Forum:Bioinformatics analogies

Question

[melissachua90]

What analogies would you use to describe Bioinformatics?

Answer 1

[Pierre Lindenbaum]

Molecular biology is 90% moving small liquids from one tube to another. Computational biology is 90% file manipulation.

— Stephen Williams (@SvenAT) August 2, 2016

Answer 2

[Istvan Albert]

almost a decade ago brentp wrote:

I've been doing bioinformatics for about 10 years now.

I used to joke with a friend of mine that most of our work was converting between file formats.

We don't joke about that anymore.

Full post here:

• Very Bad Things

Answer 3

[ngarber]

I would argue that life is, in a sense, equivalent to information. What makes a cell, a cell? Surely it's not having a bunch of protein and nucleic acids in one place, because that would just be goop. Rather, a cell is defined as a kind of program that self-assembles, replicates, etc. In fact, over time, much of the cell's atoms are exchanged for other atoms from the environment as it consumes resources, so it's not the contents that defines the cell - it's the stable program that holds it together.

What is the program? It is based on a set of rules, like any computer program, and contains an operating system written on the DNA. The operating system (DNA) is then read and held in memory by transient mRNAs, just like how a computer operating system is held in memory (RAM) at startup. Programs and executed from memory by effectors - proteins - that perform computations based on specific biochemical rules. In fact, this is how neurons work - proteins interacting with each other to send and receive signals based on a chemical intermediary.

If we accept this analogy that a cell is effectively a biological computer, then it's not surprising that we can understand its function better by using other computers! In bioinformatics, our job is to dissect the operating system (DNA sequencing), probe the memory (RNA-seq), test which programs are running (proteomics), and so on. Effectively, a bioinformatician dissects a biological computer using a simpler silicon-based computer that runs on code we can understand.

[Istvan Albert]

the original definition of bioinformatics was indeed about information.

Amusingly the Wikipedia tries to pedantically correct the original meaning

https://en.wikipedia.org/wiki/Bioinformatics

it says:

Historically, the term bioinformatics did not mean what it means today. Paulien Hogeweg and Ben Hesper coined it in 1970 to refer to the study of information processes in biotic systems

then goes on to attempt to define bioinformatics in terms of sequence processing and gene expression analysis.

As we know more and more about Bioinformatics, we realize that the original definition was the correct one.