O'Really?

January 27, 2020

Seven things to do at CERN if you’re not a Physicist

cern

Wandering the Immeasurable: A sculpture at CERN by Gayle Hermick, picture re-used with permission from the artist

Even if you’re not a Physicist, there is plenty to see and do above and below ground at the European Organization for Nuclear Research (CERN). Home to the worlds largest experiment on what is arguably the worlds largest machine near Geneva in Switzerland, CERN is a very inspiring place to visit. Consequently, CERN and the Large Hadron Collider (LHC) feature in many guidebooks like The Geek Atlas [1], the Atlas Obscura, Lonely Planet and Tripadvisor.com. So what can you actually see and do at CERN?

  1. Get a well paid engineering job. Good news for engineers, there are loads of jobs at CERN. What better way to explore a place than to work there? If you’re a student see careers.cern/students for details on summer internships and year long technical student programs. If you have already graduated, take a look at the CERN Fellowships and the doctoral student program. There are also plenty of opportunities for more experienced engineers described at careers.cern/professionals too. CERN’s mission is to “unite people from all over the world to push the frontiers of science and technology, for the benefit of all”. Part of that means providing opportunities for people from CERN’s 23 member states to learn new skills at CERN and take them back to their home country. For every research physicist at CERN, there are ten engineers. [2] To run their experiments, physicists rely on massive, novel and a very precise network of machines made with millions of parts, both moving and stationary. You need an army of engineers to build, test, run and develop such a complex machine, for example:
    • Mechanical engineers develop heating & cooling systems and mechatronics (there are quite a few robots at CERN)
    • Materials engineers test novel materials, metals, magnets, microscopes, superconductors, vacuums, X-ray diffraction and apply radiochemistry
    • Software and hardware engineers develop applications, virtualised infrastructure, distributed computing and databases using a wide range of programming and scripting languages. These applications manage data in one of the most highly demanding computing environments in the research world
    • Electrical and electronic engineers work on energy distribution, signal processing, microelectronics and radio frequency technology
    • Civil engineers and geotechnical engineers develop structures, roads, drainage, both above (and under) ground to accommodate all of the above
    • There are non-engineering jobs too, in administration careers.cern/AdminStudent-projects and Applied Physics (obviously)

So CERN is full of engineers of every flavour. But if you’re not a physicist or an engineer looking for a job, there is still plenty to see and do. So let’s reboot our listicle again: seven things to do at CERN if you’re not a physicist, an engineer or job seeker:

  1. Watch cosmic rays arrive from outer space: There are two permanent exhibitions which can be visited without booking and they both have free entry. One is housed in the aesthetically pleasing Globe of Science and Innovation (GoSI) and is called the Universe of Particles. Another is opposite the GoSI and called Microcosm. There’s plenty to see in both exhibits, including film projections, spark chambers showing cosmic rays and cloud chambers which allow you to visualise ionizing radiation.
  2. Wander the Immeasurable with Gayle Hermick: Right outside the GoSI, sits an impressive sculpture made of 15 tonnes of twisted steel, stretched out over 37 metres in length and 11 metres up into the air. Covered in mathematical equations describing physical laws, the sculpture tells the story of Physics from Mesopotamia and Ancient Greece up to present day Higgs Boson and beyond. It’s a beautiful work of art to contemplate by Gayle Hermick. Having been inspired by equations the next thing you need to do is…
  3. Crunch numbers using Einsteins famous equation: You can’t visit CERN without crunching some numbers. Many people will be familiar with Einsteins famous equation of mass–energy equivalence E=mc². What this means is that energy can be converted into mass (and vice versa) and the “exchange rate” () is a very large number – the speed of light squared. So, you can turn a small about of mass into a HUGE amount of energy. Armed with your handy mass–energy calculator, you can crunch numbers, for example 1 kg = 90,000,000,000,000,000 Joules.
  4. Thank the technology mothership: CERN is widely known as the the birthplace the Web, which we should all be thankful for. Many other technologies can trace their origin to CERN. Bent Stumpe and his colleagues developed the first touchscreens as early as 1973. [3,4] Cloud computing platforms such as Amazon Web Services, Google Cloud, Microsoft Azure have some of their roots in Grid Computing developed at CERN too. [5] Key pieces of widely used open-source software like Ceph and OpenStack have been co-developed at CERN. Where would we be without massive international collaborations? Find out more about how investment creates a positive impact on society through knowledge transfer, spin outs, startups and more at kt.cern. Many of these projects have an impact far beyond physics in areas such as medicine and consumer electronics. Thank you technology mothership. 🙏
  5. Boggle at Big Data: Data speaks louder than words. Here is some random data for your mind to boggle on:
    • When switched on, some of the LHC detectors track up to 40 million events per second.
    • The LHC Grid computing generates 30 petabytes (10¹⁵ bytes) per year, with 300 petabytes of data permanently archived in its tape libraries as of October 2018.
    • The big loop underground is 27km long. Travelling very fast, close to the speed of light, a proton laps the circuit 11,000 times every second.
    • There are 100,000 scientists from over 100 countries working at CERN
    • More boggling can be done in the CERN data centre, especially the key facts and figures. [6] Anyone can explore and play with over two petabytes of Physics data at opendata.cern.ch
  6. Contribute to the Grid: Talking of data, Physicists from all over the world work on data produced by the experiments. This requires supercomputers, very High Performance Computing (HPC) and Grid computing that no single machine can provide. This is why the Worldwide LHC Computing Grid (WLCG) exists. With the improvements of the LHC more and more computing power is required to crunch the data. Anyone can contribute by joining in the LHC@home project. Who knows? Maybe you can be a part of the discovery of the new mysterious particle or the proof that physicists have been struggling with for decades. CERN’s Grid builds on volunteered resources provided via the Berkeley Open Infrastructure for Network Computing (BOINC) middleware.
  7. Book a free tour: While the two free permanent exhibitions require no booking, the free tours do and they offer much more. Tours are typically given by knowledgeable and enthusiastic staff. You can learn a lot from the permanent exhibitions, but a tour guide brings the place to life. Tours fill up quickly and provide access to restricted parts of CERN such as mission control, the ATLAS experiment, CMS cavern, synchro-cyclotron, the CERN data centre and more. [6] The cyclotron tells the story of CERN from 1957, when the first particle accelerator arrived in pieces on the back of a few lorries. Today it spans 27 km of France and Switzerland. How did that happen? Using lights and projectors, the exhibition brings the story to life in an illuminating way. At the time of writing, limited underground visits are possible as we are in the middle of the long shutdown 2 [7]. Tunnels are accessible but you’ll need to book a tour.

If you ever get the chance to visit.cern, it is well worth it. There is nowhere else quite like it. CERN is a truly inspiring place that demonstrates what can be achieved when thousands of people collaborate on a shared vision.

Acknowledgements

I’d like to thank current and former CERN technical students from the University of Manchester for their tours (both virtual and actual) of CERN and comments on drafts of this article: Raluca Cruceru, Simeon Tsvetankov, Iuliana Voinea, Grzegorz Jacenków, Boris Vasilev, Ciprian Tomoiagă, Nicole Morgan, Paul-Adrian Gafton, Joshua Dawes and Stefan Klikovits. Did I miss anything? Let me know in the comments or by email.

Thanks to Gayle Hermick for her permission to re-use the picture of her artwork in this piece.

DISCLAIMER: You can probably tell from reading the above that I am not a Physicist, unless you count a very rusty A-level from decades ago. Any factual errors in this article are the combined fault of me and my Physics teacher!

References

    1. John Graham-Cumming (2009) The Geek Atlas: 128 places where Science & Technology come alive O’Reilly Media, Inc. ISBN: 9780596802257
    2. Did you know, CERN employs ten times more engineers and technicians than research physicists? home.cern/science/engineering Deadlines for applications are typically, end of January for summer internships and September and March for technical studentships, check careers.cern for details.
    3. Bent Stumpe and Christine Sutton (2010) The first capacitative touch screens at CERN: The story of a forerunner to today’s mobile-phone screens, cerncourier.com
    4. Bent Stumpe (2014) The ‘Touch Screen’ Revolution: 103–116. DOI: 10.1002/9783527687039.ch05 Chapter 5 of From Physics to Daily Life by Beatrice Bressan Wiley‐VCH Verlag GmbH & Co ISBN: 9783527332861
    5. Maria Alandes Pradillo and Andrzej Nowak (2013) The Grid, CERN’s Global Supercomputer Computerphile
    6. Mélissa Gaillard (2019) Key Facts and Figures – CERN Data Centre information-technology.web.cern.ch
    7. Evan Gough (2018) The Large Hadron Collider has been Shut Down, and Will Stay Down for Two Years While they Perform Major Upgrades universetoday.com

 

June 23, 2017

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

CAS

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.

July 31, 2015

Wikipedia Science Conference @WellcomeTrust in London, September 2nd & 3rd 2015 #wikisci

There is growing interest in Wikipedia, Wikidata, Commons, and other Wikimedia projects as platforms for opening up the scientific process [1]. The first Wikipedia Science Conference will discuss activities in this area at the Wellcome Collection Conference Centre in London on the 2nd & 3rd September 2015. There will be keynote talks from Wendy Hall (@DameWendyDBE) and Peter Murray-Rust (@petermurrayrust) and many other presentations including:

  • Daniel Mietchen (@EvoMRI), National Institutes of Health: wikipedia and scholarly communication
  • Alex Bateman (@AlexBateman1), European Bioinformatics Institute: Using wikipedia to annotate scientific databases
  • Geoffrey Bilder (@GBilder), CrossRef, Using DOIs in wikipedia
  • Richard Pinch (@IMAMaths), Institute of Mathematics and its Applications. Wikimedia versus academia: a clash of cultures
  • Andy Mabbett (@PigsOnTheWing), Royal Society of Chemistry / ORCID. Wikipedia, Wikidata and more – How Can Scientists Help?
  • Darren Logan (@DarrenLogan), Wellcome Trust Sanger Institute, Using scientific databases to annotate wikipedia
  • Dario Taraborelli (@ReaderMeter), Wikimedia & Altmetrics, Citing as a public service
  • … and many more

I’ll be doing a talk on “Improving the troubled relationship between Scientists and Wikipedia” (see slides below) with help from John Byrne who has been a Wikipedian in Residence at the Royal Society and Cancer Research UK.

How much does finding out more about all this wiki-goodness cost? An absolute bargain at just £29 for two days – what’s not to like? Tickets are available on eventbrite, register now, while tickets are still available. 

References

  1. Misha Teplitskiy, Grace Lu, & Eamon Duede (2015). Amplifying the Impact of Open Access: Wikipedia and the Diffusion of
    Science Wikipedia Workshop at 9th International Conference on Web and Social Media (ICWSM), Oxford, UK arXiv: 1506.07608v1

July 3, 2015

Manchester Digital, Education & Digital Skills in 2015

deemind

#DeepDream manipulated image of the Creation of Adam, some rights reserved (CC-BY) by Kyle McDonald (@kcimc) on flickr

Manchester Digital a non-profit trade assocation of around 500 digital businesses in the north west of england. Every year they hold elections at their AGM for members of their council who serve for two years. It’s time for me to stand for re-election because my two years is up. Here’s a vote-for-me pitch in 100 words:

Digital skills are crucial to the success of Manchester Digital (MD) but many members of MD struggle to recruit employees with the skills their businesses need. Key questions for MD’s growing membership are how can the skills shortage be met, and what are the responsibilities of employers and educators in addressing the digital skills shortage? As a council member, I would reboot the education special interest group to report thoroughly on these issues at a strategic level. The report would provide an overview of what digital skills young people are likely to have aged 16, 18 and 21+ and what employers can do to bridge the gaps.

If you’re interested in finding out more about Manchester Digital, and hearing from diverse bunch of 18 candidates standing for 6 places on the council, come along to the MD AGM on Thursday 9th July at 5.30pm in Ziferblat (@ziferblatedgest) – where everything is free, except time.

References

  1. #DeepDream Inceptionism: Going Deeper into Neural Networks, Google Research blog
  2. #DeepDream – a code example for visualizing Neural Networks Google Research blog
  3. Britain faces ‘growing shortage’ of digital skills” Daily Telegraph
  4. A UK digital skills gap looms, The Guardian
  5. UK failing to address digital skills shortage, says Lords report, ComputerWeekly.com

May 8, 2015

MPs with Science Degrees: How did Science & Technology do in the UK General Election 2015?

In case you missed it, the people of the United Kingdom have just democratically elected 650 Members of Parliament (MPs) to run their government for the next five years [1,2]. How many of these newly elected MPs have science backgrounds? Like many, I was inspired by Mark Henderson’s book The Geek Manifesto [3] back in 2012 after reading an article which argued that (quote) “with just one British MP having a scientific background, the people who run the country clearly need some expert advice”. So when I heard the news that the MP concerned, Julian Huppert (a.k.a. the “only scientist in the commons”) had lost his Cambridge seat, I lamented accordingly on twitter:

My lament was retweeted quite a bit, then Roger Highfield at the Science Museum in London challenged the interwebs to find if it really was true:

The sciencey MP factoid was quickly questioned by some random bloke on twitter called Richard Dawkins:

… and lots of people weighed in (see below)  – as they usually do on twitter. Thankfully Margaret Harris at Physics World, set the record straight and drew attention to the impressively large Physics Vote. Viva La Relativity!

Who knew there were so many physicists involved in the election? Not me. Turns out, the article about only one science MP, is a bit misleading. Julian Huppert was the only MP in the last government to be a “primary science worker” – that’s not quite the same as studying science at university. Julian was the only MP in the last government with scientific background at PhD level:

Members of the UK Parliament with science and technology degrees in 2015

So with help from twitter, the list of MPs with science degrees looks something like this (for a 2017 update see MPs to watch via the Campaign for Science and Engineering (CaSE)):

  1. Heidi Allen MP for South Cambridgeshire (BSc in Astrophysics)
  2. Steve Baker MP for Wycombe (BSc Aerospace Engineering, MSc Computer Science)
  3. Gavin Barwell MP for Croydon Central (BA Natural Sciences)
  4. Margaret Beckett MP for Derby South (BSc Metallurgy)
  5. Karen Bradley MP for Staffordshire Moorlands (BSc Mathematics)
  6. Tom Brake MP for Carshalton and Wallington (BSc Physics)
  7. Julian Brazier MP for Canterbury (BA Mathematics)
  8. Andrew Bridgen MP for North West Leicestershire (BSc Genetics)
  9. Alan Brown MP for Kilmarnock (BSc Civil Engineering)
  10. Therese Coffey MP for Suffolk Coastal (BSc & PhD Chemistry)
  11. David Davis MP for Haltemprice & Howden (BSc Computer Science)
  12. Robert Flello MP for Stoke-on-Trent South (BSc Chemistry)
  13. Liam Fox MP for North Somerset (Bachelor of Medicine)
  14. Mark Hendrick MP for Central Lancashire (BSc Eletrical Engineering)
  15. Carol Monaghan MP for Glasgow North West (BSc Physics)
  16. Liz McInnes MP for Heywood & Middleton (BSc Biochemistry)
  17. Chi Onwurah MP for Newcastle Central (BEng Electrical Engineering)
  18. Chris Philp MP for  Croydon South (BSc Physics)
  19. Alok Sharma MP for Reading West (BSc Physics & Electronics)
  20. Alec Shelbrooke MP for Elmet & Rothwell (BEng Mechanical Engineering)
  21. Graham Stringer MP for Blackley (BSc Chemistry)
  22. Stephen Timms MP for East Ham (MA Mathematics)
  23. Philippa Whitford MP for Ayrshire Central (Bachelor of Medicine)
  24. Sarah Wollaston MP for Totnes (Bachelor of Medicine)
  25. Valerie Vaz MP for Walsall South (BSc Biochemistry)
  26. Nadhim Zahawi MP for Stratford-on-Avon (BSc Chemical Engineering)

So there are at least 26 MPs out of 650 total who have some kind of STEM educational backgrounds, and hopefully several more. Thankfully, much better than none – but still not that high considering the proportion of STEM in the general population. This article MP’s Degrees: What do they know? claims there are many more scientific MPs, but it depends what you mean by Science of course. Over at the Science Campaign, they have counted 83 politicians with a background or “interest in” science. Doesn’t everyone have an interest in Science & Technology at some level? If so, there are 650 out of 650 MPs (100%) with an interest in science and technology then? As for MPs who have an actual science education, your mileage may vary, especially if you think Politics, Philosophy and Economics (PPE) are all sciences. Wannabe sciences? Yes. Actual Sciences? No.

In an ideal world where politicians create policies based on evidence, rather than finding evidence to fit their policies, how many scientists and technologists do we actually need in our government? Would it actually help make for better policies?

[Update: Jo Johnson MP for Orpington (BA Modern History), is the newly appointed Minister for Universities and Science [4], a post formerly held by David Willetts. Apparently, Johnson doesn’t know anything about Science. Does it matter?]

References

  1. Castelvecchi, D. (2015). Why the polls got the UK election wrong Nature DOI: 10.1038/nature.2015.17511
  2. Gibney, E. (2015). What the UK election results mean for science Nature DOI: 10.1038/nature.2015.17506
  3. Anon (2012). Books in brief: The Geek Manifesto: Why Science Matters Nature, 485 (7397), 173-173 DOI: 10.1038/485173a
  4. Gibney, E., & Van Noorden, R. (2015). UK researchers fret about downgrading of science minister role Nature DOI: 10.1038/nature.2015.17535

Thanks everyone who weighed in on twitter:

December 22, 2014

Makey Christmas and a Hacky New Year!

Christmas lectures by Ben Nuttall

Christmas lectures 2014 by @Ben_Nuttall

Our homes are full of technology that we typically take for granted and understand little. Your average smartphone or tablet, for example, is a “black box”, that deliberately discourages modification by tinkering and hacking. This Christmas, Danielle George takes three technologies we routinely take for granted – the light bulb, the telephone and the motor – and shows you how to hack your home as part of the Royal Institution Christmas Lectures broadcast on BBC Four.

Lecture 1/3 The Light Bulb Moment: First broadcast Monday 29th December

Inspired by Geordie inventor Joseph Swan, Danielle attempts to play a computer game on the windows of a skyscraper using hundreds of light bulbs. Along the way, Danielle will show the next generation how to hack, adapt and transform the technologies found in the home to have fun and make a difference to the world.

This year’s Royal Institution Christmas Lectures have been inspired by the great inventors and the thousands of people playing with technology at their kitchen tables or tinkering in their garden sheds. When Joseph Swan demonstrated the first working light bulb in 1878 he could never have dreamed that in 2014 we’d be surrounded by super-bright LED screens and lights that could be controlled using mobile phones.

In this lecture, Danielle explains how these technologies work and show how they can be adapted to help you realise your own light bulb moments. She shows how to send wireless messages using a barbecue, control a firework display with your laptop and use a torch to browse the internet. (via richannel.org/the-light-bulb-moment)

Lecture 2/3 Making Contact: First broadcast Tuesday 30th December

Inspired by Alexander Graham Bell, Danielle attempts to beam a special guest into the theatre via hologram using the technology found in a mobile phone. Along the way, Danielle shows the next generation how to hack, adapt and transform the electronics found in the home to have fun and make a difference to the world.

This year’s Royal Institution Christmas Lectures have been inspired by the great inventors and the thousands of people playing with technology at their kitchen tables or tinkering in their garden sheds. When Scottish inventor Alexander Graham Bell demonstrated the first telephone in 1876, he could never have dreamed that in 2014 we’d all be carrying wire-free phones in our pockets and be able to video chat in crystal clear HD across the world.

In this lecture, Danielle explains how these technologies work and shows how they can be adapted to help keep you connected to the people around you. She shows how to control paintball guns with a webcam and turn your smartphone into a microscope, whilst also investigating a device that allows you to feel invisible objects in mid-air. (via richannel.org/making-contact)

Lecture 3/3 A New Revolution: First broadcast Wednesday 31st December

Inspired by the Royal Institution’s very own Michael Faraday, Danielle attempts to use simple motors to construct the world’s greatest robot orchestra. Along the way, Danielle shows the next generation how to hack, adapt and transform the electronics found in the home to have fun and make a difference to the world.

This year’s Royal Institution Christmas Lectures have been inspired by the great inventors and the thousands of people playing with technology at their kitchen tables or tinkering in their garden sheds. When Michael Faraday demonstrated the first electric motor in 1822, he could never have dreamed that in 2014 we’d be surrounded by mechanical devices capable of performing nearly every human task.

In this lecture, Danielle explains how these robotic and motor-driven appliances work and shows how they can adapted to help you kick-start a technological revolution. She shows how to turn a washing machine into a wind turbine, how Lego can solve a Rubik’s Cube and how the next Mars rover will traverse an alien world. (via richannel.org/a-new-revolution)

If you miss the television broadcasts, the lectures will also be available on BBC iPlayer for 30 days then at richannel.org/christmas-lectures.

This will (probably) be the last post of the year at O’Really, so if you’ve visited, thanks for reading during 2014. Wherever you are, whatever you’re up to, have a Very Makey Christmas and a Hacky New Year in 2015.

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?

References

  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

September 9, 2014

Punning with the Pub in PubMed: Are there any decent NCBI puns left? #PubMedPuns

PubMedication: do you get your best ideas in the Pub? CC-BY-ND image via trombone65 on Flickr.

Many people claim they get all their best ideas in the pub, but for lots of scientists their best ideas probably come from PubMed.gov – the NCBI’s monster database of biomedical literature. Consequently, the database has spawned a whole slew of tools that riff off the PubMed name, with many puns and portmanteaus (aka “PubManteaus”), and the pub-based wordplays are very common. [1,2]

All of this might make you wonder, are there any decent PubMed puns left? Here’s an incomplete collection:

  • PubCrawler pubcrawler.ie “goes to the library while you go to the pub…” [3,4]
  • PubChase pubchase.com is a “life sciences and medical literature recommendations engine. Search smarter, organize, and discover the articles most important to you.” [5]
  • PubCast scivee.tv/pubcasts allow users to “enliven articles and help drive more views” (to PubMed) [6]
  • PubFig nothing to do with PubMed, but research done on face and image recognition that happens to be indexed by PubMed. [7]
  • PubGet pubget.com is a “comprehensive source for science PDFs, including everything you’d find in Medline.” [8]
  • PubLons publons.com OK, not much to do with PubMed directly but PubLons helps you “you record, showcase, and verify all your peer review activity.”
  • PubMine “supports intelligent knowledge discovery” [9]
  • PubNet pubnet.gersteinlab.org is a “web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks” aka a publication network graph utility. [10]
  • GastroPub repackages and re-sells ordinary PubMed content disguised as high-end luxury data at a higher premium, similar to a Gastropub.
  • PubQuiz is either the new name for NCBI database search www.ncbi.nlm.nih.gov/gquery or a quiz where you’re only allowed to use PubMed to answer questions.
  • PubSearch & PubFetch allows users to “store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature” [11]
  • PubScience is either “peer-reviewed drinking” courtesy of pubsci.co.uk or an ambitious publishing project tragically axed by the U.S. Department of Energy (DoE). [12,13]
  • PubSub is anything that makes use of the publish–subscribe pattern, such as NCBI feeds. [14]
  • PubLick as far as I can see, hasn’t been used yet, unless you count this @publick on twitter. If anyone was launching a startup, working in the area of “licking” the tastiest data out of PubMed, that could be a great name for their data-mining business. Alternatively, it could be a catchy new nickname for PubMedCentral (PMC) or Europe PubMedCentral (EuropePMC) [15] – names which don’t exactly trip off the tongue. Since PMC is a free digital archive of publicly accessible full-text scholarly articles, PubLick seems like a appropriate moniker.

PubLick Cat got all the PubMed cream. CC-BY image via dizznbonn on flickr.

There’s probably lots more PubMed puns and portmanteaus out there just waiting to be used. Pubby, Pubsy, PubLican, Pubble, Pubbit, Publy, PubSoft, PubSort, PubBrawl, PubMatch, PubGames, PubGuide, PubWisdom, PubTalk, PubChat, PubShare, PubGrub, PubSnacks and PubLunch could all work. If you’ve know of any other decent (or dodgy) PubMed puns, leave them in the comments below and go and build a scientific twitterbot or cool tool using the same name — if you haven’t already.

References

  1. Lu Z. (2011). PubMed and beyond: a survey of web tools for searching biomedical literature., Database: The Journal of Biological Databases and Curation, http://pubmed.gov/21245076
  2. Hull D., Pettifer S.R. & Kell D.B. (2008). Defrosting the digital library: bibliographic tools for the next generation web., PLOS Computational Biology, PMID: http://pubmed.gov/18974831
  3. Hokamp K. & Wolfe K.H. (2004) PubCrawler: keeping up comfortably with PubMed and GenBank., Nucleic acids research, http://pubmed.gov/15215341
  4. Hokamp K. & Wolfe K. (1999) What’s new in the library? What’s new in GenBank? let PubCrawler tell you., Trends in Genetics, http://pubmed.gov/10529811
  5. Gibney E. (2014). How to tame the flood of literature., Nature, 513 (7516) http://pubmed.gov/25186906
  6. Bourne P. & Chalupa L. (2008). A new approach to scientific dissemination, Materials Today, 11 (6) 48-48. DOI:10.1016/s1369-7021(08)70131-7
  7. Kumar N., Berg A., Belhumeur P.N. & Nayar S. (2011). Describable Visual Attributes for Face Verification and Image Search., IEEE Transactions on Pattern Analysis and Machine Intelligence, http://pubmed.gov/21383395
  8. Featherstone R. & Hersey D. (2010). The quest for full text: an in-depth examination of Pubget for medical searchers., Medical Reference Services Quarterly, 29 (4) 307-319. http://pubmed.gov/21058175
  9. Kim T.K., Wan-Sup Cho, Gun Hwan Ko, Sanghyuk Lee & Bo Kyeng Hou (2011). PubMine: An Ontology-Based Text Mining System for Deducing Relationships among Biological Entities, Interdisciplinary Bio Central, 3 (2) 1-6. DOI:10.4051/ibc.2011.3.2.0007
  10. Douglas S.M., Montelione G.T. & Gerstein M. (2005). PubNet: a flexible system for visualizing literature derived networks., Genome Biology, http://pubmed.gov/16168087
  11. Yoo D., Xu I., Berardini T.Z., Rhee S.Y., Narayanasamy V. & Twigger S. (2006). PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature., Current Protocols in Bioinformatics , http://pubmed.gov/18428773
  12. Seife C. (2002). Electronic publishing. DOE cites competition in killing PubSCIENCE., Science (New York, N.Y.), 297 (5585) 1257-1259. http://pubmed.gov/12193762
  13. Jensen M. (2003). Another loss in the privatisation war: PubScience., Lancet, 361 (9354) 274. http://pubmed.gov/12559859
  14. Dubuque E.M. (2011). Automating academic literature searches with RSS Feeds and Google Reader(™)., Behavior Analysis in Practice, 4 (1) http://pubmed.gov/22532905
  15. McEntyre J.R., Ananiadou S., Andrews S., Black W.J., Boulderstone R., Buttery P., Chaplin D., Chevuru S., Cobley N. & Coleman L.A. & (2010). UKPMC: a full text article resource for the life sciences., Nucleic Acids Research, http://pubmed.gov/21062818

July 29, 2014

A simple and useable classification of software by Aral Balkan via Wuthering Bytes

Three kinds of Software: Enthusiast, Enterprise & Consumer by Aral Balkan

Three kinds of Software: Enthusiast, Enterprise & Consumer by Aral Balkan

It’s getting pretty hard to do anything these days that doesn’t involve software. Our governments, businesses, laboratories, personal lives and entertainment would look very different without the software that makes them tick. How can we classify all this software to make sense of it all? The likes of this huge list of software categories on wikipedia are pretty bewildering, and projects such as the Software Ontology (SWO) [1] are attempting to make sense of swathes of software too. There’s lots of software out there.

Aral Balkan, one of the people behind the Indie Phone, has proposed a simpler classification which will appeal to many people. In his classification, there are three kinds of software (see picture top right), as follows:

  1. Enthusiast software: like a classic car. We tinker with enthusiast software, in the same way motoring enthusiasts tinker with their classic cars. To the enthusiast, it is a joy when the software breaks, because that’s part of the fun, fixing it and getting it back on the road. However, you wouldn’t drive your classic car during your day job, or commute to work. Like a classic car, enthusiast software, is largely for weekends and evenings only. Raspberry Pi software is a classic example of enthusiast software made in garages by hobbyists.
  2. Enterprise software: like a juggernaut truck. We use enterprise software, because our employers mandate that we do so. It might not be fun to drive, or work particularly quickly, but enterprise software is often a necessary evil to get work done on an industrial scale. Cynics will tell you enterprisey software is slow because the engineers have:

    “…added a delay of 3 seconds to every action and now users are feeling it’s enterprisey”.

    Cynics will also tell you, enterprise software has been made by architecture astronauts, purchased by clueless decision-makers who don’t have actually have to use the software themselves, but have been hoodwinked in notorious“vendor meetings” which could explain the unpopularity of some enterprise software. But that’s another story…

  3. Consumer software: like a family saloon car. We rely on consumer software to get the job done, it is purely functional, does the job in a reliable (and boring) way on a daily basis, just like the vehicle you commute in. Consumer software can be found on your mobile phone and most consumer software is Application Software aka “Apps”.

I came across Aral’s classification at Wuthering Bytes last summer, a small and friendly festival of technology in the Pennines. Wuthering Bytes is running again next month, August 15th -17th and is well worth attending if you’re in the North of England and fancy having your bytes wuthered [2]. It’s a great mix of talks by the likes of Sophie Wilson and many others combined with hands-on activities in beautiful Happy-Hippy-Hacky Hebden Bridge for a bargain £10 per day. It’s software (and hardware) for enthusiasts (not enterprises or consumers). What’s not to like?

References

  1. Malone, J., Brown, A., Lister, A., Ison, J., Hull, D., Parkinson, H., & Stevens, R. (2014). The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation Journal of Biomedical Semantics, 5 (1) DOI: 10.1186/2041-1480-5-25
  2. Brontë, Emily (1847) Wuthering Heights

August 7, 2013

A sweet taste of beekeeping with @Grow4ItChorlton in Chorlton-cum-Honey

busy bee

Mosaic of a busy mancunian bee in Manchester Town Hall

Down in deepest, darkest Chorlton-cum-Hardy [1] the good people of Grow for it Chorlton have been running a series of taster sessions on beekeeping (a.k.a. apiculture). Here are some notes from one of these sessions held last weekend and some info on where to find out more if you’re interested.

Bee Science

With the ongoing mystery about the decline of bee populations [2,3] and controversial pesticide bans [4], there’s been a surge of interest in bees and beekeeping. If you’re thinking about starting a hive, here’s some things you’ll need to consider:

  • Beekeeping can be very rewarding. Remind yourself how fascinating the biology of bees is: dronesworkers, queens and swarms – you couldn’t make this stuff up if you tried.
  • It’s a real buzz breaking the propolis seal on a hive full of ~60,000 bees and having a look inside, you can’t beat hands-on experience – handling bees was the highlight of the taster session.
  • Apiculture  takes lots of time, in peak season you’ll need to be inspecting hives at least once a week for any potential problems, such as the emergence of new queen cells or pests & diseases like Nosema and Varroa mites.
  • Beekeeping can be a substantial financial commitment too, depending on how resourceful you are. There’s a lot of kit you need, see thorne.co.ukbees-online.co.uk or beekeeping.co.uk for some examples of what you can buy and how much it costs.
  • One of the biggest threats to bees is irresponsible bee-keepers! If bees aren’t looked after hygienically, diseases can be spread to the  larger population. You don’t need a license (yet) to keep bees, but it’s a good idea to register hive(s) with DEFRA’s BeeBase (not to be confused with BeeBase.org) [5].

For such a tiny insect with even smaller brain, bees are surprisingly good at maths and computation. For example, bees use sophisticated vectors [6] to tell members of the hive where the food is during their famous waggle dance. Also, honeycomb is hexagonal because this is the shape that makes optimal use of beeswax – covering the maximum area using a minimum of material.

If you’re interested getting your hands on some bees in South Manchester, contact Loucas Athienites, Nancy Green or Erica Gardner at Nam-Bee-Pam-Bee Beekeepers, Chorlton based at Grow for It, Chorlton – their next (most excellent!) beekeeping session is due to run in late August 2013. Manchester & District Beekeepers Assocation (MDBKA), part of the British Beekeepers Association (BBKA), run a longer two-day course at Heaton Park (and elsewhere) which is essential if you going to take things further. [7]

References

  1. Yes, as you might expect, Chorlton-cum-Hardy suffers from the Scunthorpe problem
  2. Bill Turnbull et al (2013) What’s Killing Our Bees? A BBC Horizon Special featuring Rothamsted and BBSRC
  3. Charlotte Stoddart (2012). The buzz about pesticides: Common pesticides affect bumblebee foraging Nature DOI:10.1038/nature.2012.11626
  4. Daniel Cressey (2013). Europe debates risk to bees: Proposed pesticide ban gathers scientific support as some experts call for more field studies Nature DOI: 10.1038/496408a
  5. Munoz-Torres MC, Reese JT, Childers CP, Bennett AK, Sundaram JP, Childs KL, Anzola JM, Milshina N, & Elsik CG (2011). Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. Nucleic Acids Research, 39 (Database issue) PMID: 21071397
  6. Rossel S, & Wehner R (1982). The bee’s map of the e-vector pattern in the sky. PNAS, 79 (14), 4451-5 PMID: 16593211
  7. Ted Hooper (2010) Guide to Bees & Honey (updated): The World’s Best Selling Guide to Beekeeping Northern Bee Books, ISBN:1904846513
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