Bioinformatics

Mike the Mad Biologist

Category archives for Bioinformatics

Why Should Publishers Organize Science?

I found this post titled “What scientists really want from digital publishing“, and, after reading it, I’m pretty certain this scientist doesn’t want what’s offered. Before I get to the details, here’s what computer scientst Philip Bourne offers: “as a scientist I want an interaction with a publisher that does not begin when the scientific…

Gabe Rudy, blogging at our 2 snps, has a really good introduction to sequencing technology and its history. It’s worth the read, but I don’t entirely agree with the reason given for why ABI SOLiD lost out to Illumina: Coming to market at the same time, but seeming to have just missed the wave, was…

One of the exciting things about bacterial genomics in that, within a year, we’ll definitely be in the era of the $1,500 bacterial genome, although that’s probably an overestimate. This cost includes everything: labor, sequencing, genome assembly, and genome annotation. While sequencing is highly automated, and has been turned into a production process, akin to…

What Is a Bioinformaticist?

ScienceBlogling Sandra Porter asks a bunch of questions, including: What do you call a biologist who uses bioinformatics tools to do research, but doesn’t program? My snarky answer is: a biologist. Since I work at a genome center where I’m up to my eyeballs in computational biologists, bioinformaticists, and computational engineers (this is a good…

Should any data, not just genomic data, be held hostage by the grant award process? Hunh? Let me back up… By way of ScienceBlogling Daniel MacArthur, I came across this excellent post by David Dooling about, among other things, how different genome centers, based on size, have different release policies (seriously, read his post). Dooling…

I realize that the typical format for blogging is to find something that pisses you off and then rant about it, but I actually like the recent workshop report by NHGRI, “The Future of DNA Sequencing at the National Human Genome Research Institute.” (pdf file) While I’ll have more to say about the report overall,…

A recent article that examined the relationship between antibiotic use and antibiotic resistance in Finland made me realize one very sad fact: what is easy to do in Finland is nearly impossible in the U.S. because we lack a national healthcare system (note: I’m not talking about how healthcare is paid for which is an…

Eigenfactor and Carl Bergstrom Feature in Seed

It’s nice to see Carl Bergstrom, the driving force behind the Eigenfactor metric for measuring publication use, get written up in Seed magazine. Sez Bergstrom:

The Problem with Publication-Driven Science

Now, I realize with this title, lots of people are thinking that I’m trying to do away with scientific articles. Far from it. But the use of published articles as ‘scientific currency’ can retard the adoption of new breakthroughs. A recent personal experience is in order.

One of the things I find fascinating about the Weather Channel is that after watching it for a while, you actually start to worry about that cold front moving through some other part of the country. You become quite paranoid about things that won’t affect you. Well, I’ve got an even better way to drive…