Saturday, 1 November 2014

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.)

Wednesday, 29 October 2014

Sculpture by the sea is back

We moved to Sydney just over a year ago and one of the first things we discovered was Sculpture by the sea 2013, an annual free public arts event in which one hundred or so artists create sculptures on the eastern coast from Bondi Beach to Tamarama Beach.

Even without the sculptures, the Coogee to Bondi coastal walk is an impressive piece of coastline and we are lucky to have it on our doorstep. The sculptures really add another dimension, especially the ones that make use of the terrain as part of the art. I’ve not yet seen all of the 2014 offerings, but some of my favourites have this element, including a small army of giant ants and some strange tentacled beasts, draped over the rocks.

Another thing I really like is the use of materials by some of the sculptures. The giant tentacular monster, for example, is made from thousands of bottle tops (left). There may well have been an environmental statement here too, about the amount of plastic (and plastic bottles specifically) that wash up on beaches. There were also some fantastic wooden birds made from old bits of furniture etc.

Another material that always seems popular is super shiny metal, which reflects the viewer, landscape and/or bits of the art itself in interesting ways. Last year, for example, there were some invisible dogs on the beach. This year, the sculptures included some shiny metal cylinders that mirrored flat discs into surprisingly three dimensional images.

It was a glorious weekend for the most part and so the coastal walk sections were predictably crammed with people. If you have the opportunity (as we did last year) to go off-peak, it is highly recommended. I’m already looking forward to going back and seeing what I missed the first time around. More photos on Google+.

Monday, 20 October 2014

Do we need a bioinformatics dead links database?

Keith Bradnam on his ACGT blog has recently highlighted the irksome issue of “link rot” - the unfortunate but all-to-common scenario in which a publication points to a URL that ceases to exist after an oft-too-brief time has elapsed. (In severe cases, before the paper is even published!)

Personally, I think that journals need to take a bigger responsibility in maintaining the integrity of their publications. Surely it is not beyond a big publishing house to have a bot that systematically checks their published links once a week and reports and errors? Authors could be notified and/or online manuscripts updated. In severe cases where the URL is critical to the paper, such as databases and webservers, lack of repair could even lead to retraction.

The problem goes beyond publications, however. For (sometimes mysterious) reasons of their own, even established biological resources quite often change their URLs too. For example, Pfam embeds the Wikipedia entry for a domain into their pages. I was browsing the globin page last week and clicked on a link to see the entry in Interpro, only to be greeted with:

Sorry, the requested URL has changed

The requested URL: http://www.ebi.ac.uk/interpro/IEntry/ac=IPR002338

has moved to

/interpro/entry/IPR002338;jsessionid=BB50E35E3DD96F6C83B7AD432B8E2E2A

You will automatically be redirected to the correct URL in a few seconds. Please update your bookmarks.

It redirected OK but I wonder how long it will be before that redirect itself disappears… and how many Wikipedia articles and database cross-references run the risk of breaking.

Perhaps we need a database where bioinformaticians can report, track, update and hopefully fix all these rotten links? In the meantime, if anyone spots any in my own webpages or papers, please let me know!

The perils of having a (soft) cat

Why Evolution is True posted this cartoon from lunarbaboon last week:

It’s never stopped me going to work but I’d be lying if I said that something like this (without the shoes) had not delayed me going to bed once or twice.

Monday, 13 October 2014

Every conference should be like ABiC 2014 (#ABiC14)

Last weekend, I attended the inaugural Australian Bioinformatics Conference (ABiC 2014) in Melbourne. (Twitter tag #ABiC14 so as not to be confused with the ABIC Foundation conference in California.) I’ve been to quite a few conferences in my time, including a fair few bioinformatics conferences. The latter (in my experience) are often quite dull affairs - good for meeting people and “networking” but not so good for interesting science beyond the invited keynote speakers.

Happily, ABiC14 went far beyond expectations. I signed up because it is important for me as a relative newbie to meet more Australian bioinformaticians. This was accomplished but was only the start of the positive experience of this conference. In fact, the conference was so good that I thought it worth posting its successful attributes/decisions as a model for future conferences (and reminder to myself should I organise one).

Here then, in approximate chronological order, are my top take-home quality attributes of ABiC 2014:

Organisation. The conference website was well organised and clear prior to the meeting. The program outline was available in good time, enabling planning, with abstracts etc. available in a single PDF. The only real improvement I can think of would be to have a printed program (just the outline, not full abstracts) provided upon arrival. However, because there were no last minute changes to the program, this turned out to be a moot point.

Coffee. Science in general, and bioinformatics specifically, is fuelled by coffee. The Aussies do coffee well and ABiC 2014 had the genius idea of a sponsored barista who made a decent cup of fresh coffee to order. I took advantage of this on arrival, which really set me up for the morning session and got the whole thing off to a great start.

Venue. The Royal Children’s Hospital was a great venue. Access by public transport was easy. The lecture theatre was comfortable and a good size. Eduroam provided free WiFi access (even if HTTP sites were unavailable for some reason). Coffee breaks, lunch, and poster sessions were near to the lecture theatre and promoted mingling.

Size. I’m not sure what the final number of delegates at ABiC 2014 was but for me it was the perfect number. (I would guess around 180+/-.) There were enough people for some interesting diversity, presentations and posters but not too many to actually get to chat to people and visit all the interesting posters.

Interesting Science! This is clearly one of the most important aspects of a good conference but sadly one that is often not achieved by a bioinformatics meeting (beyond the keynotes). I think there were several contributing factors to this. First, there were not too many talks and no parallel sessions. There were twenty talks in total, in six sessions of 3-4 talks of 10-50 mins each. Each session kicked off with an invited speaker. By keeping the quantity down, the quality of the talks - and stamina of the audience - was maintained at a very high level. I was expecting to “zone out” and struggle to maintain concentration a few times but I found my attention captured by each speaker. Talk quality was further enhanced by…

No published conference proceedings. Because of the large computer science community within bioinformatics, a lot of bioinformatics conferences have the submitted work published as papers in conference proceedings or a journal special issue. Even when the journal is a good one, this massively decreases the likelihood of getting interesting science, which will normally be either (a) published in a higher impact biology or general science journal, or (b) not yet be ready for publication. As a result, talks tend to be more technical and specialist… and boring. ABiC 2104 avoided this trap.

Food. You don’t go to a conference for the food but having tasty snacks at the breaks and at lunch does add to a general vibe of happiness and satisfaction.

Beer. Scientists and computer geeks are not always the most extrovert of individuals, and a little something to grease the wheels of social interaction never goes amiss. The ABiC committee went as far as to establish the beverage categories of choice with a pre-conference questionnaire. They gained extra brownie points from me for the presence of Fat Yak among the offerings.

Posters. This is largely a composite of the above points but the poster session was one of the better ones I have attended. For a start, the posters were up for the entire conference. It really bugs me when conferences do not do this and it all comes down to choice of venue - so well done ABiC for selecting a venue with this capacity. Furthermore, the poster location had great access - being a wide corridor - and was between the auditorium and the morning/afternoon drinks and snacks, maximising quality exposure. Furthermore, restricting the number of talks saved lots of interesting science for the posters!

Conference Dinner. If you are lucky, the conference dinner will be one of the best networking points of a conference, as your table represents a fairly captive audience with whom you have to interact. Nevertheless, conferences are generally charged to grants and researchers are on a budget, so it is frustrating to be forced to spend a load of cash on a meal that rarely lives up to the expectation of the price tag. ABiC 2014 took a pragmatic solution of booking out a restaurant and bar, and everyone paying for their own meal and drinks ordered off a standard single course menu. It worked really well. The food was good (but not excessive) as was the company. There was only one course but you never need more than that when there are morning and afternoon snacks in the breaks.

Timing. As far as I could tell, the talks generally seemed to stick to time, so coffee/lunch breaks were not truncated. Again, by keeping the number of talks (and talks per sessions) low, this was easier to achieve. Nonetheless, it's still something that is not achieved by all conferences. (I remember one conference in which my talk started 5 minutes after it was supposed to finish!)

Twitter. I’m a bit sporadic on Twitter at the best of times and not entirely convinced that live tweeting in a conference is not generally more of a distraction than a benefit - for those present, at least. However, I did enjoy having the #ABiC14 twitter feed open during the meeting and felt that it added to the sense of community. Of course, the aforementioned interest of the talks (and the smallish size of the meeting) limited the distraction.

As of the end of ABiC 2014, there was no plan for an ABiC 2015. I, for one, really hope that there is one - and that the organisers are able to stick to the same model.

Sunday, 5 October 2014

Wikipedia joker almost prescient as Rabbitohs win their first NRL Grand Final for over forty years

Congratulations to the South Sydney Rabbitohs, who have just won the Australian National Rugby League Grand Final 2014. The Rabbitohs are our local team, so we watched the game (on TV) - and it was a cracker!

Although I must confess that it was the first NRL game that I’ve watched properly (being more familiar with Union back in the UK & Ireland), I must also admit that I don’t think it will be my last. It's pretty brutal but very exciting.

I decided to do a bit of reading up on the Rabbitoh’s before the match and was surprised to see that Wikipedia already listed a Rabbitohs win! It was taken down at some point but I got a screen grab first (right). The final score was 30-6, so the jokester in question was only a couple of digits out!

The game started with a crunching tackle which broke the cheekbone of Bunnies’ hero and man-of-the-match (Clive Churchill Medal winner) Sam Burgess. Burgess went on to play the entire game with a broken cheekbone, reminiscent of their 1970 victory when the skipper played 70 minutes with a broken jaw! Tough game, tough players!

Thursday, 18 September 2014

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”.