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.” 
- PubCast scivee.tv/pubcasts allow users to “enliven articles and help drive more views” (to PubMed) 
- PubFig nothing to do with PubMed, but research done on face and image recognition that happens to be indexed by PubMed. 
- PubGet pubget.com is a “comprehensive source for science PDFs, including everything you’d find in Medline.” 
- 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” 
- 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. 
- 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” 
- 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. 
- 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)  – 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.
- 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
- 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
- Hokamp K. & Wolfe K.H. (2004) PubCrawler: keeping up comfortably with PubMed and GenBank., Nucleic acids research, http://pubmed.gov/15215341
- 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
- Gibney E. (2014). How to tame the flood of literature., Nature, 513 (7516) http://pubmed.gov/25186906
- 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
- 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
- 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
- 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
- Douglas S.M., Montelione G.T. & Gerstein M. (2005). PubNet: a flexible system for visualizing literature derived networks., Genome Biology, http://pubmed.gov/16168087
- 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
- Seife C. (2002). Electronic publishing. DOE cites competition in killing PubSCIENCE., Science (New York, N.Y.), 297 (5585) 1257-1259. http://pubmed.gov/12193762
- Jensen M. (2003). Another loss in the privatisation war: PubScience., Lancet, 361 (9354) 274. http://pubmed.gov/12559859
- Dubuque E.M. (2011). Automating academic literature searches with RSS Feeds and Google Reader(™)., Behavior Analysis in Practice, 4 (1) http://pubmed.gov/22532905
- 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
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)  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:
- 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.
- 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…
- 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 . 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?
- 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
- Brontë, Emily (1847) Wuthering Heights
How to Win the World Cup: Step One: Dream on, Dreamer
Are you passionate about your football team? When I say passion I mean passion as in suffering, from the Latin verb patī meaning to suffer. World cups are passionate milestones for many people, they leave indelible marks on the psyche, you remember who you were with, where you were and how your team suffered.
Like many England supporters I’ve suffered as the english media whips up false hope about the prospects of the squad every four years. “This year could be our chance”, and “we’ve got some really good players”, “remember 1966?”, “thirty years of hurt never stopped me dreaming” bla bla bla….
Passionate English suffering at the World Cup (1982-2014)
All this hope, passionately flies in the face of reason, cold facts and history:
So if history [2,3] and mathematics (via predictwise) are anything to go by, there is (at the time of writing) a 96.5% chance that English suffering will continue and a 60% chance that the suffering will occur in the latter stages of the competition…
Wherever you are, whoever you support and whatever their chances, enjoy the inevitable suffering that comes with being passionate about zero-sum games like football. Life would be very boring without passion and suffering…
- Clemente FM, Couceiro MS, Martins FM, Ivanova MO, & Mendes R (2013). Activity profiles of soccer players during the 2010 World Cup. Journal of Human Kinetics, 38, 201-11 PMID: 24235995
- Graham McColl (2010) How to win the World Cup Bantam Press, ISBN: 0593066227
- Alex Bellos (2014) Futebol: The Brazilian Way of Life Bloomsbury Paperback ISBN: 0747561796
Sunny intervals? Really?
According to the urban myth, the eskimos have hundreds of words for snow. But meteorologists, especially British weather forecasters, have just as many words for rain. Take this typical forecast for example:
TODAY: Showers will continue in the north and west, but become more lighter and more isolated as the night progresses. Remaining dry elsewhere with clear spells and light winds.
TOMORROW: Largely dry and bright with sunny spells, the best of the sunshine in the south. A few light showers are likely for Scotland and Northern Ireland. Warm with light winds.
Many people just want to know will it rain today and should I take a brolly? Deciphering the weasel words above can be frustrating, in case you find this confusing, here’s a quick (and incomplete) translation into plain words .
|Weasel Weather Words
||Will it rain? Actual meaning in plain english
|low pressure moving in from the west
|sunshine with showers
|becoming brighter later
||yes (where you are)
I hope this clears things up a bit.
- Ernest Gowers (1954) Plain Words: A Guide to the use of English revised and updated by Rebecca Gowers ISBN: 0141975539
The Church of Banksy
Whatever your religous preferences, the Serenity Prayer by Reinhold Niebuhr captures a certain wisdom about life in general. So it is good to see that physicist Jon Butterworth at UCL has adapted it  for scientists:
“Give me grace to accept with serenity the things that cannot be understood,
Data to investigate the things which can be understood,
And the Wisdom to know the difference.”
- Jon Butterworth (2014) Giles Fraser says scientists are replacing theologians. Some thoughts on that The Gruaniad, 2014-03-31
A dojo (or a dōjō) is an event where people train to perform a given task. So for example, software engineers organise code dojos to hone their skills in making software. The term has become widely adopted, so much so, that you’ll often find many flavours of dojo in your local area. In Manchester, there are at least three variants and these often get confused, usually by me. So here’s a quick explanation of what the different dojos do and how they are different.
CoderDojo: @coderdojo & @mcrcoderdojo etc
CoderDojo.com is an open source, volunteer led, global movement of free coding clubs for young people. You’ll find Coder Dojos all over the world, the Manchester Coder Dojo meets once a month in The Sharp Project, and like many coder dojos is very popular and frequently over-subscribed.
CodingDojo: @uomcodingdojo & @codingdojodotco
A group of students at the University of Manchester organise a Coding Dojo @uomcodingdojo see fb.com/uomcodingdojo. They practise problems in TopCoder and other puzzles [1-5] in order to compete in the ACM International Collegiate Programming Contest. They do this because it’s fun, improves their skill and prepares them for the kind’s of problems that are commonly found in a Coding Interviews – a variant of the infamous Microsoft / Amazon / Google / Apple / Facebook / Twitter interviews. [6,7]
(The Manchester Coding Dojo are nothing to do with codingdojo.com an outfit in Seattle and Silly Valley who claim to “teach you programming in 2 weeks” see @codingdojodotco.)
The Manchester Codejo is monthly coding meetup in Manchester, where developers improve their skills by performing Katas – exercises designed to improve coding ability through repetition. So at their last meeting for example, Gemma Cameron @ruby_gem recently ran a Codejo session on the Class-responsibility-collaboration card at manchester.techhub.com.
In other words…
So @coderdojo ≠ @uomcodingdojo ≠ @manc_codejo ≠ @McrCoderDojo etc. Hope this clears up some confusion…
- http://en.wikipedia.org/wiki/Dining Philosophers
- http://en.wikipedia.org/wiki/Eight queens puzzle
- http://en.wikipedia.org/wiki/Tower of Hanoi
- http://en.wikipedia.org/wiki/Travelling salesman problem
- http://en.wikipedia.org/wiki/Two Generals’ problem
- McDowell, Gayle Laakman (2011) Cracking the Coding Interview: 150 Programming Questions and Solutions Career Cup ISBN:098478280X
- Poundstone, William (2013) Are You Smart Enough to Work at Google? Fiendish Puzzles And Impossible Interview Questions From The World’s Top Companies Oneworld Publications ISBN:1851689559
I’m Sorry I Haven’t A Clue, also unavailable on Samsung Android devices.
I’m Sorry I Haven’t A Clue (ISIHAC) is a superbly funny comedy show broadcast by the BBC since 1972 and currently airing it’s sixtieth (yes 60th!) series. Unlike many other BBC programmes, ISIHAC is mysteriously unavailable as a podcast, which makes it difficult to listen to offline. Why is this? Professor Google doesn’t give a definitive answer and the BBC aren’t saying much about it either. So in the spirit of public broadcasting, this post poses the question, where’s the podcast? Currently there are a two theories floating around on the interwebs:
- The podcast was destroyed by the lovely Samantha when she exceeded her bandwidth after … [insert smutty innuendo here]
- There is no podcast because Random Entertainment Ltd, the company behind ISIHAC, make a tidy profit from ISIHAC merchandise (mostly CDs, audiobooks, Uxbridge English Dictionary etc). This makes enough money for Graeme Garden and Jon Naismith to have a lifetime supply of Swanee whistles and Kazoos funded by tax-payers money. Consequently, the BBC don’t have the rights to podcast it or something, probably…
If all you want is an ISIHAC MP3 of the broadcast that can be listened to offline at your leisure, then the lack of a podcast is frustrating. Of course, there various workarounds and hacks to roll your own using using get_iplayer, a digital recorder, XBMC or similar but this will be a lot of unnecessary hassle for most listeners. None of this seems to be in the spirit of public broadcasting and there’s a bigger (unanswered?) question about how the BBC decides what to podcast (and what not to).
So Jon Naismith, Graeme Garden and anyone at the BBC, if you’re reading this, please can ISIHAC be made available as an MP3 via a podcast? Much obliged.
[Update July 2015: the BBC iPlayer Radio app now supports downloads – the next best thing in the absence of podcasts. Hooray!]
Manchester Town Hall by Richard Hopkins, creative commons licensed picture via Flickr
The term Manchester is a misnomer, mutated from it’s original form. The name Mamchester might be more appropriate, but only if the pedants get their way.
The Man in Manchester is misleading and has little to do with Manhood or Masculinity. Instead, the word is thought to come from the name given to city by the romans of “Mamucium”, meaning breast-shaped hill. Somewhere down the line Mamucium morphed into Manchester and the Mam became a Man. That’s mam, not man, as in Mammary or as the Miserable Mancunian Morrissey put it,
“Let me get my hands on your mammary glands.”
So don’t be a boob, remember the Man in Manchester is a Mam. Mamchester, you talk so hip, you’re twistin my melon man…
Tweeting down Twitter Lane, Waddington, Lancashire
While passing through the beautiful Forest of Bowland the other day, I chanced upon a remarkable place known as Twitter Lane in the village of Waddington, Lancashire. Twitter Lane is an interesting place because of the people you find there and they way they behave . For example, the residents of Twitter Lane are characterised by:
- Open-ness: residents share all sorts of information without anyone who will listen, from the banal to the profound, from the libellous to the incriminating, from the funny to the informative. All humanity is there, the good, the bad and the ugly.
- Serfdom: most of the residents on twitter lane are serfs who rent their property much like tenant farmers or sharecroppers. The rent they pay to their landlords is not a financial one, but an informational one. Residents volunteer numerous personal details: IP addresses, mobile phone numbers and address books in return for a place to stay. Some people are calling it digital serfdom.
- Short attention-span: although a friendly and open bunch, the residents of Twitter Lane have very short … where was I … ah yes, short attention spans and communicate in even shorter messages. Residents are typically obsessed with news, celebrities and sport. They are well supplied with the very latest real-time information on all of these things and more. However, sometimes the cacophony on Twitter Lane means it feels like everyone is talking, but few are listening.
So, Twitter Lane is an extraordinary place, with a large and a burgeoning population. Two important questions currently hang over it, how much is it worth and how many more people are going to want to live there on a long-term basis?
- Rappa M., Jones P., Freire J., Chakrabarti S., Kwak H., Lee C., Park H. & Moon S. (2010). What is Twitter, a social network or a news media?, WWW ’10 Proceedings of the 19th international conference on World Wide Web conference, 591-600. DOI: 10.1145/1772690.1772751