Saaien Tist: 2007

What makes code beautiful?

Saw this webcast a couple of weeks ago where Marcel Molina explains the notion of beautiful code. And I really recommend anyone writing code to have a look at it (totally irrespective of the fact he uses a ruby example...). If you look at the progress bar of the presentation, it looks like it's really long, but only the first half is the actual presentation, followed by a lengthy discussion. (The last few minutes have a nice wrap-up by Chad Fowler.)

The talk is basically split into two parts: (a) what is beauty, and (b) how does that apply to coding?

What is beauty?

After going into the history of what philosophers like Plate, Rousseau and others found beautiful, Molina focusses on the three rules set out by Thomas Aquinas: proportion, integrity and clarity.

Nov

Named arguments in ruby

One of the main disadvantages of using ruby that I bump into is the absence of named arguments (or keyword parameters). That's no problem for methods taking just two or three arguments, but it does get confusing when you have to be able to pass more than that.

For example, the Bio::Graphics::Panel::Track::Feature#new method takes six arguments: the track it belongs to, a label, a type, the location, an array of subfeatures and a url. (Note: there's only four in the released version.

Oct

The state of bioruby (or: how can bioruby grow?)

A number of people asked me recently about the usability of ruby/bioruby and if it would be worthwhile for them to take the plunge and investigate bioruby more. So I thought writing up here would be a good idea...

First a disclaimer: this is my own personal view on bioruby, based on experiences in the last year-and-a-half. In addition, this is about the bioruby project, not the code or the people.

Let's first see what bioruby does.

Oct

Using rake to manage your software project

Do you have some of those projects where you have to be sure that you jump the same loops every time you edit some code? Take a look at the bio-graphics code. Every time I change anything in the code, I have to do the following things:

regenerate the RDoc documentationregenerate the ruby gemcheck SVN statusdo an SVN updateperform the SVN commitupload the new documentation to the websiteThat's a prime candidate for rake. Rake does the same as GNU make, which is dependency-based programming.

Sep

Bio::Graphics and rails

As a follow up to my post on Bio::Graphics, I tried integrating this library in a rails application. After all, you'd get your data either from a file (like GFF) or a database. And let me tell you: it took me just 30 minutes or so to get a proof-of-concept running. This included installing rails itself, creating the rails app, creating the database, loading dummy data, and doing the coding itself.

Sep

Graphics, genomics and ruby

Having known and used the Generic Genome Browser (aka gbrowse, see here) for years now, it occured to me a while ago that it should be o so simple to create the same functionality with a much easier setup if we could use ruby instead of perl.

Gbrowse depends on bioperl's Bio::Graphics module. Although gbrowse has been instrumental for many people's research, it does take a bit of work to get it installed. Apart from bioperl, it depends on Apache for showing the results in a browser.

Sep

ActiveRecord - all vs all relationships

Modeling genetics or genomics data presents its own challenges. One of the issues is that the actual definition of things change over time. A database system can only be based on the scientific knowledge at the time of conception. The prime example of course is the definition of a gene over the years. Before 1997, it was believed that the vast majority of these encoded proteins. As a result, 'genes' tables in databases typically had columns to store information on the start and stop codon.

Aug

A ruby API to the Ensembl database

"Joy to the world, lalaa la laaaa." I can finally announce that I've released the ruby API to the Ensembl core database under the bioruby-annex umbrella. Go here for the release.

What is it?

The Ensembl database stores genetic and genomic data on a variety of species: sequences of chromosomes and positions of features such as genes and polymorphisms. This data is browseable using their genome browser, but is also directly accessible if you connect to their mysql database.

Jul

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.

Saaien Tist

On data visualization, bioinformatics, quantified health and personal productivity