Simon Cockell | Archive Uncategorized

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Stack Overflow, BioStar and – shock, horror – some code

Stack Overflow reached critical mass a few months ago now. The site gets upwards of 6 million unique visitors a month. The chances are, if you write code, you know it exists, and you’ve received some sort of help there, whether directly or by proxy. In its wake, Stack Overflow has spawned Stack Exchange, a question and answer platform that anyone can buy into, and set up a site. So there’s now Stack Overflow type sites for any number of topics.

Amongst these sites, there have been a couple of attempts to set up science Stack Exchanges (http://asksci.com/ & http://science.stackexchange.com/), but to my mind, science as a whole is not specific enough, even biology is probably too broad an area for Stack Exchange to work as a platform. As a result questions are too hand-wavy, and communities have not really seemed to build. The key to Stack Overflow’s success is that it has very tightly defined boundaries, only questions about programming are accepted, anything else is removed for being off-topic. The site’s creators even set up more sites, Super User, and Server Fault, to keep Stack Overflow on topic.

It seems, then, that bioinformatics is the perfect use case for Stack Exchange. A more narrow domain than science or biology, with an already web savvy community ready to coalesce around a useful focal point. Until recently, however, no one had made the site. Then a couple of weeks ago, http://biostar.stackexchange.com/ started to get some attention on Twitter and FriendFeed. It’s early days, but the site has made a good start, some interesting questions, with some good, intelligent, answers. My main concerns would be:

Not enough users, no critical mass achieved.
- The site seems to be gaining some traction, and getting more active by the day.
Not enough questions, no reason for users to keep coming back.
- This does remain an area for concern, but is also starting to pick up a little.
No financial backing, the site may disappear after the test period comes to an end.
- Stack Exchange is not a cheap platform, and a site like this will need funding to continue. However, the administrator, Istvan Albert, has insisted on the Google Group, set up for ‘meta’ discussion surrounding the site, that the site is funded for a year at least.

Finally, the real motivation for this post… A question on BioStar made me revisit some semi-abandoned code in order to post an answer, and I thought it was quite a nice snippet. About 15 lines of Python that utilises the UniProt ID Mapping service to automate protein ID conversion. I’ve stuck the code into a gist, and I thought I’d stick it up here too.

Posted via email from Simon’s posterous

Friday, March 12th, 2010 Uncategorized No Comments

A geeky selection of birthday books

“Beautiful Data”, “Coders at Work” and “xkcd volume 0″

Posted via web from Simon’s posterous

Monday, December 14th, 2009 Uncategorized No Comments

Randomness, statistics and understanding

So here I am, sitting in a statistics workshop, having finished all the exercises ahead of time, musing on how much easier all this stuff is once you understand where it all comes from. This made me think that I have found this workshop more understandable and simpler to tackle because I have pretty much finished reading a marvellous little book called ‘The Drunkard’s Walk’ by Leonard Mlodinow.

Photo from http://www.flickr.com/photos/sixmilliondollardan/3193613357/

Mlodinow aims to educate the reader about randomness and statistics, by way of history and illustrative example, and he succeeds admirably. The book is a walk through mathematics from the Greeks and Romans, by way of the renaissance, to Einstein and the modern day. Each important advance toward the modern day study of statistics is illustrated with excellent examples and anecdotes, many of them personal to the author. The Monty Hall problem, the anomoly of Jeanne Calment, who reverse-mortgaged her apartment to a 47 year old lawyer when she was 90, only to outlive him (and he died aged 77), even the author’s own (false) positive AIDS test makes for an intriguing case study, and illustrates the importance of understanding prior probabilities when reporting the results of a test.

The setting of all this stuff in context has really helped my brain with the basic concepts, and even without this current course, I feel like I’ve got a much better grip on statistics in general. A remarkable claim for a popular science book. I look forward to the remaining 30 or so pages.

Tags: book, randomness, Review, statistics