BIOINFORMATICS AND THE INTERNET

Genome Technology Branch National Human Genome Research Institute National Institutes of Health Bethesda, Maryland 

Once the machines on a network have been connected to one another, there needs to be an unambiguous way to specify a single computer so that messages and files actually find their intended recipient. To accomplish this, all machines directly connected to the Internet have an IP number. IP addresses are unique, identifying one and only one machine. The IP address is made up of four numbers separated by periods for example, the IP address for the main file server at the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH) is 

Examples oe top-level domain names used outside the Untied States ca Canadian site 

Generic top-level domains proposed by lAHC firm Firms or businesses 

A complete listing of domain suffixes, including country codes, can be found at http //www.currents.net/ resources/directory/noframes/nf.domains.htnil. 

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Anonymous, Bioinformatics and the Effective Use of the Internet for Rapid Drug Discovery, Proceedings of IBC s International Conference held 3—4 March 1997, in San Diego, California, IBC, Southborough, MA, 1997. 

It is well known that the resources available on the Internet are in constant flux, with new sites appearing on a daily basis and established sites disappearing almost as frequently. This also holds true for the dedicated tools used in biochemical and biophysical studies. New tools are constantly becoming available, and established tools, obsolete. Such rapid change makes it difficult to stay current with the state-of-the-art technologies in the areas of bioinformatics and computational biochemistry and biophysics. 

The computer has become an essential tool in biochemical research. A computer may be used for the routine jobs of word processing and data collection and analysis. In addition, if a computer is connected to the Internet, then it may be used for biochemical literature searching, accessing information about nucleic acid and protein sequences, predicting protein structure, and seeking research methodology. In this experiment, students will be introduced to all of these skills in bioinformatics. 

The Internet resources have provided great impetus to an advancement of bioinformatics and computational biochemistry. They contribute greatly in the collection and dissemination of biochemical information. The Internet resources of biochemical interest and their uses to acquire biochemical information are described. 

Several databases for metabolic pathways are available currently from the Internet, and some major representatives are listed in Table 1. KEGG (Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan), BRENDA (Institute... 

In this paper we describe the basic design of a microarray gene expression database to help microarray users and their informatics teams set up their information services. The first version of the microarray database object model ArrayExpress, which is described here, was developed at the European Bioinformatics Institute (EBI) in collaboration with the German Cancer Research Centre (DKFZ) and posted on the Internet in November, 1999 (see (http //www.ebi.ac.uk/arrayexpress)). A relational database implementation maxd based on the ArrayExpress object model was conducted at the University of Manchester (http //bioinf.man.ac.uk/microarray/resources.html) and is widely used for microarray laboratory informatics support. 

As computer science and molecular biology merge in the new field of bioinformatics, the use of pattern expression syntax like regular expressions has been introduced to the life scientists. They see it in databases like PROSITE. They also see it in the Internet search engines like Google. 

Tavema supports the creation of workflows that utilize the large number of databases and computational tools that are publicly available to bioinformatics users on the Internet. 

Distribution of data Bioinformatics uses over 500 data resources and analysis tools found all over the Internet [5]. They often have Web interfaces through which biologists enter data for analysis, cut and paste results to new Web resources, or explore results through rich annotations with cross-links [21... 

As bioinformatics evolves and matures, more and more information beyond sequences of DNAs and amino acids is added to the database. The amount of data that can be generated is phenomenal. It is reported that the growth in bioinformatics data exceeded even the well-known Moore s Law for electronics, which states that the number of transistors on a chip doubles every 18 months. The Internet has played a central role in the growth of bioinformatics. It provides a comprehensive and easily accessible means for information storage, retrieval and analysis. 

The rescent advances made in bioinformatics as well as in proteomics are particularly impressive, and a number of proteomic databases dealing with plasma and/or blood cells are now available on the Internet (Table 1). 

An important factor in the progress of bioinformatics has been the constant increase in computer speed and memory capacity of desktop computers and the increasing sophistication of data processing techniques. The computation power of common personal computers has increased within 12 years approximately 100-fold in processor speed, 250-fold in RAM memory space and 500-fold or more in hard disk space, while the price has nearly halved. This enables acquisition, transformation, visuahsation and interpretation of large amounts of data at a fraction of the cost compared to 12 years ago. Presently, bioanalytical databases are also growing quickly in size and many databases are directly accessible via the Internet One of the first chemical databases to be placed on the Internet was the Brookha-ven protein data bank, which contains very valuable three-dimensional structural data of proteins. The primary resource for proteomics is the ExPASy (Expert Protein Analysis System) database, which is dedicated to the analysis of protein sequences and structures and contains a rapidly growing index of 2D-gel electrophoresis maps. Some primary biomolecular database resources compiled from spectroscopic data are given in Tab. 14.1. 

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