Matrix algebra routines for the Acorn Archimedes microcomputer: example applications

A set of matrix algebra routines have been written, as BASICVprocedures, for the Acorn Archimedes microcomputer. It is shownthat these procedures are executed so quickly that programs,which require matrix algebra computations, can be written ininterpreted BASIC. Two example applications, reciprocal averagingand principal components analysis, are demonstrated. Received on January 19, 1988; accepted on February 9, 1988     

Cycle-triggered averaging of respiration-related neuronal activity

A computer system is presented which provides off-line computation of cycle-triggered histograms (CTH) of respiration-related neuronal activity. Binwidths of the histograms are freely selectable by software from 10 ms to 100 ms. For special evaluation purposes, CTHs can be standardized in different ways concerning cycle duration as well as amplitude. Time incidence of maximum frequency, center of gravity and expiration-to-inspiration phase transition within the respiratory cycle are computed. The system employs special hardware interfaces to an 8-bit microcomputer which are briefly described. Data acquisition, data manipulation and output handling of the results are performed by chaining 3 compiled BASIC programs. Some comments on peculiarities of the BASIC language concerning combined application of a BASIC interpreter and a BASIC compiler are brought up. The usefulness of the method is demonstrated by examples of CTHs computed from the activity of medullary respiration-related neurons as well as of the corresponding phrenic nerve mass activity.     

A computerized system for scoring primate behavior using standard keyboards

A scoring system has been developed for primate behavior which uses standard keyboards and minicomputers or microcomputers. The mnemonic, alphanumeric code used is easily learned, highly flexible, and can be recorded in longhand for later entry into a computer if a keyboard is not immediately available. The software consists of two programs, both of which can be written in BASIC. SCORE is used for data acquisition and appends the test time to each behavioral sequence. DATSUM decodes and summarizes the test data using table-driven logic. The minimum hardware required is a 16K microcomputer, an alphanumeric keyboard, a display, and cassette storage.     

A flexible system for microscope fluorometry served by a personal computer

Summary An automated microscope fluorometer based on a modified Leitz MPV I system is described. Automation is mainly attained by the use of a cheap, commercially available personal computer system programmed in extended BASIC supplemented by a few assembly-level subroutines. The automation has resulted in simplified measuring procedures and increased measuring speed. The statistical precision is enhanced because greater cell populations can be analysed within reasonable time. Programs for several biological applications are described. Routines for cell population analysis, including storage of data on disk files, has proved especially useful. Programs for recording of corrected fluorescence emission spectra and of time-dependent fluorescence variables have also been developed. A high flexibility is achieved, as the BASIC programs can readily be modified for specific purposes. Some data on the sensitivity and reproducibility of the instrument alone, and in combination with a staining method, are also presented.Supported by grants from the Swedish Medical Research Council (Project No. 2235) and from the Faculty of Medicine, University of Linköping     

Electron paramagnetic resonance in biochemistry. Computer simulation of spectra from frozen aqueous samples.

Two computer programs are described; they can be used to simulate e.p.r. spectra of effective spin-1/2 systems in frozen aqueous samples. One program is written in BASIC and the other in FORTRAN IV. Both programs are deposited as a Supplementary Publication (SUP 50082; 27 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7QB, U.K. References are given to the applications of these programs in biochemical work.     

Collection and analysis of kinetic data from a stopped-flow spectrophotometer using a microcomputer

A method of interfacing an inexpensive microcomputer to a stopped-flow kinetics spectrophotometer is described. It allows software-selectable sampling frequencies between 0.1 ms and 8 s and large numbers of data points to be collected. Machine language routines to use the interface are described and these allow the sampling frequency to be altered during data collection to ensure adequate numbers of points in critical regions of the kinetic profile. BASIC programs for collection and analysis of multicomponent kinetic data using this system are also described. Due to the large number of data points that can be collected and the ability to selectively sample transmittance values in regions where the signal is rapidly changing with time, relatively unsophisticated methods of data analysis can be used. These methods are suitable for use by microcomputers and mean that data analysis and acquisition can be performed on the same microcomputer in real time. To illustrate this, multicomponent analysis of kinetic transients is performed on simulated data and on the dissociation kinetics of the ethidium-DNA complex.     

IBM microcomputer programs that analyze DNA sequences for tRNA genes

A set of four computer programs that search DNA sequence datafiles for transfer RNA genes have been written in IBM (Microsoft)BASIC for the IBM personal computer. These programs locate andplot predicted secondary structures of tRNA genes in the cloverleafconformation. The set of programs are applicable to eukaryotictRNA genes, including those containing intervening sequences,and to prokaryotic and mitochondrial tRNA genes. In addition,two of the programs search up to 150 residues downstream oftRNA gene sequences for possible eukaryotic RNA polymerase IIItermination sites comprised of at least four consecutive T residues.Molecular biologists studying a variety of gene sequences andflanking regions can use these programs to search for the additionalpresence of tRNA genes. Furthermore, investigators studyingtRNA gene structure-to-function relationships would not needto do extensive restriction mapping to locate tRNA gene sequenceswithin their cloned DNA fragments. Received on October 29, 1985; accepted on January 28, 1986     

A BASIC computer program for calculation of photosynthesis,stomatal conductance,and related parameters in an open gas exchange system

Computer programs written in BASICA (IBM'S VERSION OF BASIC) language were developed for the calculation of the gas exchange parameters of CO₂ assimilation, leaf conductance, stomatal conductance, residual conductance, intercellular CO₂ concentration, transpiration, water use efficiency and transpiration ratio in an open system. Formulas are discussed in both an algebraic and in a BASIC computer program form. Calculations based on mole fractions of CO₂ and water vapor are explained and both molar and mass fluxes are included in the program output to facilitate comparisons with data from the literature. Corrections are made in the program to account for under-estimation of CO₂ assimilation due to the increase in flow rates out of sample chambers caused by simultaneous transpiration. A sample output is included to illustrate the formatting capability of the program.Michigan Agricultural Experiment Station Journal Article No. 11576.Michigan Agricultural Experiment Station Journal Article No. 11576.     

Microcomputer control of behavior and the acquisition of digital and analog data

Advances in technology and decreasing costs are enabling microcomputers to displace more traditional devices in the scientific laboratory. The availability of various approaches to software-system development for the use of microcomputers in the on-line control of experiments has contributed to the trend. This report describes a software system developed to control conditioned behavior during schedules of reinforcement while simultaneously accumulating behavioral data and physiological (analog) data using a hardware system based on the Radio Shack TRS-80 Model I microcomputer. The software utilizes a high-level interpretive language (Microsoft BASIC), assembly language and compiled BASIC to attain an acceptable execution speed and ease of programming.     

Analysis of twin data using SAS

Summary .  Twin studies are essential for assessing disease inheritance. Data generated from twin studies are traditionally analyzed using specialized computational programs. For many researchers, especially those who are new to twin studies, understanding and using those specialized computational programs can be a daunting task. Given that SAS (Statistical Analysis Software) is the most popular software for statistical analysis, we suggest that the use of SAS procedures for twin data may be a helpful alternative and demonstrate that we can obtain similar results from SAS to those produced by specialized computational programs. This numerical validation is practically useful, because a natural concern with general statistical software is whether it can deal with data that are generated from special study designs such as twin studies and if it can test a particular hypothesis. We concluded through our extensive simulation that SAS procedures can be used easily as a very convenient alternative to specialized programs for twin data analysis.     

An automated program to find animals and crop photographs for individual recognition

Detailed data on individual animals are critical to ecological and evolutionary studies, but attaching identifying marks can alter individual fates and behavior leading to biases in parameter estimates and ethical issues. Individual-recognition software has been developed to assist in identifying many species from non-invasive photographic data. These programs utilize algorithms to find unique individual characteristics and compare images to a catalogue of known individuals. Currently, all applications for individual identification require manual processing to crop images so only the area of interest remains, or the area of interest must be manually delineated in each image. Thus, one of the main bottlenecks in processing data from photographic capture-recapture surveys is in cropping to an area of interest so that matching algorithms can identify the individual. Here, we describe the development and testing of an automated cropping program. The methods and techniques we describe are broadly applicable to any system where raw photos must be cropped down to a specific area of interest before pattern recognition software can be used for individual identification. We developed and tested the program for use with identification photos of wild giraffes.     

Modeling and artificial intelligence approaches to enzyme systems

Modeling is a means of formulating and testing complex hypotheses. Useful modeling is now possible with biological laboratory microcomputers with which experimenters feel comfortable. Artificial intelligence (AI) is sufficiently similar to modeling that AI techniques, now becoming usable on microcomputers, are applicable to modeling. Microcomputer and AI applications to physiological system studies with multienzyme models and with kinetic models of isolated enzymes are described. Using an IBM PC microcomputer, we have been able to fit kinetic enzyme models; to extend this process to design kinetic experiments by determining the optimal conditions; and to construct an enzyme (hexokinase) kinetics data base. We have also used a PC to do most of the constructing of complex multienzyme models, initially with small simple BASIC programs; alternative methods with standard spreadsheet or data base programs have been defined. Formulating and solving differential equations in appropriate representational languages, and sensitivity analysis, are soon likely to be feasible with PCs. Much of the modeling process can be stated in terms of AI expert systems, using sets of rules for fitting and evaluating models and designing further experiments. AI techniques also permit critiquing and evaluating the data, experiments, and hypotheses being modeled, and can be extended to supervise the calculations involved.     

Conception d'un logiciel de traitement et d'interrogations statistiques de donnees logist

This paper presents a general program which cannot only be used for the treatment and the statistical interrogations, but also for basic operations, such as validity check and the preparation of data which is often necessary for other programs. Its use language is simple, suitable and accessible to non-specialists. The program is sufficiently complete so that it can treat some complex problems without requiring complementary programs. It can treat several problems simultaneously. This allows one to gain data-reading time and the program is therefore economical. Its domain of use is large: epidemiological studies, psychological and sociological investigations, biological studies, clinical research, chronological follow-up, examinations of faculties, ….The program is written in FORTRAN IV and thus transferable. It contains more than 25 000 instructions but needs limited place in the core memory (less than 64 000 words). Its structure allows further evolution and addition of new procedures or new methods. A transformation into a conversational form is considered.     

Comparison of sequence profiles. Strategies for structural predictions using sequence information

Distant homologies between proteins are often discovered only after three-dimensional structures of both proteins are solved. The sequence divergence for such proteins can be so large that simple comparison of their sequences fails to identify any similarity. New generation of sensitive alignment tools use averaged sequences of entire homologous families (profiles) to detect such homologies. Several algorithms, including the newest generation of BLAST algorithms and BASIC, an algorithm used in our group to assign fold predictions for proteins from several genomes, are compared to each other on the large set of structurally similar proteins with little sequence similarity. Proteins in the benchmark are classified according to the level of their similarity, which allows us to demonstrate that most of the improvement of the new algorithms is achieved for proteins with strong functional similarities, with almost no progress in recognizing distant fold similarities. It is also shown that details of profile calculation strongly influence its sensitivity in recognizing distant homologies. The most important choice is how to include information from diverging members of the family, avoiding generating false predictions, while accounting for entire sequence divergence within a family. PSI-BLAST takes a conservative approach, deriving a profile from core members of the family, providing a solid improvement without almost any false predictions. BASIC strives for better sensitivity by increasing the weight of divergent family members and paying the price in lower reliability. A new FFAS algorithm introduced here uses a new procedure for profile generation that takes into account all the relations within the family and matches BASIC sensitivity with PSI-BLAST like reliability.     

The computer-assisted spatial reconstruction of the hip acetabulum

Computer aided design is a useful method in presenting graphics. By 2 simple computer programs written in BASIC and running on most home computers very clear plots of the 3-dimensional (3D) structure of joints like the acetabulum can be drawn quickly. By orthogonal transformations the 3D-body may be easily regarded from every possible point of view. The surface of the acetabulum may be emphasized by an optional automatic hatching between adjacent cutting bows. Further methods of automatic data entering from given joints are discussed.     

Individual Effects of Seasonal Changes,Visitor Density,and Concurrent Bear Behavior on Stereotypical Behaviors in Captive Polar Bears (Ursus maritimus)

Stereotypical behaviors in captive polar bears (Ursus maritimus) can be detrimental to their welfare. These behaviors can be reduced through enrichment programs but are often not completely eliminated, so identifying potential triggers is important. The present study investigated the influences of seasonal changes, visitor density, and concurrent bear activity on stereotypical behaviors exhibited by 3 captive polar bears at the Toronto Zoo. All bears exhibited these behaviors; however, individual differences were found in duration and form. The male exhibited less stereotypical behavior during spring, and the females exhibited less stereotypical behavior during winter. An increase in visitor density was associated with more stereotypical behavior in 1 female but less stereotypical behavior in the other 2 bears. All bears engaged in more stereotypical behaviors when the other bears were inactive, and 1 female engaged in more stereotypical behaviors when the other bears were out of sight. Further, when conspecifics were active, all bears engaged in less stereotypical behaviors. Given the variability among individual bears, future enrichment programs must be tailored to the needs of individuals to maximize efficacy.     

Assembly of overlapping DNA sequences by a program written in BASIC for 64K CP/M and MS-DOS IBM-compatible microcomputers.

The SEQALIGN programs1 described in this report aid in the assembly of up to 100 individual overlapping DNA sequences generated by M-13 subcloning and sequencing methods. The program produces a printout of the aligned sequences presented in register. Use of the program will be facilitated because 1) it is written with the Microsoft BASIC interpreter, 2) sequence data may be entered and edited using WORDSTAR or similar word processing programs, and 3) hardware requirements for execution of the program on CP/M or MS-DOS (IBM-PC compatible) systems are minimal.     

Energetics of feeding,social behavior,and life history in non-human primates

Energy is a variable of key importance to a wide range of research in primate behavioral ecology, life history, and conservation. However, obtaining detailed data on variation in energetic condition, and its biological consequences, has been a considerable challenge. In the past 20 years, tremendous strides have been made towards non-invasive methods for monitoring the physiology of animals in their natural environment. These methods provide detailed, individualized data about energetic condition, as well as energy allocations to growth, reproduction, and somatic health. In doing so, they add much-needed resolution by which to move beyond correlative studies to research programs that can discriminate causes from effects and disaggregate multiple correlated features of the social and physical environment. In this review, I describe the conceptual and methodological approaches for studying primate energetics. I then discuss the core questions about primate feeding ecology, social behavior, and life history that can benefit from physiological studies, highlighting the ways in which recent research has done so. Among these are studies that test, and often refute, common assumptions about how feeding ecology shapes primate biology, and those that reveal proximate associations between energetics and reproductive strategies.     

The recognition site of type II restriction enzyme BglI is interrupted

The Type II restriction endonuclease BglI recognizes the interrupted DNA sequence 5'-G-C-C-N-N-N-N-N-G-G-C-. This sequence occurs at all locations in over 33 000 base pairs of DNA sequence where the enzyme was found to cut DNA and nowhere else. All six of the specified bases are essential parts of the site since all groups of five of the six bases occur in the DNA sequences tested and none of them are cut by BglI. The length of the block of intervening unspecified positions must be exactly five since all other sizes between zero and 15 occur in the DNA sequences searched and none are cut by BglI. The 5'-terminal nucleotides of BglI cleaved phage G4 replicative form DNA and plasmid pER18 DNA were compared with the DNA sequences near the BglI sites on these DNAs. These results indicated that BglI cuts within the intervening unspecified region and produces single-stranded 3' termini that are three bases long. The BglI recognition site and cleavage points can thus be represented as follows: (Formula: see text). This study of the BglI recognition site was facilitated by the use of inexpensive microcomputers. A system of programs was developed that allowed analysis of over 33 kb of DNA sequences stored on flexible magnetic disks or audio cassettes. While these programs were generally written in the higher level language BASIC, some assembly language subroutines were utilized to reduce execution time.     

Programs simulating a I lost eric and other enzyme kinetics for computer-aided teaching

Two programs have been written in BASIC as a teaching aid for instruction of HNC, HND, and degree students in a strategy of experimentation, taking enzyme kinetics as a particular example. Little prior knowledge is required to use the programs. One of the programs (ENZY) simulates the action of a non-allosteric enzyme as (a) a simple case with or without inhibitors including substrate inhibition (b) a two-substrate case with either random-order or ping-pong kinetics. The other program (ALLO) simulates the action of an allosteric enzyme with or without activators or inhibitors or both. A detailed example of an investigation using ALLO is given.