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2011 March 20

Real bioinformaticians write code

Filed under: Uncategorized — gasstationwithoutpumps @ 22:32
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The What You’re Doing Is Rather Desperate blog has a post Real bioinformaticians write code, which makes the point that bioinformaticians have to program.  It will never be the case that every interesting question can be answered by applying a pre-existing tool. I find myself writing code a lot, even when there are tools or packages that supposedly do the job for me.  Quite often, I find that the existing tools only do 80% of the job I need, and adding the extra 20% of functionality is more work than starting over from scratch.  That is not always the case, though, and I do appreciate well-written tools and packages when I can find them.

I used to do most of my programming in large systems I wrote in C++, but lately I find myself doing more rapid prototyping in Python, as it is easier for doing small programs in, and there are some nice general-purpose packages that are easy to use (like NumPy for numerical work).

The post was a response to the frequent form of request on BioStar: “I’m looking for a resource … “, which usually has one of two answers: “Let me Google that for you” or “you’ll have to write a program to do that yourself”.  If you do have a good bioinformatics question, the BioStar website can be a good place to get it answered, though.

One of the comments on the original blog post points to BioMart, an open-source data management system for biologists, for those looking for some of the standard data handling and query stuff.  I’ve never used the tool, as I almost always have questions that require scanning entire data sets, not ones that can be answered by single-point queries, as BioMart is designed for.

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