Saaien Tist: July 2007

ActiveRecord and mysql: show my databases

Working on a ruby API for the Ensembl databases, I bumped into the issue of having to connect to a database without knowing its name.

The ensembl database server hosts databases for each species. Every two months or so, there's a new release which means a new database for every single species. To see what databases are there, you can login to the ensembl server with mysql:

mysql -h ensembldb.ensembl.org -u anonymous

(for more information, see here).

Jul

How do you process literature?

A quick glance at the side of my desk reveals two stacks of manuscripts to read; each stack about 20cm high. Sounds familiar? There seems to be a major task in front of me to process all that.

First thing to do is to identify what caused those piles in the first place. The answer: no system that I'm satisfied with for reference management. Of course, there is software like Reference Manager and EndNote as well as websites like Connotea and CiteULike.

Jul

Documenting one-off parsers

A lot of day-to-day work consists of parsing data files to transform the contents from one format into another or to create statistics. However, when you have to get back to those scripts at a later stage - you need something similar in another project or you notice that something along the way must have gone horribly wrong - it can often be quite hard to figure out what the script actually did. Having meaningless script filenames like ParseBlast.rb doesn't help either.

Jul

A choice of databases, or PostGres vs SQLite

When managing data in bioinformatics, one of the main tools you use is databases to store the stuff. In many cases, flatfiles are sufficient, but sometimes you need the flexibility and reliance of a nice relational database. (Note: Excel is not a database). Actually, in quite a few cases it does make sense to use flat text files instead of databases, but that's the subject of another post.

Jul

Bioinformatics and labbooks

What I've really struggled with in the first years after I ended up in bioinformatics (still in denial back then), was how to record what I'd done. Researchers in a wet-lab environment typically use a labbook in which they write down what protocols they used for an experiment, together with the results and nice pictures of their PCR electrophoresis gels. This is a bit more difficult for bioinformaticians.

Jul

Six months of Getting Things Done

It's the start of July and about 6 months after I started implementing the Getting Things Done meme. And, man, did it change things... In this post, I'll share some of my experiences and the obstacles I encountered.

What is that Getting Things Done already?

I'm not going to explain the whole thing here. There are better resources for that (for a list of URLs, see the bottom of this post). Most importantly: get the book "Getting Things Done: The Art of Stress-Free Productivity" by David Allen.