Naming conventions. You bump into them every single minute of the day. Naming new directories in your project folder, naming new tables in your database, ... Recently, the issue of naming convention came more to the foreground for me as I'm trying to write a ruby API to one of our databases (see later).

Two of the most-often-encountered naming schemes are CamelCase (ThisIsACamelCaseString) and snake_case (this_is_a_snake_case_string). And in the case of CamelCase: do you make the very first letter a capital or not? If I'm not mistaken, variables in java are often CamelCase, except the first letter (thisCouldBeAJavaVariable).

When thinking of names for directories and files (read also "Organizing yourself as a dry-lab scientist" on BioinformaticsZen), i.e.

An important part of genomics and genetics research is to know where your genes of interest lie on the genome and what the gene model looks like. In other words: to know where do the exons start and stop, what the UTR boundaries are, and where there are any polymorphisms in those genes. That's called genome annotation, that is.

With the sequencing of any new genome, the annotation of its genes is the logical next step.
2

Just bumped into a really nice O'Reilly blog article that combines two of the things I like to work with: GTD and ruby.

As a bioinformatician, I often have to handle quite a lot of data, which I tend to put into databases.
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The paper "Anatomy of data integration" by Brazhnik & Jones (J Biomed Inf 40:252-269 (2007)) gives a clear high-level overview of what is involved in the process of acquiring data from different sources and how to integrate them. Apart from talking about information pipelines and conceptual data models, it delves deeper into the concept of types of data elements (DEs). It really all speaks for itself, but it's nice to be able to name things in a meaningful way.
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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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