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BioStar users update: using mechanize to fetch user IP addresses
In my previous post I outlined a clumsy, manual method to retrieve user IP addresses from BioStar, using Javascript. Jukka left a helpful comment, explaining how to send an authentication cookie to a...
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How open source and BioStar saved a project
This is the story of how an open source project and a science communication tool combined to save the day. 1. November 2nd 2010 I receive an email from colleagues at my previous workplace. They are...
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Real bioinformaticians write code
A lot of questions at BioStar begin along these lines: Where can I find…? I am looking for a resource…? Is there some database…? I tweeted some concerns about this: Many #biostar questions begin “I am...
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New publication: analysis of large protein assemblies in macrophage cytoplasm
First for 2011: Proteomic and electron microscopy survey of large assemblies in macrophage cytoplasm. Maco, B., Ross I.L., Landsberg, M., Mouradov, D., Saunders, N.F.W., Hankamer, B. and Kobe, B....
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Popular topics at the BioStar Q&A site
Which topics are the most popular at the BioStar bioinformatics Q&A site? One source of data is the tags used for questions. Tags are somewhat arbitrary of course, but fortunately BioStar has quite...
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Boring, monotonous day-to-day tasks? That’s synonymous with bioinformatics.
In response to this question, I can only point out that J.C.R. Licklider figured it out over 50 years ago: Despite the fact that there is a voluminous literature on thinking and problem solving,...
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Proteins in the PDB that differ by one amino acid
A question at BioStar: how to “return all pdb ids to a given one that differ only by one amino acid”? My answer began: “I think it is not too much work to craft a solution using a few tools”, followed...
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How to: remember that you once knew how to parse KEGG
Recently, someone asked me if I could generate a list of genes associated with a particular pathway. Sure, I said and hacked together some rather nasty code in R which, given a KEGG pathway identifier,...
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A minor update to my “apply functions” post
One of my more popular posts is A brief introduction to “apply” in R. Come August, it will be four years old. Technology moves on, old blog posts do not. So: thanks to BioStar user zx8754 for pointing...
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Create your own gene IDs! No wait. Don’t.
Here’s a new way to abuse biological information: take a list of gene IDs and use them to create a completely fictitious, but very convincing set of microarray probeset IDs. This one begins with a...
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