Bio Informatics

Well they'll clone you when you're try'na be so good >sounds of 2 partiers< And they'll clone you just like they said they would >sounds of 4 partiers< And they'll clone you when you're drivin' in your car >sounds of 8 partiers< And they'll clone you when you're playin' your guitar >sounds of 16 partiers< But I would not feel so all alone >sounds of 32 partiers< Eeeeverybody must get cloned

Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving business with a questionable basis in science. Genome sequencing projects are producing vast amounts of poorly organized, error-ridden, and mostly jumbled biological data for many different organisms, and, increasingly, storing these data in public databases. Such biological databases are growing exponentially, along with the biological jargon-base. It's impossible for even the most zealous researcher to understand the different experimental ontologies or stay on top of necessary information in the field even with the aid of modern computer-based tools. BioInformatics is failing horribly in building new tools. It's all too dimensional, too complex, and too dynamic.

But if you want an arbitrary projection that will support your pet clinical theory or help you publish and get cited to avoid perishing, have we got a deal for you!

More on the tools angle: Bioinformatics provides tools for storing, analyzing, mining and visualizing the huge amount of scientific data currently being generated. Another way to look at it is doing biology through computers. -- AngsumanChakraborty

I recently met with a group of cancer researchers. As they put it, until recently, they had thousands of patients and collected a few signals: blood pressure, height, weight... With the rise of new technologies, they have dozens of patients (for each area of research) and analyze millions of signals. They agreed to call it "data fishing".

Q: There are those who have collected measurements of old bones to determine that America was first populated by Pacifics, then Asian Caucasians, then Mongolians. They did it by statistically analyzing many sets of bone feature measurements. Is this an example of BioInformatics? or just plain old Biometrics?

A: It's biometrics. Bioinformatics is more the use of computational power to determine previously unsuspected relationships. For example, you have no idea what gene does process X in humans, but you have five different proteins from organsisms a, b, c, d, and e that do it. You computationally extract the structurally similar 3-dimensional geometry based on the sequences of the five known proteins, and scan the human genome database for sequences that could form a similar geometry. Essentially bioinformatics is more than just biostatistics.

What does this mean? A geneticist is sitting next to me, gainfully employed by a leading biotechnology concern, who is doing what he is attempting to describe on a daily basis. Her answer to this is "This guy doesn't know what he is talking about". The NIH says that BioInformatics is "Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data." (http://grants.nih.gov/grants/bistic/bistic.cfm).

Another definition is at http://www.biology.gatech.edu/bioinformatics/whatis.html -- "Bioinformatics is an integration of mathematical, statistical and computer methods to analyze biological, biochemical and biophysical data."

I find that many of these terms are more bioscience buzzwords than words with well-defined, or even generally agreed-upon, meaning. For example, there is a lot of talk about things like "functional genomics" these days. I have no idea what that means. "Bioinformatics" is another such example - is this different from "computational biology"? -- AndyPierce

I read through these links, in particular the NIH link above. It seems to me like the distinction that is made there, and in general, goes something like this: that bioinformatics is to computational biology as information technology is to computer science. That is, bioinformatics tends to refer to the ugly, practical details of dealing with biological data in the real world, whereas computational biology is more theoretical, abstract, less practical. Or, to put it more cynically, people who do bioinformatics tend to be people who have some data and just want to analyze it, to get some useful answers, whereas people who do computational biology are just looking for excuses to think up clever algorithms. -- JosephDale

The OpenBioInformaticsFoundation? promotes the development of OpenSource software for BioInformatics. Some of the projects they support and sponsor are BioPerl, BioPython, BioJava? and BioCorba?. See http://www.open-bio.org/

"There are those who have collected measurements of old bones to determine that America was first populated by Pacifics, then Asian Caucasians, then Mongolians."

Can you point to some references for this? I have heard the stuff about KennewickMan?, but this about Pacifics is new to me. -- PeteHardie

The "who was the first American" debate is as old as the hills. But my reference was a PbsNova episode. -- PhlIp

CategoryBiology