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Bioinformatics

A leading application in which search, analysis, and visualization are intimately linked into a comprehensive computational environment under a Web browser is the Biology Workbench. The Biology Workbench provides a point-and-click access to all the leading biology molecular sequence and structure databases integrated with analysis and visualization tools. The Workbench architecture is a new way of dealing with information on the Web and was so recognized by a patent awarded on January 12, 1999.

To understand the educational significance of the Workbench, it is necessary to consider the scientific context. The raw material of biology is information, the results of experiments in the laboratory and observatoins in the field. The science of biology is all about constructing meaning from the information. In the last couple of decades, an enormous new category of information has become available about living systems. An array of technical revolutions in molecular biology, still ongoing, have made it possible to get enormous amounts of information about the sequences of amino acids in proteins and the sequences of bases in nucleic acids. To construct meaning from the sequence information, the array of computer techniques called bioinformatics has been developed. To understand the basic idea of bioinformatics, one might think of a written language. The text you are reading consists of a series of letters, words, sentences, and paragraphs. If you did not know the meanings of the words and the rules of the language, this page would just be a collection of meaningless symbols. Similarly, the first time scientists saw gene and protein sequences, they saw a string of symbols with no clear meaning in terms of biological function. But now, bioinformatics is showing us many things about what sequences mean. Using bioinformatics, sequences are being used to reveal relationships among different life forms that we could not find out any other way. Bioinformatics is revealing the rules and meaning of a language that is new to human beings but in fact is a billion years old - the Language of Life.

Bioinformatics is not a separate area of study in biology. Rather, the importance of bioinformatics to biology is that it adds value and new dimensions to everything else that biologists do. Consider for example structural biology - the determination of protein structures by x-ray crystallography or nuclear magnetic resonance spectroscopy. Because of bioinformatics analysis of sequences, when one determines the structure of one protein, one has a very good idea of the structure of many related molecules. For example, the first structure of a class of proteins called potassium channels was determined last year. These proteins selectively permit the passage of potassium ions accross cell membranes for modulation of electrical signals and maintenance of appropriate ionic environments inside and outside ceslls. Because of the ability bioinformatics gives us to compare sequences from various cells, tissues, and organisms, knowledge of the one known structure can be used to provide insights into the structural correlates of ionic selectivity, permeability regulation, toxin sensitivity, etc., of potassium channels from all forms of life. Potassium channels are just one example; bioinformatics multiplies many-fold the insights obtainable from any biomolecular structure determination. This knowledge is not only useful for basic knowledge in biology. It also pertains to such practical considerations as drug design, understanding the mechanisms of action of environmental pollutants, and understanding the mechanisms of a plethora of diseases such as cancer, sickle-cell disease, cystic fibrosis, etc. There is always value to understanding the molecular basis of disease, and bioinfirmatics always multiplies the insights obtainable from any particular molecular biology experimental information. Today, the vast majority of research papers published in molecular biology have a bioinformatics component in which the sequence of the molecule being studied is compared and contrasted with the sequences of related molecules to extend and generalize the insights directly obtainable from experiment.


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