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. That 30 minutes was interrupted for a couple of hours, because I needed some advice from Kouhei Sutou, the author of rcairo, on how to write PNG images in memory instead of to a file.
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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.
7

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.
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Welcome
Hi there, and welcome to SaaienTist, a blog by me, for me and you. It started out long ago as a personal notebook to help me remind how to do things, but evolved to cover more opinionated posts as well. After a hiatus of 3 to 4 years (basically since I started my current position in Belgium), I resurrect it to help me organize my thoughts. It might or might not be useful to you.

Why "Saaien tist"? Because it's pronounced as 'scientist', and means 'boring bloke' in Flemish.
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