pathmatrix: a geographical information system tool to compute effective distances among samples

pathmatrix is a tool used to compute matrices of effective geographical distances among samples using a least‐cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. Punctual locations (e.g. individuals) or zones encompassing sample data points (e.g. demes) are used in conjunction with a species‐specific friction map representing the cost of movement through the landscape. Matrices of effective distances can then be exported to population genetic software to test, for example, for isolation by distance. pathmatrix is an extension to the geographical information system (GIS) software arcview 3.x.     

Interfacing a flow cytometer computer with a PC-based patient information system

We have established an interface between our flow cytometer's computer and the personal computer (PC) which supports our patient database system. The PC has been equipped with a commercially available IEEE-488 bus interface board which is connected to the interface bus of the cytometer's Hewlett-Packard 9000/300 computer (HP). The PC is set as a bus device with the same address as that of the HP's printer. It is programmed to examine the stream of data sent to the printer and extract from it and store in an MS-DOS text file selected information which subsequently may be transferred to the database system.     

An computer information system for genetic engineering

The article describes the vectors data base and the software for its use (the VECTOR-PC system). At present the prototype versions of data base and VECTOR-PC exist and are in test exploitation. The original data base entry format contains 17 main fields for specific genetic engineering information. The VECTOR-PC system includes programs for data base search and support, and also the "genetic engineering designer", which allows the user to design his own hypothetic structures from the objects of data base and to receive detailed information about them. The system is destined for IBM PC or compatible computers.     

A simple coding method for computer storage and handling of drug information

An ever-growing body of knowledge in pharmacology has created a need for devising improved methods for handling drug information. We have developed an eleven digit comprehensive cardiovascular number to represent vital information on the effects of a drug on the cardiovascular system. Each digit of the number signifies an important cardiovascular phenomenon, and can vary from 0 to 9. This coding method provides a simmple technique for computer handling of vital information on the effects of pharmacoactive agents in a semi-quantitative manner. Using this procedure, similar numbers for neuromuscular and immune systems can be easily developed.     

A semiautomatic image analyzing system based on an APPLE II or IIe personal computer

A new semiautomatic image analyzing system based on an APPLE II or IIe personal computer is described. The configurations of the hardware and software are extensively explained. The possibilities of applying the system are demonstrated by different examples taken from various projects in biological research and clinical pathology. The system is designed to fulfil the following requirements: (1) stepwise realization as a unit-by-unit system according to individual needs and interests, (2) acquisition and calculation of morphometric parameters, (3) provision of solutions for the greatest possible number of given problems in clinical and experimental pathology, (4) direct connection of the system to host computers for on-line data transfer and evaluation, and (5) optimum cost-benefit ratio by manifold application possibilities for the individual hardware and software elements. The advantages of the unit-by-unit system with personal computers outweigh in many respects the disadvantages (for example, increased file handling and limited capacity) in comparison with the closed automatized image evaluation system, particularly with regard to costs, flexibility and compatibility. The system is being further developed in collaboration with Kontron Bildanalyse GmbH, Eching/Munich, FRG.     

Prediction of Prosopis species invasion in Kenya using geographical information system techniques

Tree species from Prosopis genus were widely planted for rehabilitation of degraded drylands of Kenya. However, they have invaded riverine ecosystems where they cause negative socio‐economic and ecological impacts. GIS was used to estimate the reverine area threatened by Prosopis invasion in Kenya. Landsat satellite images, field surveys and past studies were also used to assess the resulting potential ecological impacts in the Turkwel ecosystem in Kenya. The study revealed that 3.0 to 27.7 million hectares are threatened by invasion, based on documented riverine forests width of 0.5–3 km. Image analysis showed that 34% of the sites under positive change were invaded, with most invasions occurring in natural forests and abandoned farms. Prosopis had overall occurrence of 39% in all the sampled sites in 2007, in contrast to 0% in 1990 that was reported in an earlier study. In these areas, Acacia tortilis occurrence dropped from 81% in 1990 to 43% in 2007, suggesting that Prosopis could be displacing it. Utilization of Prosopis for fodder, fuel wood and pods for animal feeds is recommended as a management tool to reverse the trend. The methods used in this study are also recommended for invasion prediction and management in other similar ecosystems.     

Analog computer studies of a simple enzyme-catalyzed reaction

Analog computer studies of an enzyme-catalyzed reaction in its most simple form, according to the scheme E + S ⇋ ES → E + X have shown that appreciable deviations from a steady state of intermediary enzyme-substrate complex occur. The earlier developed theory in which an exponential breakdown of this in the presteady-state phase of the reaction to a maximum value increasing complex was postulated proved to be a reasonable good approximation.     

A personal computer system for observation and analysis of copulatory behavior in small rodents

A personal computer system was developed for measuring values of copulatory behavior of small laboratory rodents. This system enabled us to get the analysis data of copulatory behavior of male rats as soon as possible after observation. This present system could be useful to measure other reproductive behavior of small rodents.     

A simple polymerase chain reaction apparatus based on a computer printer.

We describe a very simple laboratory-made polymerase chain reaction (PCR) apparatus. The reaction tubes are placed in a holder fixed through a mechanical arm to the tape cartridge of a computer printer. A computer controls the horizontal movement of the tube carrier by sending the proper printing commands. The holder is raised or lowered by a frame fixed to the paper-advancing roller of the printer. The system allows the programmed movement of the test tubes within the holder, successively through three thermal baths placed in front of the printer. DNA from single lambda gtll lysis plaques was successfully amplified with this system in our laboratory.     

Topographical brain electrical activity mapping on an IBM-compatible personal computer

A new system for computing brain electrical activity maps on a standard IBM-compatible computer has been developed. The EEG is recorded using a CED1401 intelligent laboratory interface and stored in the computer; colour coded maps are generated using softwave developed in Turbo PASCAL and displayed on the EGA graphics screen. An acceptable computation time of 1.2 s for a 64 × 64 map displayed as a 128 × 128 pixel image has been achieved by incorporating assembly language routines and a maths coprocessor. The system may be readily upgraded as improved hardware becomes available and further software can be added. In addition to triggering auditory, visual and somatosensory stimulators, it provides the potential for the generation of complex stimuli for cognitive experiments by means of mass RAM and digital-to-analogue converters.     

euGenes: a eukaryote genome information system

euGenes is a genome information system and database that provides a common summary of eukaryote genes and genomes, at http://iubio.bio.indiana.edu/eugenes/. Seven popular genomes are included: human, mouse, fruitfly, Caenorhabditis elegans worm, Saccharomyces yeast, Arabidopsis mustard weed and zebrafish, with more planned. This information, automatically extracted and updated from several source databases, offers features not readily available through other genome databases to bioscientists looking for gene relationships across organisms. The database describes 150 000 known, predicted and orphan genes, using consistent gene names along with their homologies and associations with a standard vocabulary of molecular functions, cell locations and biological processes. Usable whole-genome maps including features, chromosome locations and molecular data integration are available, as are options to retrieve sequences from these genomes. Search and retrieval methods for these data are easy to use and efficient, allowing one to ask combined questions of sequence features, protein functions and other gene attributes, and fetch results in reports, computable tabular outputs or bulk database forms. These summarized data are useful for integration in other projects, such as gene expression databases. euGenes provides an extensible, flexible genome information system for many organisms.