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:

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Setting up NCBI wwwblast on Ubuntu 8.04 (Hardy), Apache 2

Recently I needed to install NCBI wwwblast on my local workstation to enable some software that needed to interface with BLAST via the web service. It was straightforward to install, but I took some notes, because there were a few changes required with respect to the official wwwblast documentation at NCBI. These instructions are for Ubuntu 8.04, but probably will work with many recent flavours of Debian.
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Mako templates in Google App Engine: seems to work for me

For some reason which I can’t really articulate, I’m not a huge fan of Django templating. I’d actually prefer to use Genshi with Google App Engine, but I need to wait until all the kinks are ironed out, since as far as I can tell it’s not quite working painlessly yet. Another templating option is Mako, which I’ve barely used, but I still prefer to Django templates. One nice thing about Mako: it’s faster than most Python templating engines out there. So, here’s a quickie on how I got Mako working with Google App Engine. It wasn’t tricky at all, but I thought I’d document it anyway.

Checkout Mako from SVN and copy the directory mako/lib/mako to the path of your application, eg, on Linux:

$ cp -r mako/lib/mako myapp

(where myapp is the directory that your GAE app lives in).

In your app, obviously you’ll need to import some parts of mako:

from mako.template import Template

Then, whenever you want to render a template as output (say, at the end of a ‘get’ or ‘post’ method .. see the GAE templating example for some context), call something like:

# a dictionary of variables to send to the template namespace
foo, bar = "some", "enthralling text"
template_values = {
  ‘some_foo’: foo,
  ‘some_bar’: bar

# index.mako is the template file in our GAE app directory
path = os.path.join(os.path.dirname(__file__), ‘index.mako’)
# make a new template instance
templ = Template(filename=path)
# unpack the dictionary to become keyword arguments and render

An example of some template text that could go into index.mako could be:

<html><body>${some_foo} likes the ${some_bar}<br/></body></html>

One possible modification: I need to look into it, but defining your Template class (eg templ in the example above) in the main() function (maybe as a global) rather than instantiating it every time it is rendered would probably give better performance.