Is this the shortest abstract ever?

I’m currently writing a new program as part of a comparative genome analysis, which has the working title of “Snapper”. Unusually (but not uniquely) for me, this is not an acronym, but is instead a simple contraction of “SNP Mapper”.

Before doing too much, it is always wise to check for existing tools with the same name, especially if they might do similar things. A quick Google search for “Snapper bioinformatics” threw up this paper:

• Kolesov G, Mewes HW & Frishman D (2002). SNAPper: gene order predicts gene function. Bioinformatics 18(7):1017-9.

The abstract:

SNAPper is a network service for predicting gene function based on the conservation of gene order.

AVAILABILITY:
The SNAPper server is available at http://pedant.gsf.de/snapper. SNAPper-based functional predictions will soon be offered as part of the PEDANT genome analysis server http://pedant.gsf.de.

I know that Bioinformatics application notes are pretty concise - the idea is that the described software has the documentation you need - but that has to be one of the shortest abstracts that I have ever seen!

SNAPper itself is not an acronym, although the SNAP part is: Similarity Neighbourhood APproach. For such a common acronym as “SNAP”, that one needs some work, I think.

PEDANT, on the other hand, is a full ORCA-worthy acronym: Protein Extraction, Description and ANalysis Tool. It reminds me a bit of a defunct classic of my own, PIRATE: Protein Identification, References, Annotation and Tissue Extraction (or something like that, lost in the mists of time) that was basically just a parser for Uniprot entries that tabulated certain data, after I discovered that a PhD student in the department had spent several days copying and pasting data from Uniprot into Excel. Happy days!

Increase your mailbox and get a new massage

I just can’t understand the authors of phishing emails. Why go to all that trouble to mimic an Outlook full mailbox message and then not even bother to proof-read the English. Don’t con artists have any standards? It’s just insulting. (A massage would be nice, though.)

Why are kinases called kinases?

Kinases are one of the biggest and most important classes of enzymes (i.e. protein with catalytic activity) in biology. You can always recognise an enzyme because of the suffix “-ase”. What comes before the -ase then indicates the nature of the enzymatic activity.

The major classes of enzyme have names that give a good clue as to the general nature of this activity. Oxidoreductases, for example, catalyse oxidation-reduction (“redox”) reactions. Transferases transfer chemical groups from one molecule to another. Kinases are transferases: they transfer a phosphate group from one organic molecule (usually ATP, the cell’s primary energy carrier) to another (a protein, lipid or carbohydrate). And this is actually the origin of the kin- part of the name: from the Greek kinein “to move”.

For those wondering, there is also such as thing as a Phosphorylase but this does something subtly different; whereas a kinase transfers organic phosphate groups (i.e. phosphates attached to carbon-based biomolecules), a phosphorylase transfers inorganic phosphate groups (i.e. phosphate+hydrogen) to acceptor biomolecules.

But why -ase? This stems from the ending of diastase, the first enzyme ever discovered. According to Wikipedia:

“The name “diastase” comes from the Greek word διάστασις (diastasis) (a parting, a separation) because when beer mash is heated, the enzyme causes the starch in the barley seed to transform quickly into soluble sugars and hence the husk to separate from the rest of the seed.”

So there you have it. A kinase is an early example of an enzyme that moves something from one molecule to another, hence a name that literally means “an enzyme to move”.

20% off The Cabbages of Doom

Yesterday was apparently International Waffle Day, which sounds a bit made-up to me but is excuse enough for Lulu.com to have a 20% sale until the 31st of March. Just use WAFFLESSAY20 to get 20% off The Cabbages of Doom (just 80p!) or for some graphic entertainment, I can recommend Jesus ‘n’ Mo.

Christmas cracker jokes are bad and don't always work in the wrong continent

Dodgy Christmas cracker jokes are a Christmas tradition. Apparently, the jokes are deliberately bad. The alleged psychology behind this is that everyone groans and gangs up on the joke, thus are unified by their common disdain for the poor pun. If, on the other hand, the joke showed true wit and humour then it is highly likely that some people would not understand it and/or simply find it unfunny, thus creating a schism between those who get the joke and those who don’t.

It’s an interesting theory and I am not sure who first told me of it nor from whence it originated. What I am sure of, however, is that even the bad jokes need to be told in the right culture to stand a chance of doing their job. We had our departmental Christmas party yesterday (on a boat in the harbour and very nice too) but the crackers had clearly been imported from the UK and did not work Down Under.

The first one is not so bad. Presumably, Australian birds would migrate north for the winter but I think the meaning is still clear even if the geography is confused. The latter, however, completely fails on the basis that the penguins referred to do not exist here. There is a similar biscuit - the Tim Tam - but it is superior to the humble penguin and possibly why the latter has never taken off.

Even without the carbon footprint considerations, importing your crackers from halfway round the world is not a good move.

From the ancient Greeks to the modern Geeks - the #Nerdlympics

This weekend I joined with people from all over the world to witness Olympic history in the making. It was a pleasure to see science and technology celebrated on the world stage and pay a wonderful tribute to the creation of the World Wide Web.

No, I am not talking about the opening ceremony (although I did very much like the cauldron). I am, of course, referring to the #Nerdlympics on Twitter!

I've been on Twitter for a while now and contribute to a couple of trending topics but never got in on one at the beginning and watch it take off before.

Perhaps ironically, I had not really checked my Twitter feed for a while when I logged on last night, Alex Wild (@Myrmecos) had just posted a couple of geeky Olympic event puns with the hashtag #Nerdlympics. ("Star Trek and Field" was one of the early ones.) Never one to resist a good pun (as readers of The Cabbages of Doom could testify!), I tweeted "PCRchery" back (an event to be held in the velodrome with the rest of the thermal cycling). There were then a trickle of tweets, including some of my own contributions:

☺"Modem pentathlon"
☺"Circadian Rhythym Gymnastics" and
☺"Geeko-Roman Wrestling".

A couple of my favourites were tweeted at this time, including:

☺"Periodic table tennis" (@Myrmecos),
☺"Kreb's Cycling" (also @Myrmecos),
☺"Higgs Field Hockey" (@paulcoxon) and
☺<table>Tennis</table> (@gr33ndata).

Then, it suddenly took off and tweets were flying in, causing Alex to tweet:

The good news is, I've finally created my first successful hashtag. The bad news is, it's #Nerdlympics

As I replied at the time - I don't see the bad news here! Top work, Alex - you gave many nerds (including me) an entertaining evening.

It was quite interesting to see the different approaches taken. I was definitely of the "pun" class but there was a clear set of proposed events from an actual Nerdlympic competition. (Alex himself posted both types, e.g. "Synchronized Centrifuging".) At this point it became hard to keep up but here are a few more of my favourites (in no particular order):

☺@artologica: Tenure Track and Field,
☺@SuzeMarsupial: Basketball Galactica
☺@RalphCipolla: Heavy Water Polo
‏☺@skepticCanary: Petri Discus.
☺@CarolMorton: Beach bucky ball
☺@eric_andersen: Angry Birdminton
☺@abdelrahmanG: Spammer throw
‏☺@scientelle: Logarithmic Gymnastics
☺@marvel_matt: TATA-Boxing
☺@JamieBeach: Floppy Discus Throw
☺@JoeyMcMorrow1: Molecular weight lifting

Well done, all! It made me proud to be a nerd.

I am sure that there were some other classics that I have missed. To get a few more, try searching Twitter for #Nerdlympics - the early posts are all events but then later posts start referring to summaries of the event (recursive trending?) - or check out the Storify summaries by Bug Girl and Tarek Amr.

The Glossariser 1.0 is here

A while ago, I made a molecular evolution glossary page in case it was of use to anyone. Being a geek and a programmer, rather than actually making the webpage myself, I made a program to make the webpage for me. From a plain text set of terms and definitions, this program will construct a formatted web page, including hyperlinks between terms (if so desired).

As I now need to make another glossary for MapTime, I thought I would throw together a quick cgi script to make the code available online, and the Glossariser was born.



It's rather crude at present and, in particular, contains no documentation - trial and error only, I'm afraid! Input is, again, raw text with a number of delimiter options. (It only splits on the first occurrence of the chosen delimiter, so periods can be used quite happily.) There are currently a limited selection of output styles available. Unless "tabs" is chosen, terms will be split up according to their first letter and output alphabetically:



The "Header" or "bold" style refers to the formatting for the letters A-Z. The "table" output is similar but has each letter in a row of a table. The tabs style was a bit experimental and doesn't really work that well, so I won't bother to explain it here. (Feel free to try it!)

If you just want a standalone HTML page, you can (hopefully) just save the output directly. Otherwise, you will either want to copy and paste the text into a Word document or, to use in Blogger or other existing framework, just "view source" and copy the bits you need. (That's how I made the molecular evolution glossary.)

I have some plans for improvements - there are a few bugs to iron out and I would like to add URLs etc. - but, as with most things, they will probably wait until I, or someone else, really wants them in place. So, if it is useful but doesn't quite do what you want, let me know and I might be able to update it. There's also no reason that its use should be limited to a glossary. Any list of names/keywords and associated short paragraphs will do - perhaps I should make the alphabetical arrangement optional in this case?

The Glossariser is available at: http://bioware.soton.ac.uk/glossariser.html.

(If it ever saves you an evening of writing HTML and you want to say thanks, buy The Cabbages of Doom for just 99p! ☺ (You can't blame a guy for trying!))

CGI, where've you bin all my life?

I'd been meaning to play around with CGI (Common Gateway Interface) programming for some time as a way of making simple functional websites. I finally got round to it last month, thanks to a great introductory page at Tutorials Point. What I did not realise is quite how easy it was.

I've still only really scratched the surface and scanned over the page to get something up quickly but, in essence, you only need three things:

1. A webserver that supports CGI.

2. An html page containing some "form" code that contains a submit button and (optionally) some input options (e.g. text boxes or checkboxes).

3. A python script (or another language) that generates HTML code based on the variables and values from the form.

And that's essentially it. Actually, you don't even need (2), as you can feed variables directly to the cgi script, but it makes it easier for the user, I think.

My first attempt at this can be found here. It's a bit of silly fun but it shows what can be done with just a few simple lines of code. I've cheated a little bit by using an existing python module to generate the middle of the HTML code but, in a way, that's the point - you can easily adapt existing functional code to output text.

In this case, I use the random "Zen wisdom" text strings that are generated in my code to lighten up error messages when I'm debugging. (If you ever use one of my programs, you sometimes come across such an error message, which always causes confusion (and usually embarrassment for me!) but I think it's a small price to pay for making debugging more fun!) The scary thing is how often the random Zen Wisdoms sound deep and meaningful, e.g.

"It is bold to play jenga with blocks of passion."

Well, maybe not that deep and meaningful!

Flying squirrel Google Psyche

Following my earlier post on Flying Squid, I thought I'd do a bit of Google Psyche on the subject, just out of curiosity. I'd got as far as "flying squi", however, when I realised that flying squirrels were much more intriguing Google Psyche subjects!

I think "pet" and "facts" speak for them themselves. I had also known about the "flying squirrel suit", although I did not realise that it came in a "cuddly" Halloween variant.



The pizza is probably most disturbing thought but it turns out to be the name of a Seattle pizza restaurant, rather than a particularly avant garde topping. Meanwhile, "flying squirrel wrestling" is also not quite as cruel as it sounds but is instead the name of a wrestling move. What a weird and wonderful place the world is!

Google Psyche: 'Dinosaurs Are Jesus Ponies' and other fun revelations

Thanks to Twitter (and Ed Yong), I just stumbled across "Google Psyche":

Great moments in Autocomplete, courtesy of Google search and collective consciousness

Google Psyche is an exploration of the stories that the world's Internet searches tell. The company's autocomplete algorithm predicts the word a random web searcher is most likely to type next, providing a statistical probe for our collective consciousness.

This week's offering is a search starting "Dinosaurs are...", which features (among other things) "Dinosaurs Are Jesus Ponies" at number 5.

I'm not entirely sure what this this tells us about our collective consciousness - it's just what people search a lot - and I really don't think that I would describe it as a "statistical probe" but it's still kind of interesting and fun. There must be a local factor in the Google search prediction algorithm, though, because the Jesus Ponies search does not appear in the top 5 for me:



I wonder if this says something about Americans! Of course, it could just be due to a famous quote that I am not aware of - according to the comments on the Google Psyche page, "Dinosaurs Were Made Up by the CIA to Discourage Time Travel" is a song by "Math the Band", which might account for number 3.

I tried it for "Cabbages of..." and was pleased to see "Doom" at number 2, although that might be just due to me lazily using the autocomplete to find my own homepage from time to time. I'm not sure what other people would get. Fourth on the list is very disturbing, though. The mind boggles.

The Cabbages of Doom: Kindle Edition out now!

My fictional folly is complete (for now) and The Cabbages of Doom is now available in a Kindle Edition too.

I thought it was going to be priced at £1.49 for the UK market but there seems to have been a glitch somewhere. I did find it a bit odd that the cheapest UK price allowed was lower than the USD or EUR prices. Oh well. If the extra 22p puts you off, the PDF and ePub versions are still only £1.44.

Over Christmas, I shall hopefully blog the full e-publishing experience. It's been interesting and I am sure I could do it better next time! (Content aside, that is.)

I eat waffles, therefore I waffle

I just changed my profile picture to this one of me eating a lovely Belgian waffle in Bruges and it got me thinking about food/verb homonyms - words that are food but also verbs. Like waffle. I like waffle. And, I like to waffle, as you (and my poor students) can tell.

But then I got thinking about other ones: cake, chip, chop, cream, fish, jam, juice, milk, toast... all yummy things. Sprout. Hmm. (Actually, I like sprouts.)

Some of these of course, are foods named after verbs. Chips, for example, are chips because they were chipped from potatoes. Likewise, chops were chopped and toast was toasted. Some are the other way round: you fish to get fish, milk to get milk and juice to get juice. Not so sure about cake, though. And back to waffle... Where does that come from?

Then we can cast the net wider with homophones: I drink wine, I whine; I eat meat, I meet; I eat a plum, I plumb. OK, so I might be scraping the barrel with that one. (I'm a bad plumber, clearly.) I'm sure I had some better ones when I started writing this post but my mind's gone blank. Oh well. Perhaps they will come back to me. In the meantime, I think I shall go and chock a lot.