June 23, 2017

Nine ideas for teaching Computing at School from the 2017 CAS conference


Delegates at the Computing at School conference 2017 #CASConf17 answering diagnostic questions, picture by Miles Berry.

The Computing At School (CAS) conference is an annual event for educators, mostly primary and secondary school teachers from the public and private sector in the UK. Now in its ninth year, it attracts over 300 delegates from across the UK and beyond to the University of Birmingham, see the brochure for details. One of the purposes of the conference is to give teachers new ideas to use in their classrooms to teach Computer Science and Computational Thinking. I went along for my first time (*blushes*) seeking ideas to use in an after school Code Club (ages 7-10) I’ve been running for a few years and also for approaches that undergraduate students in Computer Science (age 20+) at the University of Manchester could use in their final year Computer Science Education projects. So here are nine ideas (in random brain dump order) I’ll be putting to immediate use in clubs, classrooms, labs and lecture theatres:

  1. Linda Liukas demonstrated some intriguing ideas from her children’s books and HelloRuby.com that are based on Montessori education. I shall be trying some of these out (particularly the storytelling stuff) at code club to keep girls involved
  2. Sue Sentance and Neil Brown from King’s College London gave an overview of some current research in pedagogy.  They discussed research questions that can be tackled in the classroom like (for example) do learners make more progress using visual programming languages (like Scratch and Blockly) or traditional text-based languages (like Python and Java etc)? Many of these research questions would make good projects for undergraduate students to investigate in secondary schools, see research on frame based editors, for example.
  3. Michel Wermelinger from the Open University demonstrated using iPython notebooks for teaching data literacy at the Urban Data School. Although I’m familiar with iPython, it had never occurred to me to actually use iPython in school for teaching. It is a no-brainer, when you think about it, even for primary, because you have your code, inputs and outputs all in one window, and can step through code execution instead of (or as well as) using more conventional tools like Trinket, Thonny or IDLE. Data literacy is fun to teach.
  4. Miles Berry from the University of Roehampton demonstrated Diagnostic Questions in Project Quantum. These are a collection of high quality quizzes to use interactively for example as hinge questions, where teaching is adapted depending on answers given, like this multiple choice question:
    Consider the following Python code:
    a = 20
    b = 10
    a = b
    What are the values of a and b?
    A: a = 10, b = 10
    B: a = 20, b = 20
    C: a = 30, b = 10
    D: a = 10, b = 20

    You’ll have to try these five questions to check your answer. The useful thing here is that DiagnosticQuestions.com (the platform on which this is built) allows you to see lots of responses, for example each answer (A, B, C or D) above was selected by 25% of participants. You can also view explanations which illuminate common misconceptions (e.g. the classic mistake of confusing assignment with equality) as well as providing a bank of free questions for use in the classroom.

  5. Mark Guzdial from GeorgiaTech discussed using learning sciences to improve computing teaching. He demonstrated predictive questions (e.g. ask students What do you think will happen when we run this code? before actually executing it) alongside what he called subgoal labelling. These are simple ideas (with proven benefits) that can be put to use immediately. I’ll also be trying the Live Coding (with Sonic Pi) and Media Computation he demonstrated asap.
  6. Laurence Rogers demonstrated Insight: Mr. Bit  this looks like a good app for using BBC microbits in the classroom, connected to a range of sensors, provided you’ve got access to iPads.
  7. A copy of Hello World magazine was in the conference bag. The summer 2017 issue has an unusual article from Ian Benson from Kingston University and Jenny Cane describing their use of the Haskell programming language to teach 5-7 year olds to reason symbolically and learn algebra before arithmetic with help from Cuisenaire rods. The Scratch Maths project at University College London are doing similar things, building mathematical knowledge using Scratch, rather than Haskell. These are experimental ideas you could try out on unsuspecting (junior) family members.
  8. Lee Goss from Barefoot Computing, described the free CPD for primary school teachers on offer from BT. I’ve signed up and hope to plug some of the shortcomings in the Code Club Curriculum.
  9. Richard Jarvis demonstrated appJar, a handy Python library for teaching Graphical User Interfaces (GUIs). That’s Jar as in Jarvis and Jam, not JAR as in Java ARchive BTW. I’ve not tried GUIs at code club yet, but appJar looks like a good way to do it.

There were lots more people and projects at the conference not mentioned here including tonnes of workshops. If you’re interested in any of the above, the CAS conference will be back in 2018. Despite the challenging problems faced by Computer Science at GCSE level, it was reassuring and inspiring to meet some members of the vibrant, diverse and friendly community pushing the boundaries of computing in schools across the United Kingdom. Thanks again to everyone at CAS for putting on another great event, I will definitely consider attending next year and maybe you should too.

June 18, 2013

Peter Suber’s Open Access book is now freely available under an open-access license

Peter Suber's Open Access book

Open Access by Peter Suber is now open access

If you never got around to buying Peter Suber’s book about Open Access (OA) publishing [1] “for busy people”, you might be pleased to learn that it’s now freely available under an open-access license.

One year after being published in dead-tree format, you can now get the whole digital book for free. There’s not much point writing yet another review of it [1], see Peter’s extensive collection of reviews at cyber.law.harvard.edu. The book succinctly covers:

  1. What Is Open Access? (and what it is not)
  2. Motivation: OA as solving problems and seizing opportunities
  3. Varieties: Green and Gold, Gratis versus libre 
  4. Policies: Funding mandates (NIH, Wellcome Trust etc)
  5. Scope: Pre-prints and post-prints
  6. Copyright: … or Copyfight?
  7. Economics: Who pays the bills? Publication fees, toll-access paywalls and “author pays”
  8. Casualties: “OA doesn’t threaten publishing; it only threatens existing publishers who do not adapt”
  9. Future: Where next?
  10. Self-Help: DIY publishing

Open Access for MACHINES!

A lot of the (often heated) debate about Open Access misses an important point about open access being for machines as well as humans, or as Suber puts in Chapter 5 on Scope:

We also want access for machines. I don’t mean the futuristic altruism in which kindly humans want to help curious machines answer their own questions. I mean something more selfish. We’re well into the era in which serious research is mediated by sophisticated software. If our machines don’t have access, then we don’t have access. Moreover, if we can’t get access for our machines, then we lose a momentous opportunity to enhance access with processing.

Think about the size of the body of literature to which you have access, online and off. Now think realistically about the subset to which you’d have practical access if you couldn’t use search engines, or if search engines couldn’t index the literature you needed.

Information overload didn’t start with the internet. The internet does vastly increase the volume of work to which we have access, but at the same time it vastly increases our ability to find what we need. We zero in on the pieces that deserve our limited time with the aid of powerful software, or more precisely, powerful software with access. Software helps us learn what exists, what’s new, what’s relevant, what others find relevant, and what others are saying about it. Without these tools, we couldn’t cope with information overload. Or we’d have to redefine “coping” as artificially reducing the range of work we are allowed to consider, investigate, read, or retrieve.

It’s refreshing to see someone making these points that are often ignored, forgotten or missed out of the public debate about Open Access. The book is available in various digital flavours including:


  1. Suber, Peter. Open Access (MIT Press Essential Knowledge, The MIT Press, 2012). ISBN:0262517639
  2. Clair, Kevin. (2013). Kevin Michael Clair reviews Open Access by Peter Suber The Journal of Academic Librarianship, 39 (1) DOI: 10.1016/j.acalib.2012.11.017

August 3, 2012

June 8, 2012

From Useful Trees to Powerful Networks: A talk by Manuel Lima from Microsoft

It’s Friday, so here’s another one of those cool RSA Animate videos by Cognitive Media. This one is narrated by Microsoftie Manuel Lima and describes how the tree structures that we know and love, such as the infamous tree of life are becoming inadequate for organising knowledge, despite having been useful for thousands of years.

Trees are, according to Lima, being replaced by networks of various kinds [1] as they are often a better way to organise the huge complexity [1] of the world around us.


  1. Manuel Lima (2011) Visual Complexity: Mapping Patterns of Information Princeton Architectural Press.

May 11, 2012

Journal Fire: Bonfire of the Vanity Journals?

Fire by John Curley on Flickr

Fire by John Curley, available via Creative Commons license.

When I first heard about Journal Fire, I thought, Great! someone is going to take all the closed-access scientific journals and make a big bonfire of them! At the top of this bonfire would be the burning effigy of a wicker man, representing the very worst of the vanity journals [1,2].

Unfortunately Journal Fire aren’t burning anything just yet, but what they are doing is something just as interesting. Their web based application allows you to manage and share your journal club online. I thought I’d give it a whirl because a friend of mine asked me what I thought about a paper on ontologies in biodiversity [3]. Rather than post a brief review here, I’ve posted it over at Journal Fire. Here’s some initial thoughts on a quick test drive of their application:


On the up side Journal Fire:

  • Is a neutral-ish third party space where anyone can discuss scientific papers.
  • Understands common identifiers (DOI and PMID) to tackle the identity crisis.
  • Allows you to post simple anchor links in reviews, but not much else, see below.
  • Does not require you to use cumbersome syntax used in ResearchBlogging [4], ScienceSeeker and elsewhere
  • Is integrated with citeulike, for those that use it
  • It can potentially provide many different reviews of a given paper in one place
  • Is web-based, so you don’t have to download and install any software, unlike alternative desktop systems Mendeley and Utopia docs


On the down side Journal Fire:

  • Is yet another piece social software for scientists. Do we really need more, when we’ve had far too many already?
  • Requires you to sign up for an account without  re-using your existing digital identity with Google, Facebook, Twitter etc.
  • Does not seem to have many people on it (yet) despite the fact it has been going since at least since 2007.
  • Looks a bit stale, the last blog post was published in 2010. Although the software still works fine, it is not clear if it is being actively maintained and developed.
  • Does not allow much formatting in reviews besides simple links, something like markdown would be good.
  • Does not understand or import arXiv identifiers, at the moment.
  • As far as I can see, Journal Fire is a small startup based in Pasadena, California. Like all startups, they might go bust. If this happens, they’ll take your journal club, and all its reviews down with them.

I think the pros mostly outweigh the cons, so if you like the idea of a third-party hosting your journal club, Journal Fire is worth a trial run.


  1. Juan Carlos Lopez (2009) We want your paper! The similarity between high-end restaurants and scientific journals Spoonful of Medicine, a blog from Nature Medicine
  2. NOTE: Vanity journals should not to be confused with the The Vanity Press.
  3. Andrew R. Deans, Matthew J. Yoder & James P. Balhoff (2012). Time to change how we describe biodiversity, Trends in Ecology & Evolution, 27 (2) 84. DOI: 10.1016/j.tree.2011.11.007
  4. Shema, H., Bar-Ilan, J., & Thelwall, M. (2012). Research Blogs and the Discussion of Scholarly Information PLoS ONE, 7 (5) DOI: 10.1371/journal.pone.0035869

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

March 11, 2011

Drop the Digital Dummy!

Pacifier anyone?Here is an experiment to investigate dependence on your “digital dummy”. A digital dummy is any computer, smartphone or other digital device on which you suckle data like a baby. What you need to do is:

  1. Delete all your so-called “social networks” on LinkedIn, Facebook etc. Being sat in front of a computer is distinctly unsociable.
  2. Delete your twitter account.
  3. Don’t bother reading your email (90% of email is useless noise).
  4. Blast your blog into oblivion.
  5. Ignore your feed reader, or “mark all items as read” because if Internet Addiction Disorder (IAD) actually exists and you are a sufferer [1], the currently best known cure is to go cold turkey.

After completing all these steps, wait for at least one week and observe results. Hasn’t it gone quiet?  Is your life any better? Repeat as necessary until sanity returns…


  1. Flisher, C. (2010). Getting plugged in: An overview of Internet addiction Journal of Paediatrics and Child Health, 46 (10), 557-559 DOI: 10.1111/j.1440-1754.2010.01879.x

June 22, 2010

Impact Factor Boxing 2010

Golden Gloves Prelim Bouts by Kate Gardiner[This post is part of an ongoing series about impact factors. See this post for the latest impact factors published in 2012.]

Roll up, roll up, ladies and gentlemen, Impact Factor Boxing is here again. As with last year (2009), the metrics used in this combat sport are already a year out of date. But this doesn’t stop many people from writing about impact factors and it’s been an interesting year [1] for the metrics used by many to judge the relative value of scientific work. The Public Library of Science (PLoS) launched their article level metrics within the last year following the example of BioMedCentral’s “most viewed” articles feature. Next to these new style metrics, the traditional impact factors live on, despite their limitations. Critics like Harold Varmus have recently pointed out that (quote):

“The impact factor is a completely flawed metric and it’s a source of a lot of unhappiness in the scientific community. Evaluating someone’s scientific productivity by looking at the number of papers they published in journals with impact factors over a certain level is poisonous to the system. A couple of folks are acting as gatekeepers to the distribution of information, and this is a very bad system. It really slows progress by keeping ideas and experiments out of the public domain until reviewers have been satisfied and authors are allowed to get their paper into the journal that they feel will advance their career.”

To be fair though, it’s not the metric that is flawed, more the way it is used (and abused) – a subject covered in much detail in a special issue of Nature at http://nature.com/metrics [2,3,4,5]. It’s much harder than it should be to get hold of these metrics, so I’ve reproduced some data below (fair use? I don’t know I am not a lawyer…) to minimise the considerable frustrations of using Journal Citation Reports (JCR).

Love them, loathe them, use them, abuse them, ignore them or obsess over them … here’s a small selection of the 7347 journals that are tracked in JCR  ordered by increasing impact.

Journal Title 2009 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
RSC Integrative Biology 34 0.596 57 0.00000
Communications of the ACM 13853 2.346 3.050 0.350 177 >10.0 0.01411 0.866
IEEE Intelligent Systems 2214 3.144 3.594 0.333 33 6.5 0.00447 0.763
Journal of Web Semantics 651 3.412 0.107 28 4.6 0.00222
BMC Bionformatics 10850 3.428 4.108 0.581 651 3.4 0.07335 1.516
Journal of Molecular Biology 69710 3.871 4.303 0.993 916 9.2 0.21679 2.051
Journal of Chemical Information and Modeling 8973 3.882 3.631 0.695 266 5.9 0.01943 0.772
Journal of the American Medical Informatics Association (JAMIA) 4183 3.974 5.199 0.705 105 5.7 0.01366 1.585
PLoS ONE 20466 4.351 4.383 0.582 4263 1.7 0.16373 1.918
OUP Bioinformatics 36932 4.926 6.271 0.733 677 5.2 0.16661 2.370
Biochemical Journal 50632 5.155 4.365 1.262 455 >10.0 0.10896 1.787
BMC Biology 1152 5.636 0.702 84 2.7 0.00997
PLoS Computational Biology 4674 5.759 6.429 0.786 365 2.5 0.04369 3.080
Genome Biology 12688 6.626 7.593 1.075 186 4.8 0.08005 3.586
Trends in Biotechnology 8118 6.909 8.588 1.407 81 6.4 0.02402 2.665
Briefings in Bioinformatics 2898 7.329 16.146 1.109 55 5.3 0.01928 5.887
Nucleic Acids Research 95799 7.479 7.279 1.635 1070 6.5 0.37108 2.963
PNAS 451386 9.432 10.312 1.805 3765 7.6 1.68111 4.857
PLoS Biology 15699 12.916 14.798 2.692 195 3.5 0.17630 8.623
Nature Biotechnology 31564 29.495 27.620 5.408 103 5.7 0.14503 11.803
Science 444643 29.747 31.052 6.531 897 8.8 1.52580 16.570
Cell 153972 31.152 32.628 6.825 359 8.7 0.70117 20.150
Nature 483039 34.480 32.906 8.209 866 8.9 1.74951 18.054
New England Journal of Medicine 216752 47.050 51.410 14.557 352 7.5 0.67401 19.870

Maybe next year Thomson Reuters, who publish this data, could start attaching large government health warnings (like on cigarette packets) and long disclaimers to this data? WARNING: Abusing these figures can seriously damage your Science – you have been warned!


  1. Rizkallah, J., & Sin, D. (2010). Integrative Approach to Quality Assessment of Medical Journals Using Impact Factor, Eigenfactor, and Article Influence Scores PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010204
  2. Abbott, A., Cyranoski, D., Jones, N., Maher, B., Schiermeier, Q., & Van Noorden, R. (2010). Metrics: Do metrics matter? Nature, 465 (7300), 860-862 DOI: 10.1038/465860a
  3. Van Noorden, R. (2010). Metrics: A profusion of measures Nature, 465 (7300), 864-866 DOI: 10.1038/465864a
  4. Braun, T., Osterloh, M., West, J., Rohn, J., Pendlebury, D., Bergstrom, C., & Frey, B. (2010). How to improve the use of metrics Nature, 465 (7300), 870-872 DOI: 10.1038/465870a
  5. Lane, J. (2010). Let’s make science metrics more scientific Nature, 464 (7288), 488-489 DOI: 10.1038/464488a

[Creative Commons licensed picture of Golden Gloves Prelim Bouts by Kate Gardiner ]

May 21, 2010

myExperiment: The Videos

myExperiment is a research project that is exploring models, techniques and infrastructure for sharing digital items associated with  research , especially scientific workflows. The project is funded by the Joint Information Standards Committee (JISC) as part of a series of projects building Virtual Research Environments (VRE’s) and is run by Dave De Roure and Carole Goble at the Universities of Southampton and Manchester in the UK.

Last year, JISC made some professional videos describing the project. Needless to say, the videos were much more fun to make than the accompanying papers [1,2,3] and a probably more informative too. The best way of linking the research papers to the videos on youtube is to blog about them, so here they are. The first video (below) talks about the project generally:

The second video (below) discusses the data used in tackling African trypanosomiasis (sleeping sickness) in cattle.

The videos include interviews with Carole Goble, Dave De Roure, Paul Fisher, Andy Brass and yours truly.


  1. David De Roure, Carole Goble, & Robert Stevens (2007). Designing the myExperiment Virtual Research Environment for the Social Sharing of Workflows IEEE International Conference on e-Science and Grid Computing, 603-610 DOI: 10.1109/E-SCIENCE.2007.29
  2. David De Roure, Carole Goble, Jiten Bhagat, Don Cruickshank, Antoon Goderis, Danius Michaelides, & David Newman (2008). myExperiment: Defining the Social Virtual Research Environment IEEE Fourth International Conference on eScience, 2008. eScience ’08., 182-189 DOI: 10.1109/eScience.2008.86
  3. Goble, C., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., & De Roure, D. (2010). myExperiment: a repository and social network for the sharing of bioinformatics workflows Nucleic Acids Research DOI: 10.1093/nar/gkq429

December 5, 2009

Adrenaline: Entity of the Month

XML Summer School, Oxford, U.K.December’s entity of the month at ChEBI is Adrenaline, for all the adrenaline junkies out there. This accompanies ChEBI release 63, containing 536,978 total entities, of which 19,501 are annotated entities and 678 were submitted via the ChEBI submission tool. Text reproduced below from the ChEBI website:

Adrenaline (CHEBI:33568), also known as epinephrine, is a catecholamine that acts as a hormone and neurotransmitter.

It was first isolated from an extract of the suprarenal (adrenal) gland as its mono-benzoyl derivative by the American biochemist and pharmacologist John Jacob Abel in 1889 [1] who later also crystallised it as a hydrate. The pure compound was produced in 1901 by the Japanese industrial chemist Jokichi Takamine [2] and patented as ‘Adrenalin’. Two chemists, Stolz and Dakin, independently reported the synthesis of the compound in 1904 [3,4].

Adrenaline is a potent ‘fight-or-flight’ hormone, which is produced in stress situations. When produced in the body, it leads to an increase in heart-rate, vasodilation and the supply of both glucose and oxygen to the muscles and the brain, thus preparing the body for rapid action if needed. The increase in glucose supply is achieved through the binding of adrenaline to β-adrenergic receptors in the liver. This triggers the adenylate cyclase pathway, which, in turn, leads to increased glycogenolysis activity. On the other hand, adrenaline suppresses both digestive processes as well as immune responses. As such, it can be used in the treatment of anaphylactic shock [5] as well as for the treatment of cardiac arrest and cardiac disrythmias [6].

The biosynthesis of adrenaline is regulated by the central nervous system. It is ultimately derived from L-tyrosine, which is converted into L-dihydroxyphenylalanine (L-DOPA) by the action of tyrosine 3-monooxygenase (EC Adrenaline is produced through the conversion of L-DOPA into dopamine into noradrenaline into adrenaline itself.


  1. Abel, J.J. (1899) Ueber den blutdruckerregenden Bestandtheil der Nebenniere, das Epinephrin. Z. Physiol. Chem. 18, 318–324.
  2. Takamine, J., (1902) The isolation of the active principle of the suprarenal gland. J. Physiol. 27 (Suppl), xxix–xxx.
  3. Stolz, F. (1904) Ueber Adrenalin und Alkylaminoacetobrenzkatechin. Ber. Dtsch. Chem. Ges. 37, 4149–4154.
  4. Dakin, H.D. (1905) The synthesis of a substance allied to noradrenaline. Proc. Roy. Soc. Lon. Ser. B 76, 491–497.
  5. ANCHOR, J. (2004). Appropriate use of epinephrine in anaphylaxis The American Journal of Emergency Medicine, 22 (6), 488-490 DOI: 10.1016/j.ajem.2004.07.016
  6. Rainer TH, & Robertson CE (1996). Adrenaline, cardiac arrest, and evidence based medicine. Journal of accident & emergency medicine, 13 (4), 234-7 PMID: 8832338

[CC licensed picture of dan wakeham pipe by jeffcapeshop]

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