Bioinformatics FAQ (Frequently Asked Questions) - What is bioinformatics

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"New" bioinformatics

The greatest achievement of bioinformatics methods, the Human Genome Project, is currently being completed. Because of this the nature and priorities of bioinformatics research and applications are changing. People often talk portentously of our living in the " post-genomic" era. My personal view is that this will affect bioinformatics in several ways:

• Now we possess multiple whole genomes we can look for differences and similarities between all the genes of multiple species. From such studies we can draw particular conclusions about species and general ones about evolution. This kind of science is often referred to as comparative genomics.
• There are now technologies designed to measure the relative number of copies of a genetic message (levels of gene expression) at different stages in development or disease or in different tissues. Such technologies, such as DNA microarrays will grow in importance.
• Other, more direct, large-scale ways of identifying gene functions and associations (for example yeast two-hybrid methods) will grow in significance and with them the accompanying bioinformatics of functional genomics.
• There will be a general shift in emphasis (of sequence analysis especially) from genes themselves to gene products. This will lead to:
  • attempts to catalogue the activities and characterize interactions between all gene products (in humans): proteomics ).
  • attempts to crystallize and or predict the structures of all proteins (in humans): structural genomics.
  • fewer DNA double-helices in bad sci-fi movies.
• What some people refer to as research or medical informatics, the management of all biomedical experimental data associated with particular molecules or patients---from mass spectroscopy, to in vitro assays to clinical side-effects---will move from the concern of those working in drug company and hospital I.T. (information technology) into the mainstream of cell and molecular biology and migrate from the commercial and clinical to academic sectors.

Definitions of Fields Related to Bioinformatics

What is Biophysics?

Molecular biology itself grew out of biophysics.The British Biophysical Society defines biophysics as:

"an interdisciplinary field which applies techniques from the physical sciences to understanding biological structure and function"

Mike Goodrich wrote to ask what the status of biophysics was given the definition of computational biology submitted by Paul Schulte (below). A recent article in The Scientist [free registration required] dealt with this question---thanks to Jo Wixon (Managing Editor of Comparative and Functional Genomics) for the reference.

What is Computational Biology?

Computational biologists might object (please do), but, I find that people use "computational biology" when discussing that subset of bioinformatics (in the broadest sense) closest to the field of classical general biology.

Computational biologists interest themselves more with evolutionary, population and theoretical biology rather than cell and molecular biomedicine. It is inevitable that molecular biology is profoundly important in computational biology, but it is certainly not what computational biology is all about (see next paragraph). In these areas of computational biology it seems that computational biologists have tended to prefer statistical models for biological phenomena over physico-chemical ones. This is often wise...

One computational biologist (Paul J Schulte) did object to the above and makes the entirely valid point that this definition derives from a popular use of the term, rather than a correct one. Paul works on water flow in plant cells. He points out that biological fluid dynamics is a field of computational biology in itself. He argues that this, and any application of computing to biology, can be described as "computational biology" (see also the "loose" definition of bioinformatics below). Where we disagree, perhaps, is in the conclusion he draws from this---which I reproduce in full:

"Computational biology is not a "field", but an "approach" involving the use of computers to study biological processes and hence it is an area as diverse as biology itself."

Richard Durbin, Head of Informatics at the Wellcome Trust Sanger Institute, expressed an interesting opinion on this distinction in an interview:

"I do not think all biological computing is bioinformatics, e.g. mathematical modelling is not bioinformatics, even when connected with biology-related problems. In my opinion, bioinformatics has to do with management and the subsequent use of biological information, particular genetic information."

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