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A program (TAXOKEY.EXE), requiring only a few keystrokes to use, is described as a universal taxonomic key in the identification of plant and animal species by IBM-compatible personal computers. A DOS text file serves as the database for a key that can be dichotomous or with multiple choices. TAXOKEY can optionally display colour or monochrome screen pictures to illustrate the keys. Additional programs are described that are used to make the keys and check for errors, as well as convert .PCX graphic images for use with TAXOKEY. A second text file can be searched by TAXOKEY for information on particular species descriptions, notes and references.

Algorithms for simulating the response of a benthic animal community and several abiotic environmental variables to organic pollution are described. An IBM PC compatible computer program incorporating these methods has been written. The program simulates the abundance response of 23 species, the redox potential depth profile and several other sediment variables at any distance from a point source of pollution. The program has been designed as a teaching tool and examples of its use to study pollution biology and biometrics are given.

MetaModel is a user-friendly program for calculating steady-state fluxes and metabolite concentrations of metabolic systems on the IBM PC and compatible computers. For any steady state that is obtained, one can then calculate a matrix of elasticity coefficients at that steady state, or a matrix of control and response coefficients. It thus offers a simple way to calculate the control structure of a pathway: it provides not only an educational tool that allows the student to verify empirically the classic summation relationships of metabolic control analysis but also a research tool for addressing 'what if?' questions about the behaviour of metabolic systems. Results can not only be printed or stored in a file, but can also be written to a special file that can be read by popular spreadsheet programs, thereby giving access to rapid, flexible and powerful methods for subsequent analysis and plotting of these results.

A computer program, coded in QuickBASIC ® language, is used to make a non-redundant list of references, in alphabetical order, that are found in a scientific manuscript (formatted as a DOS text file). The program can extract either direct or indirect citations as in the following : Byers (1983a, b, 1984) and Miller and Keen, 1960; Byers et l., 1984; Byers 1984) An IBM-compatible personal computer is required to run the executable program

TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists. Some phylogeny programs, such as PAUP (Swofford, 1993) and MacClade (Maddison and Maddison, 1992) already provide excellent tree drawing and printing facilities, however at present these programs are restricted to Apple Macintosh computers. Furthermore, they require the user to load a data set before any trees can be displayed which is inconvenient if the user simply wants to view the trees. More portable programs, such as DRAWGRAM and DRAWTREE in the PHYLIP package (Felsenstein, 1993) can run on both MacOS and Windows computers, but make little, if any use of the graphical interface features available under those operating systems. TreeView runs as a native application on either MacOS or Windows computers, enables the user to use the standard fonts installed on their machine, their printer, and supports the relevant native graphics format (PICT and Windows metafile) for either creating graphics files or pasting pictures to other applications via the clipboard. The program also supports standard file operations, such as 'drag and drop' whereby dragging a file's icon onto the program opens that file. TreeView can read a range of tree file formats (see below) and can display trees in a range of styles (Fig. 1). Additional information, such as edge lengths and internal node labels can also be displayed. The order of the terminal taxa in the tree can be altered, and the tree can be rerooted. If the tree file contains more than one tree the user can view each tree in turn. The program can also save trees in a variety of file formats, so that it can be used to move trees between programs that use different file formats.

GelMetric employs a 2-D digitizer to determine band and loading well positions, then constructs a calibration curve, calculates unknown molecular sizes, and prints the calibration curve and a tubular summary of the results. The user is guided through steps in which gel and lane headings are entered and in which well, band and mobility standard positions are marked

An IBM-compatible package for asynchronous communication with Perkin-Elmer fluorimeters is described. Data are displayed graphically and stored on diskette. They can be re-called for various types of analysis, and the results are sent to the screen or a compatible matrix printer

An algorithm to simulate DNA sequence evolution under a general stochastic model, including as particular cases all the previously used schemes of nucleotide substitution, is described. The stimulation is carried out on finite, variable length, DNA sequences through a strict stochastic process, according to the particular substitution rates imposed by each scheme. Five FORTRAN programs, running on an IBM PC and compatibles, carry out all the tasks needed for the simulation. They are menu driven and interfaced to the system through a principal menu. All sequence data files used and generated by the SDSE package conform to the standard GenBank database format, thus allowing the use of any sequence retrieved from this databank, as well as the application of other packages to analyse, manipulate or retrieve stimulated sequences.

With the advent of increasingly integrated, powerful and inexpensive digital electronics, relatively powerful computers have become available to the general public. Along with this technological boom there has been a concomitant increase in the availability of over-the-counter software packages which can be used by research scientists for program development. In the past, the development of computer programs for the collection of large amounts of time-based data was expensive and time consuming; however, the introduction of the current generation of 16-bit microcomputers and associated hardware and software packages has enabled investigators with only a rudimentary knowledge of computers and interfacing to begin to design programs. The schemes and algorithms, developed using BASICA on an IBM-Personal Computer, which are described in this article can serve other investigators as models for the assembly of their own programs for the collection, manipulation and plotting of time-based data. The incorporation of inexpensive computer graphics hardware and software, which provided a simple solution to the problem of analysis and presentation of large amounts of data, will also be discussed.

A manual integration system for the analysis of chromatographic data is described. The analog output produced by an HPLC absorbance monitor is passed to a non-inverting signal amplifier. This amplified signal is sent to an IBM PC where an analog to digital converter is used to digitize the data. A set of six computer programs which collect, store and analyze these data are presented. This system was used to analyze the nucleotide content of the anaerobic organism Clostridium acetobutylicum by strong anion-exchange HPLC.

We have developed a new algorithm 'Complete sentences compatibility' (CSC) which uses single and double digestion fragments to rapidly determine restriction maps of circular DNA. From possible combinations of fragments of each simple digestion, which we call 'sentences of decomposition', we construct a restriction map which combines the sentences while taking into account compatibility rules. The algorithm can also deal with experimental errors of fragment weight and can suggest solutions that account for non-readable bands (fragments of zero length or multiple bands) on the gel. Because experiments using pairs of restrictive enzymes often result in multiple solutions, a complementary algorithm tries to reduce the number of proposed solutions by establishing consensus maps. The restriction map construction algorithm was tested on real cases, some containing more than fifteen fragments. Execution times range from 1-10 s on an IBM PC compatible microcomputer.

A branch and bound algorithm is described for searching rapidly for minimal length trees from biological data. The algorithm adds characters one at a time, rather than adding taxa, as in previous branch and bound methods. The algorithm has been programmed and is available from the authors. A worked example is given with 33 characters and 15 taxa. About 8 x 10(12) binary trees are possible with 15 taxa but the branch and bound program finds the minimal tree in less than 5 min on an IBM PC.

A BASIC program to assist the instruction of steady-state enzyme kinetics has been developed for the IBM PC microcomputer. Its purpose is to simulate laboratory experiments in order to minimize the time required to obtain kinetic data from which students deduce kinetic mechanisms and determine kinetic constants of enzyme-catalyzed reactions. The program randomly selects a kinetic scheme from various sequential, ping pong, and iso reaction sequences as well as values for the kinetic constants. The scheme and kinetic constants are unknown to the student at this time; the only thing he or she knows is the stoichiometry of the catalyzed reaction which can have two or three substrates and products. The student is prompted to enter values for concentrations of substrates and products; several different concentrations for each substrate and product can be entered in a single experiment. The program then calculates, displays and prints (if desired) the corresponding initial steady-state velocities. The student can perform as many experiments as desired until enough information is obtained to determine the kinetic mechanism and to calculate values for the kinetic constants.