mrcreek: Pikaia, a distant relative (pic#265175)
[personal profile] mrcreek2010-05-14 01:08 am

bioinformatics in fiction?

I am looking for good examples of bioinformatics in fiction. Biotechnology and genetics are major themes in stories ranging from science fiction to crime thrillers. Most of the time, though, either the focus is on cloning or modifying DNA rather than interpreting it, or else the part where DNA is compared to a database is mentioned in a throwaway sentence but there is no discussion of how it was analyzed. Even though bioinformatics is complicated, there is no reason why parts of it couldn't be explained to a lay audience. I have easily followed plenty of plots, from Sherlock Holmes to Contact to the Da Vinci Code, which revolve around characters figuring things using fields of study in which I had very little prior knowledge.

Here are a few examples I can think of so far (I haven't read any of these in a while, so my summaries might be slightly off):

Darwin's Radio by Bear. Studies of endogenous viruses in the modern human genome and in Neandertal DNA play a pivotal role in the plot.

Relic by Preston and Child. In at least one scene, a sassy computer program talks a researcher through the process of taxonomically identifying the source(s) of a DNA sample.

Jurassic Park by Crichton. Although the main event is of course cloning and minor genetic modification, the book does a fairly good job explaining how the scientists made sense of dinosaur DNA.

Please help me think of more. Movies and TV shows are okay, too, although it's usually possible to fit more scientific details into novels or short stories. I'm definitely interested in amateur fiction, also; give me the links.
foxfirefey: Look at this wee octopus! LOOK AT IT! (squee)
[personal profile] foxfirefey2009-12-31 02:32 pm
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Zinc Fingers Could Be Key to Reviving Gene Therapy - NYTimes.com

In New Way to Edit DNA, Hope for Treating Disease

I give data our lab processes to Sangamo sometimes! (Although I have no way of knowing if it's involved in this particular aspect.)
foxfirefey: Fox stealing an egg. (Default)
[personal profile] foxfirefey2009-12-22 06:05 pm
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O'Reilly's Bioinformatics for Python: a disappointment on first glance

I got really excited when I saw Bioinformatics Programming Using Python pop up on Safari O'Reilly, only to get kind of disappointed at first glance. At first I thought it would by a Pythonic version of the classics like Beginning Perl for Bioinformatics. But, it doesn't have any mention at all of BioPython, it seems, not even as a footnote.

Now I'm left wondering why not. I know that BioPerl is still more expansive, but is BioPython so lacking that it doesn't even merit a mention? That's a very sobering thing to think about, as somebody who's been really enjoying using Python over Perl lately.

In any case, this book mainly seems to center over basic language concepts, which is sad in some ways, because many of the examples are doing things that I imagine are "reinventing the wheel" if you're using a library like BioPython. Reinventing the wheel for learning has its merits, but it's not very useful to someone like me, who would find a primer that included an introduction into a powerful library that takes care of some of the drudge work more useful.

It's possible that this book is more useful (to people of my type) than my skimming indicates, but unfortunately I probably won't delve into it to find out.
foxfirefey: Fox stealing an egg. (mischief)
[personal profile] foxfirefey2009-12-21 11:38 pm
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Gel electrophoresis cookies

Got this link from [personal profile] azurelunatic! Not So Humble Pie: Science Cookies: Gel Eletrophoresis. Not the most serious of topics, but soon I hope to post on a project involving SVMs.
yvi: Kaylee half-smiling, looking very pretty (Default)
[personal profile] yvi2009-10-09 08:19 pm

Intro post?

Let's have the standard who are you and why are you here round, shall we? :)