Bioinformatics FAQ (Frequently Asked Questions) - What is bioinformatics

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(Continued from previous part...)

The span of academic cheminformatics is wide and is exemplified by the interests of the cheminiformatics groups at the Centre for Molecular and Biomolecular Informatics at the University of Nijmegen in the Netherlands. These interests include:

• Synthesis Planning
• Reaction and Structure Retrieval
• 3-D Structure Retrieval
• Modelling
• Computational Chemistry
• Visualisation Tools and Utilities

Trinity University's Cheminformatics Web page, for another example, concerns itself with cheminformatics as the use of the Internet in chemistry.

What is Genomics?

Genomics is a field which existed before the completion of the sequences of genomes, but in the crudest of forms, for example the oft-re-referenced estimate of 100 000 genes in the human genome derived from a(n) (in)famous piece of "back of an envelope" genomics, guessing the weight of chromosomes and the density of the genes they bear. Genomics is any attempt to analyze or compare the entire genetic complement of a species or species (plural). It is, of course possible to compare genomes by comparing more-or-less representative subsets of genes within genomes.

What is Mathematical Biology?

Mathematical biology is easier to distinguish from bioinformatics than computational biology. Mathematical biology also tackles biological problems, but the methods it uses to tackle them need not be numerical and need not be implemented in software or hardware. Indeed, such methods need not "solve" anything; in mathematical biology it would be considered reasonable to publish a result which merely establishes that a biological problem belongs to a particular general class.

The distinction between bioinformatics and mathematical biology was illuminated by an email I received from Alex Kasman at the College of Charleston. According to his working definition, he distinguished bioinformatics which (under the tight definition at least)...

"...seems to focus almost exclusively on specific algorithms that can be applied to large molecular biological data sets..."

...from mathematical biology which...

"...includes things of theoretical interest which are not necessarily algorithmic, not necessarily molecular in nature, and are not necessarily useful in analyzing collected data."

What is Proteomics?

A recent review on proteomics in the journal Nature defined the field this way:

"The term proteome was first coined to describe the set of proteins encoded by the genome1. The study of the proteome, called proteomics, now evokes not only all the proteins in any given cell, but also the set of all protein isoforms and modifications, the interactions between them, the structural description of proteins and their higher-order complexes, and for that matter almost everything 'post-genomic'."

Michael J.Dunn, the Editor-in-Chief of Proteomics defines the "proteome" as:

"the PROTEin complement of the genOME"

and proteomics to be concerned with:

"qualitative and quantitative studies of gene expression at the level of the functional proteins themselves"

that is:

"an interface between protein biochemistry and molecular biology"

Characterizing the many tens of thousands of proteins expressed in a given cell type at a given time---whether measuring their molecular weights or isoelectric points, identifying their ligands or determining their structures---involves the storage and comparison of vast numbers of data. Inevitably this requires bioinformatics. Here is a constructively skeptical review by Lukas Huber.

(Continued on next part...)

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