Delicious geohashes … mmmm … tagging *drool*

Since I got a new toy for Christmas, I’ve become interested in geolocation and the fun things you can do when you have an internet-connected GPS-enabled device in your pocket. I’m also a compulsive delicious tagger, so I quickly discovered the existing practice for geotagging delicious bookmarks.

Essentially, this seems to be: add the tag ‘geotagged‘, along with the tags ‘geo:lat=X.xxx‘ and ‘geo:lon=X.xxx‘, where the X.xxx‘s are the latitude and longtitude numbers that are likely to come straight out of your GPS, in decimal degrees (WGS84).

This is all very nice, but the problem with tags in this format is that there is no easy or efficient way to use them to retrieve all items tagged for a particular locality. Sure, if I’m standing right on top of the Eureka Tower at -37.821362,144.964213, I can search for tags geo:lat=-37.821362 and geo:lon=144.964213 to find all the geotagged links for that exact location, but what if I’m standing 50 metres across the street looking up at the tower and want to search for links near my current location ? Continue reading

Naming in molecular biology: get comfortable with meaninglessness !

I noticed an interesting post over on BoingBoing: “Comfort with meaninglessness the key to good programmers“. It outlines some research by Dehnadi and Bornat on attributes that can predict aptitude in computer programming. They conclude that a “deep comfort with meaninglessness” is an important predictor of programming aptitude.

I think comfort with meaninglessness is an important skill in studying biology (and probably other sciences too). Many times, during the description of a system, various acronyms are thrown about as labels for entities (or ‘actors’) in that system. An important skill of the scientist is being able to follow how all the actors in the system relate to each other, without necessarily knowing anything about the specific properties of those actors. There are lots of protein and gene names which often bear very little meaning relative to the biological entity that they label, and fixating on what ‘the name’ means simply distracts from the true nature of the entity.

Continue reading

That Science Blog Meme Thing Going Around

Something broke out of the picket-fence surrounding Nature Networks Blogs. I’ve never participated in a blog meme … but this one appealed to me simply because I liked the questions. I haven’t read anyone else’s answers yet, to avoid biasing my own.

1. What is your blog about?

I often ask myself this question. Being a scientist, I always feel like it should be about science, and the various biological systems I work with. I reality, it is about programming, bioinformatics, the web with the tiniest bit of structural biology thrown in. I used to blog about Linux related things occasionally, but I split that off into another blog (which gets 10 times more traffic :)).

Continue reading

Searching bioinformatic databases with YubNub

You may already be familiar with YubNub; it describes itself as “the social command line for the web”. Most commands consist of two (or more) words … one for the search engine, the other for the query.

For example, typing:

gg open science on friendfeed

into the YubNub search box searches Google for “open science on friendfeed“, via YubNub.

I thought I’d highlight a few life science- and bioinformatics-related YubNub commands I find myself using quite often in my day-to-day work. Some are commands I created, others someone else created. This is the beauty of YubNub … often someone has already made the ‘obvious’ command … it’s worth just trying to search with a command you expect to exist, since it often does.

Onward, with the list:

Continue reading

Synthetic Biology 4.0 : highlights and reflections

Update: The videos of the talks from Synthetic Biology 4.0 are here !

Around three weeks ago I attended the Synthetic Biology 4.0 meeting in Hong Kong, hosted by the Hong Kong University of Science and Technology. I’ve taken a little time to allow all the new and exciting ideas to sink in. I really enjoyed the meeting, and while it was a little short it was an effective way to quickly sample the current developments in synthetic biology, as it stands.

Continue reading