Optimal alignments of biological sequences on a microcomputer

An algorithm and a program have been developed which enableoptimal alignments of biological sequences on an 8–bitmicrocomputer. The compiled program can process sequences upto 1000 residues on a Commodore 64. Since this program was writtenoriginally in the BASIC language, it may readily be adaptedto other microcomputers with small changes. Received on March 11, 1985; accepted on March 14, 1985     

A general purpose non-linear curve fitting program for the British Broadcasting Corporation Microcomputer

Software for non–linear curve fitting has been writtenin BASIC to execute on the British Broadcasting CorporationMicrocomputer. The program uses the direct search algorithmPattern–search, a robust algorithm that has the additionaladvantage of needing specification of the Junction without inclusionof the partial derivatives. Although less efficient than gradientmethods, the program can be readily configured to solve low–dimensionaloptimization problems that are normally encountered in lifesciences. In writing the software, emphasis has been placedupon the ‘user interface’ and making the most efficientuse of the facilities provided by the minimal configurationof this system. Received on March 4, 1985; accepted on March 14, 1985     

A non-linear regression program in BASIC for estimating Km and Vmax

This paper gives a program in BASIC for calculating the kineticparameters K_m and V_max for an enzyme reaction from a set ofpaired values of reaction velocity at given substrate concentrations.An initial estimate of the two parameters is made using a weightedlinear regression, these values are then used in an iterativeprocess to fit the data to the Michaelis–Menten equationand give final values of K_m and V_max with their associated standarderrors. Received on July 15, 1986; accepted on November 13, 1986     

Sample size calculation, power analysis and randomization: research project design in Windows

Single estimates of sample size for a study may be easily obtainedby use of a hand calculator or from published tables. In contrast,performing multiple calculations is a tedious and time-consumingtask, which is greatly simplified by a computer program. Thecomputer program presented here assists the investigator incalculating sample size estimates, determining statistical powerand creating randomization tables for a study. The program isdesigned primarily for clinical trials and thus includes somefeatures not found in other software packages performing similartasks. Sample size calculation and power analysis are performedfor dichotomous, continuous Coammetric and non–parametrictests) and time–to–failure (exponential distributionand log-rank test) response variables, and for correlation coefficients.Sample size estimates and significance levels may be adjustedfor multiple participating centers, non compliance, interimanalyses and multiple testing. The randomization subroutinegenerates tables for studies with up to nine treatment armsand with any valid block size. As a Windows application, theprogram runs in a multitasking environment, allowing switchingbetween programs and easy pasting of results into word–processingdocuments and other applications. It is very simple to use,with a completely menu–driven interface and sufficientbuilt–in help to obviate the use of a manual.     

Component manufacturing analysis

To date, numerous simplified Life Cycle Assessment methods and techniques have been developed to reduce complexities associated with practical application. However, these methods often identify critical elements according to subjective considerations. In this paper, we develop and apply a new type of Life Cycle Inventory method — Component Manufacturing Analysis (CMA) — that is easy to implement and less arbitrary. Application of CMA requires identification of all product components and their associated weights, which are then entered into a factory-type database. Because the factory database has a rigorous yet generic structure and because calculation is done automatically, the application of CMA tends to be less arbitrary and more complete than other simplified methods. Results of a case study on beverage vending machines show that the manufacturing stage is a significant phase in the whole life-cycle inventory of a product. We conclude that CMA shows promise for further development and future application.     

A microcomputer program for the identification of tRNA genes

A microcomputer program which locates tRNA genes within longDNA sequences is described. The search is performed either byidentifying tRNA-like secondary structures or by locating eukaryoticRNA polymerase III promoter consensus sequences. The programis also useful in finding inverted repeats allowing the formationof stem-loop secondary structures in tRNA. The program has beendeveloped in BASIC and 6502 Assembler and runs on the AppleII plus and He microcomputers. The execution is quite fast;all the operations are carried out in 1–90 s, dependingon the required task and on the sequence length. Received on March 1, 1985; accepted on April 25, 1985     

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.     

Profile sequence analysis and database searches on a transputer machine connected to a Macintosh computer

An implementation of Profilesearch (a technique to search forrelationships between a protein sequence and multiply alignedsequences) for a parallel computer is described. The numbercrunchingmachine, consisting of 21 T800 transputers, is connected toa Macintosh IIcx host computer. The program utilizes a standardMacintosh application as its user–interface, resultingin a transparent and user–friendly environment for addressingthe parallel computer. The program is independent of the nwnberof available processors and exceeds the speed of a VAXstation3200 with only one transputer in operation, thus allowing cheapand fast database searches with a PC frontend. For a largernwnber of processors, the speed increase is approximately linearwith no obvious symptoms of saturation with the available maximwnof 21 transputers. The program and environment are usefid tosearch quickly and easily for similarities between a singlesequence or sequence set and individual sequences containedin a large database. The alignment is determined by typicaldynamic programming techniques.     

Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison

A platform program that performs biological sequence comparisonprovides a case study to compare the relative advantages ofa machine–independent approach to parallel computationversus a machine-specific approach. The program consists oftwo routines: (i) PSCANLIB, which compares a single biologicalsequence against a database of sequences, and (ii) PCOMPLJB,which compares a database of sequences against another databaseof sequences, or against itself. The program was first parallelizedto run on the Intel Hypercube parallel computer using nativeHypercube commands to coordinate the parallel computation. Theparallelization logic of the program was then translated intoa machine–independent parallel programming language, Linda.Tliese two approaches to parallelization are contrasted in termsof: (i) the expressive power of the logic that coordinates theparallel computation, (ii) the portability of the machine–independentversion to other parallel machines and (Hi) the relative efficiencyof the two versions of the program. In the benchmark tests reported,the benefits of the machine–independent approach wereachieved with only a modest sacrifice in efficiency.     

Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis

It is widely accepted that parallel computers, which have theability to execute different parts of a program simultaneously,will offer dramatic speed–up for many time–consumingbiological computations. The paper describes how the use ofthe machine–independent parallel programming language,Linda, allows parallel programs to run on an institution^'s networkof workstations. In this way, an institution can harness existinghardware, which is often either idle or vastly underutilized,as a powerful ‘parallel machine’ with supercomputingcapability. The paper illustrates this very general paradigmby describing the use of Linda to parallelize three widely usedprograms for genetic linkage analysis, a mathematical techniqueused in gene mapping. The paper then discusses a number of technical,administrative and social issues that arise when creating sucha computational resource.     

H-EXCRETION: a program for microcomputers to aid in calculation of acid or base excretion

H-EXCRETION is a program written in BASIC language for microcomputers and designed to facilitate the calculation of excretion for acid or base from a tissue into the surrounding media. The program is designed in such a way to allow considerable variability in different experimental parameters. Five examples of calculation of H+ excretion in the urinary bladder of the toad Bufo marinus are presented.     

Implementations of BLAST for Parallel Computer

The BLAST sequence comparison programs have been ported to avariety of parallel computers – the shared memory machineCray Y–MP 8/864 and the distributed memory architecturesIntel iPSC/860 and nCUBE. Addi–tionally, the programswere ported to run on workstation clusters. We explain the parallelizationtechniques and consider the pros and cons of these methods.The BLAST programs are very well suited for parallelizationfor a moderate number of processors. We illustrate our resultsusing the program blastp as an example. As input data for blastp,a 799 residue protein query sequence and the protein databasePIR were used.     

Two Hypercard calculators for molecular biology

Two calculators built in Macintosh Hypercard are described.GelFragSizer estimates and plots DNA restriction fragment sizes,using the local reciprocal or cubic spline methods. Enzyme Kineticsestimates the Michaelis–Menton rate parameters for enzyme–catalyzedreactions, and plots data versus estimated curve in a varietyof formats. These stacks help to demonstrate the ease and sophisticationof calculation tools that scientists can develop with Hypercard. Received on January 16, 1990; accepted on January 24, 1990     

Covariance adjustment of survival curves based on Cox's proportional hazards regression model

Cox^'s proportional hazards regression model is a useful statisticaltool for the analysis of ‘survival data’ from longitudinalstudies. This multivariate method compares the ‘survivalexperience’ between two or more exposure groups whileallowing for simultaneous adjustment of confounding due to oneor more covariates. In addition to the summary regression statistics,further insight on the exposure–response relationshipcan be gained by visually examining the covariates–adjustedsurvival curves in the respective comparison groups. Covariates–adjustedsurvival curves are usually computed by the ‘average covariatemethod’. This method is, however, subject to potentialdrawbacks. A method that avoids these drawbacks is to estimateadjusted survival curves by the corrected group prognostic curvesapproach. We have written a computer program to construct survivalcurves by the latter method. The program is coded in the InteractiveMatrix Language of SAS.     

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.     

Computer data recording and DATAC 6, a BASIC program for continuous and interval sampling studies

We review aspects of the design and use of computer data recorders in field research and describe the structure and operation of a BASIC language program for the Tandy Model 100/102 notebook computers. The program is flexible and open in that it does not force the use of preconfigured codes. It is intended for research designs that employ continuous (focal-animal) sampling, interval (scan) sampling (Altmann, J., Behaviour49: 227–267,1974), or the focal-time sampling paradigm of Baulu and Redmond (Primates19: 391–400, 1978). The program has been tested by a number of undergraduate and graduate students under field and zoo observational conditions.     

A BASIC microcomputer program to calculate the secondary structure of proteins from their circular dichroism spectrum

A BASIC program (CDPROT) has been developed to calculate thesecondary structure of proteins from their far UV circular dichroismspectrum. This implementation can use different reference spectra,calculated either from model polypeptides or proteins of knowntertiary structure. Apart from obtaining the a-helical, ß-structure,ß-turns or random percentages which would generatethe spectrum of best fit with respect to the experimental measures,CDPROT represents on screen both theoretical and experimentalspectra indicating the root-mean-square error. The provisionof additional reference spectra by the user is also considered,and another program (STOREREF) performs the editing in an adequateformat for CDPROT. Received on March 8, 1988; accepted on June 3, 1988     

Statistical inference on associated fertility life table parameters using jackknife technique: computational aspects

Knowledge of population growth potential is crucial for studying population dynamics and for establishing management tactics for pest control. Estimation of population growth can be achieved with fertility life tables because they synthesize data on reproduction and mortality of a population. The five main parameters associated with a fertility life table are as follows: (1) the net reproductive rate (Ro), (2) the intrinsic rate of increase (rm), 3) the mean generation time (T), (4) the doubling time (Dt), and (5) the finite rate of increase (lambda). Jackknife and bootstrap techniques are used to calculate the variance of the rm estimate, which can be extended to the other parameters of life tables. Those methods are computer-intensive, their application requires the development of efficient algorithms, and their implementation is based on a programming language that encompasses quickness and reliability. The objectives of this article are to discuss statistical and computational aspects related to estimation of life table parameters and to present a SAS program that uses jackknife to estimate parameters for fertility life tables. The SAS program presented here allows the calculation of confidence intervals for all estimated parameters, as well as provides one-sided and two-sided t-tests to perform pairwise or multiple comparison between groups, with their respective P values.     

PROLANG: an expandable software in protein chemistry

PROLANG is an improved version of the PROSOFT program. Improvementsto the old commands were made and new ones were added, PROLANGis an open software that users with BASIC programming experiencecan easily expand. Received on May 9, 1989; accepted on May 23, 1989     

A nonlinear regression program for small computers

A BASIC computer program for performing weighted nonlinear regression is described and a listing of the program is given. The program, which is small and simple to use, has been designed to be run by users with little knowledge of mathematics or computers. Robust methods of analysis are described which may be applied to data in which experimental errors are not normally distributed, and the program incorporates one such method. It is shown that the program is useful for the analysis of data conforming to the Michaelis-Menten equation, a single exponential, and to binding equations, and other applications are discussed.