuman athletes, Nature, 487 (7407) 289. DOI: 10.1038/487287a
  4. Timothy Noakes & Michael Spedding (2012). Olympics: Run for your life, Nature, 487 (7407) 296. DOI: 10.1038/487295a
  5. Juan Enriquez & Steve Gullans (2012). Olympics: Genetically enhanced Olympics are coming, Nature, 487 (7407) 297. DOI: 10.1038/487297a
  6. Mariano Loza-Coll (2012). Piled too high, Nature, 486 (7403) 431. DOI: 10.1038/nj7403-431a
  7. Michael Brooks (2011). Free Radicals: The Secret Anarchy of Science ISBN:1846684056

Update: The real games started on a scientific and technical note with help from Tim Berners-Lee

#OlympicScience didn’t really take off, but #Nerdlympics (Olympics for Nerds) did much better – a selection below. 

http://twitter.com/Myrmecos/status/229330962205519873

http://twitter.com/artologica/status/229347539047030785

http://twitter.com/neilswainston/status/229355212706570240

July 19, 2012

Is word play friendly branding the key to successful technology?

βατόμουρο / Raspberries by Fir0002/Flagstaffotos

The Raspberry Pi (not pictured above) is currently blowing raspberries at its competitors at an impressive rate of four thousand per day. Creative Commons licensed picture of Rasberries by Fir0002/Flagstaffotos on wikipedia.

The key to successful technology is not just the tricky combination of innovation, determination and investment but also word play friendly branding.

Consider two technology companies, Google and Raspberry Pi:

So is word play really the key to technological success? Successful technologies often encourage word play, but word play does not make technology successful. Correlation does not imply causation and the examples above are very anecdotal.

Still, word play is fun and probably helps brands without doing them any harm [2]. Raspberry Pi is a particularly ripe brand for punning, are there any other #TechnoWordPlay examples?

References

  1. Rory Cellan-Jones (2012). Raspberry Ripples from the Raspberry Pi Foundation, BBC News
  2. Guy Swillingham (2005). Shop Horror: The Best of the Worst in British Shop Names, Harper Collins ISBN:0007198132

July 13, 2012

Animation 2012: Computer Science for Schools

Animation 2012 at the University of Manchester

Computer Science as a subject in mainstream UK secondary education is in a pretty sorry state [1,2,3] but it’s not all doom and gloom. While many long suffering school children are being force-fed a nauseating diet of Excel, PowerPoint and Access others are enjoying a nutritious platter of Raspberry Pi, Hack to the Future and Animated fun.

Here’s a brief report on one of these tasty appetisers: Animation 2012, a UK schools animation competition now in its fifth year.

The day kicked off with prizes being awarded for the animation competition. To get a flavour of the creativity and skill involved, you can see winning examples online.

Following the prize giving there was a carousel of activities which included:

Animation 2012 was great fun for all involved, congratulations to all this years winners, hope to see you again next year. There were 526 Schools involved from across the UK, with 914 entries. 58 students were involved in the 35 winning entries from 31 different schools. Thanks to Toby Howard, all the organisers, supporters (Google, Electronic Arts and NESTA) and associates (Computing at School, CS4FN and BAFTA young game designers) for putting on an impressive show.

References

  1. Steve Furber et al (2012). Computing in Schools: Shut down or restart? Royal Society Report
  2. James Robinson (2011). Eric Schmidt, chairman of Google, condemns British education system: criticising division between science and arts, The Guardian
  3. Keith Stuart (2011). Michael Gove admits schools should teach computer science: education secretary recognises the failings of ICT courses, The Guardian

July 6, 2012

Delicious Parthenon Marbles Cake, stolen from Athens

Parthenon by K_Dafalias on Flickr

The Parthenon at night by Konstantinos Dafalias, creative commons licensed picture available on Flickr. If you look carefully, you can see the inscription “Elgin woz ‘ere, 1801” where the Marbles were stolen from.

Here is a recipe and serving suggestion for delicious Parthenon Marbles cake, originally developed by Thomas Bruce, better known as Lord Elgin.

Recipe

  1. Buy a return ticket from the UK to Athens, Greece
  2. On arrival in Athens, find the most spectacular and beautiful cake you can
  3. Remove and vandalise the tastiest looking parts of the cake
  4. If anyone asks what you are doing, tell them you are an “ambassador”
  5. When you have finished vandalising, return to the UK with your souvenir cakes, leaving the leftovers in Greece.

Serving suggestion

These cakes are traditionally enjoyed in London. They are often decorated with large servings of patronising propaganda and a sprinkling of insults against the Greek nation. See for example Elgin Marbles: Relocation Debate on wikipedia and the Parthenon Marbles at the British Museum website.

Some people will tell you these cakes are many decades past their best before date. Ignore them if you can, while you enjoy the cakes at a safe distance from any Greeks who will legitimately demand that you return them to Athens immediately.

This is a controversial recipe as the ownership of the ingredients is keenly contested [1,2,3,4,5]. Consequently, it may not be possible to enjoy these cakes in the UK for much longer so enjoy them while you can.

References

  1. The Parthenon Marbles Should Be Returned to Athens, Intelligence Squared Debate, June 2012
  2. MarblesReunited.org.uk: promoting the case for the reunification of the Parthenon sculptures
  3. Trevor Timpson (2012) Stephen Fry’s Parthenon Marbles plea backed in debate vote, BBC News.
  4. Trevor Timpson (2012) To sue or not to sue? Parthenon Marbles activists debate, BBC News.

June 29, 2012

Impact Factor Boxing 2012

Rocky Balboa  Philadelphia, PA

Rocky Balboa, Philadelphia, PA. Creative Commons licensed picture by seng1011 (steve eng) on Flickr.

[This post is part of an ongoing series about impact factors]

In the world of abused performance metrics, the impact factor is the undisputed heavyweight champion of the (publishing) world.

It has been an eventful year in the boxing ring of scientific publishing since the last set of figures were published by Thomson-Reuters. A brand new journal called PeerJ launched with a radical publish ’til you perish business model [1]. There’s another new journal on the way too in the shape of eLifeSciences – with it’s own significant differences from current publishing models. Then there was the Finch report on Open Access. If that wasn’t enough fun, there’s been the Alternative metrics “Altmetrics” movement gathering pace [2], alongside suggestions that the impact factor may be losing its grip on the supposed “title” [3].

The impact factors below are the most recent, published June 28th 2012, covering data from 2011. Love them or loathe them, use them or abuse them, game them or shame them … here is a tiny selection of impact factors for the 10,675 journals that are tracked in Journal Citation Reports (JCR) ordered by increasing punch power.

WARNING: Abusing these figures can seriously damage your Science – you have been warned! Normal caveats apply, see nature.com/metrics.

Journal 2011 data from isiknowledge.com/JCR Eigenfactor™ Metrics
Total Cites Impact Factor 5-Year Impact Factor Immediacy Index Articles Cited Half-life Eigenfactor™ Score Article Influence™ Score
Russian Journal of Cardiology* 3 0.005 0.000 75 0.00000
BMC Bioinformatics 14268 2.751 3.493 0.293 557 4.2 0.07757 1.314
PLoS ONE 75544 4.092 4.537 0.437 13781 2.4 0.50216 1.797
Briefings in Bioinformatics 2859 5.202 7.749 0.692 65 4.3 0.01129 2.857
PLoS Computational Biology 8924 5.215 5.844 0.710 407 3.1 0.06968 2.722
OUP Bioinformatics 43380 5.468 6.051 0.666 707 6.2 0.15922 2.606
Nucleic Acids Research 106520 8.026 7.417 2.016 1230 7.4 0.30497 3.003
Genome Biology 15556 9.036 7.896 1.550 151 5.2 0.08221 4.124
PLoS Biology 20579 11.452 13.630 2.461 180 4.6 0.14975 7.830
Science 480836 31.201 32.452 6.075 871 9.4 1.41282 17.508
Nature 526505 36.280 36.235 9.690 841 9.4 1.65658 20.353
New England Journal of Medicine 232068 53.298 50.075 11.484 349 7.8 0.66466 21.293
CA – A Cancer Journal for Clinicians** 10976 101.780 67.410 21.263 19 3.8 0.04502 24.502

* The Russian Journal of Cardiology is included here for reference as it has the lowest non-zero impact factor of any science journal. A rather dubious honour…

** The Cancer Journal for Clinicians is the highest ranked journal in science, it is included here for reference. Could it be the first journal to have an impact factor of more than 100?

References

  1. Richard Van Noorden (2012). Journal offers flat fee for ‘all you can publish’, Nature, 486 (7402) 166. DOI: 10.1038/486166a
  2. Jason Priem, Heather Piwowar and Bradley Hemminger (2012).  Altmetrics in the wild: Using social media to explore scholarly impact arxiv.org/abs/1203.4745
  3. George Lozano, Vincent Lariviere and Yves Gingras (2012). The weakening relationship between the Impact Factor and papers’ citations in the digital age arxiv.org/abs/1205.4328

June 28, 2012

June 22, 2012

The Silicon Valley Meme: Coming to a Technology Cluster Near You …

Oracle by (nz)dave

Oracle Inc. Headquarters, Silicon Valley, California. CC-licensed Picture by (nz)dave on Flickr.

… if it hasn’t done already

In California the streets aren’t paved with Gold, they are paved with Silicon. Many a Californian has made their fame and fortune from Silicon-based commerce. Facebook, Google, Twitter, Oracle, Apple the list goes on and on. Silicon paves the streets of Silicon Valley.

Silly Valley is often imitated but rarely bettered. Here is a small selection of imitators from a fully blown stamp collection of silicon valley places in wikipedia:

  • Silicon Alley, New York
  • Silicon Fen, Cambridge UK
  • Silicon Roundabout, London
  • Silicon Glen, Glasgow and Edinburgh, Bonnie Scotland
  • Silicon Gorge,  M4 Corridor-ish (Bristol, Swindon, Oxford etc)
  • Silicon Mill, Manchester and North West England
  • Silicon Shipyard, Newcastle, Middlesborough etc

If you don’t have a Silicon Valley cluster near where you live, there’s an easy part and a hard part to creating one. The easy part is, just prefix the name of your local area with the magic S word Silicon. Easy. The hard part is building the universities, businesses, technology, communities, start-ups and investment that makes a technology cluster like Silicon Valley successful [1,2,3]. How can it be done?

Refererences

  1. Mietek Jaroniec (2009). Silicon beyond the valley Nature Chemistry, 1 (2), 166-166 DOI: 10.1038/nchem.173
  2. Paul Graham (2006). How to be Silicon Valley paulgraham.com
  3. Chris Vallance (2012). Silicon Britain: Inside the country’s tech clusters BBC News
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