ODDC and MULTIGRAPH: programs for spectrophotometer data collection and manipulation using a microcomputer

A software package is described that collects, graphs, performs peak sensing, and prints data from a spectrophotometer interfaced to an Apple II microcomputer with an ADALAB analog-to-digital converter card. Data collection and storage is performed by an interpreted BASIC program with machine language subroutines. Recalling, graphing, and printout of the data is accomplished by a separate compiled BASIC program. Both of these programs, as well as assisting utility programs, are under control of a menu program. The programs take advantage of all available memory in the 64-K Apple II computer to allow for storage of up to 12 600 data points (7 hours of data collection at a sampling rate of 1 sample every 2 s). As the data collection program provides peak sensing, and the capability of annotating various time points, the programs are ideally suited for use in column chromatography.     

ANTHEPROT: a package for protein sequence analysis using a microcomputer

A simple microcomputer package is described to make the theoretical analysis of protein sequences. Several methods designed to compare two sequences, to model proteolytic reactions and to predict the secondary structure, the hydrophobic/hydrophilic regions and the potential antigenic sites of proteins have been included in an Apple II microcomputer software. The package comprises 21 programs as well as the secondary structure database of Kabsch and Sander (1983).     

Framework for evaluation and selection of the software packages: A hybrid knowledge based system approach

Evaluation and selection of the software packages is complicated and time consuming decision making process. Selection of inappropriate software package can turn out to be costly and adversely affects business processes and functioning of the organization. In this paper we describe (i) generic methodology for software selection, (ii) software evaluation criteria, and (iii) hybrid knowledge based system (HKBS) approach to assist decision makers in evaluation and selection of the software packages. The proposed HKBS approach employs an integrated rule based and case based reasoning techniques. Rule based reasoning is used to capture user needs of the software package and formulate a problem case. Case based reasoning is used to retrieve and compare candidate software packages with the user needs of the package. This paper also evaluates and compares HKBS approach with the widely used existing software evaluation techniques such as analytic hierarchy process (AHP) and weighted scoring method (WSM).     

Considering perception and cognition in the design of an instructional software package

An instructional multimedia software package was developed for use by students taking introductory physics courses. Studies have indicated that many of these students possess a set of common misunderstandings of graphs describing the motion of objects. The software described here was constructed as a student tool which would specifically address these difficulties. The impact of educational psychology, cognitive science, and human factors research on software design and user interface development are described. This work was supported by NSF grant MDR-9154127 with additional support from the RasterOps Corporation, Sony Corporation of America, and Apple Computer, Inc.     

A low cost system for the graphical display of space-filling models of proteins

An inexpensive system for creating and displaying high resolution color images of space-filling models of proteins is described. The system software consists of two BASIC programs, CONVERT and MOLVIEW, which allow the user to create two-dimensional projections of space-filling models of protein molecules, using data contained in standard Protein Data Bank files. By modifying certain subroutines in the BASIC programs, the user can specify color highlightning to emphasize certain aspects of the molecule. The user can interactively specify the viewing angle or store displayed images on diskettes. The software can be implemented on any MS-DOS personal computer that supports color graphics and GW-BASIC.     

An interactive/graphics software system for function minimization

An interactive/graphics based software package for solving unconstrained function minimization problems is described. The intent of the package (called INTEROPT) is to provide a computing environment which properly matches the experimental nature of the function minimization problem. A number of multidimensional minimization algorithms are provided for the user, together with a number of linear search algorithms. Through a simple command language, the user is able to make selections from among the available options and to specify values for the various parameters which control the program execution. This dialog is carried out with the user on a graphics CRT screen. Various types of graphical output are available in INTEROPT both to assist the user in evaluating the progress of the minimization trial and to enable him to interact with it, if he so chooses. The INTEROPT system also includes provisions for the interior penalty function approach to handling problems with constraints. The package therefore has a wide range of applicability.     

An improved sequence handling package that runs on the Apple Macintosh

We report improvements to our sequence analysis package and adaptation to run on the Apple Macintosh range of machines. The 'standard' version of the programs, which run on a VAX, has been given a new user interface that makes the programs very much easier to work with and has facilitated the move to the Macintosh. The reorganization of the code should simplify moves to other systems that offer WIMP user interfaces. In addition to a large number of small but useful extra features, some important new analytical functions have been devised. These include sequence and contig editors; optimal alignment and comparison methods; and a new method for comparing the observed and expected frequencies of selected oligonucleotides.     

An automated coding and process planning system using a DEC PDP-10

A semi-generative system has been developed to perform automated process planning using DEC PDP-10 computer. The proposed Automated Coding and Process Selection (ACAPS) package makes use of Group Technology concepts to interactivity assign a code number to a part, generate a machining sequence, from part families, and specify operation details for a manufacturing route sheet. Primary consideration is given to rotational components, though others can be accommodated. ACAPS is designed to lead the planner step-by-step toward a complete process plan, with a minimum of confusion. The program could be adapted to any computer system having FORTRAN capabilities.     

The design of a user friendly interactive personal computer package for quality control charts, project management, and linear programming applications

This paper describes the design of a user friendly interactive software package which can easily be used in both educational and industrial environments. The package contains applications for Quality Control Charts, Project Management, and Linear Programming. It is written in the BASIC programming language using the IBM Disk Operating System (DOS version 3.1). An IBM Personal Computer (PC, XT or AT) or compatible with one disk drive, a monochrome VDT and a line or dot matrix printer are required. The programs incorporate human factors considerations and the user is not required to have any previous computer programming experience. The package has data management options for adding new data, deleting data, listing data, storing data on a disk file and printing data collection forms for each program. The programs have been extensively validated using text book examples and comparisons with similar packages on main frame computer systems (such as EZLP, PPERT, LPRG, etc.). Based upon testing, this package was found to be easier to use and produced the desired results in approximately one third of the total time required by using the main-frame packages.     

Mercury: An evidential reasoning image classifier

MERCURY is a multisource evidential reasoning classification software system based on the Dempster-Shafer theory of evidence. The design and implementation of this software package is described for improving the classification and analysis of multisource digital image data necessary for addressing advanced environmental and geoscience applications. In the remote-sensing context, the approach provides a more appropriate framework for classifying modern, multisource, and ancillary data sets which may contain a large number of disparate variables with different statistical properties, scales of measurement, and levels of error which cannot be handled using conventional Bayesian approaches. The software uses a nonparametric, supervised approach to classification, and provides a more objective and flexible interface to the evidential reasoning framework using a frequency-based method for computing support values from training data. The MERCURY software package has been implemented efficiently in the C programming language, with extensive use made of dynamic memory allocation procedures and compound linked list and hash-table data structures to optimize the storage and retrieval of evidence in a Knowledge Look-up Table. The software is complete with a full user interface and runs under Unix, Ultrix, VAX/VMS, MS-DOS, and Apple Macintosh operating system. An example of classifying alpine land cover and permafrost active layer depth in northern Canada is presented to illustrate the use and application of these ideas.     

SignatureClust: a tool for landmark gene-guided clustering

Over the last several years, many clustering algorithms have been applied to gene expression data. However, most clustering algorithms force the user into having one set of clusters, resulting in a restrictive biological interpretation of gene function. It would be difficult to interpret the complex biological regulatory mechanisms and genetic interactions from this restrictive interpretation of microarray expression data. The software package SignatureClust allows users to select a group of functionally related genes (called ‘Landmark Genes’), and to project the gene expression data onto these genes. Compared to existing algorithms and software in this domain, our software package offers two unique benefits. First, by selecting different sets of landmark genes, it enables the user to cluster the microarray data from multiple biological perspectives. This encourages data exploration and discovery of new gene associations. Second, most packages associated with clustering provide internal validation measures, whereas our package validates the biological significance of the new clusters by retrieving significant ontology and pathway terms associated with the new clusters. SignatureClust is a free software tool that enables biologists to get multiple views of the microarray data. It highlights new gene associations that were not found using a traditional clustering algorithm. The software package ‘SignatureClust’ and the user manual can be downloaded from .     

The Design and Specification of a Visual Language: An Example for Customising Geographic Information Systems Functionalities

In this paper the design of a visual program editor and its specification using formal grammars are discussed. We consider an environment to specify, analyse and execute visual programs for a Geographical Information System (GIS). The lack of sophisticated user interfaces is one of the major drawbacks to Geographical Information Systems, particularly for people without a sound background in computer science. The use of a visual language approach is useful in order to hide the plethora of basic GIS functions, while providing ready- to-use tools to solve users' tasks. The visual environment provides users with higher level interfaces; it is based on the module concept, which is conceived as a software building block that implements a solution to a general basic task and is presented to the user through an interactive frame. Complex GIS queries can be carried out by interconnecting modules into flow networks, using a direct manipulation approach.     

Microcomputer-based programs for calculating mean and variance residence time by the method of prospective areas

A published package of microcomputer-based pharmacokinetic programs has been expanded to include programs to calculate mean and variance above the residence time (MRT and VRT) using the method of prospective areas. Three programs, one for plasma concentration time data, one for urinary excretion data, and one for in-vitro dissolution data, are available. All programs were tested with the data obtained from original articles or from simulated theoretical data. These programs were written in a modular fashion in such a way that they form an integrated software package. In conjunction with the programs previously developed, the user can choose/select how extensively the data are to be analyzed without reentry of data. This is particularly important since proper pharmacokinetic data analysis can only be made by using different calculations with different assumptions. Graphic display and linear regression subroutines are included in each module to simplify operation for the user. The modular design also facilitates modifications, upkeep, and accommodation to new methods of calculation.     

A general purpose adaptivity driver for FE software

This paper describes a tool that serves as an automatic mesh adaptivity driver program for general purpose finite element (FE) software packages. Many commercially available FE programs lack a feature to control the numerical solution's accuracy properly. Our tool implements a mesh adaptive method that, in conjunction with separate finite element software, allows one to fully automatically improve the quality of the numerical solution up to a user specified accuracy. We demonstrate the use of the package with selected computational examples performed with a commercial FE package, ANSYS, and with our FE program FEMEngine. Copyright © 2003 John Wiley & Sons, Ltd.     

Program generation for Ada — a case study

Program generation software is increasingly being used, not only to assist non-computer professionals to produce their own applications, but also to provide tools for programmers and designers. As part of the toolkit for an Ada dialogue development system, a program generator has been written in Ada to generate the package which codes the dialogue manager for a specified user interface. The input specifications and the method of generation are described. The advantages and disadvantages of Ada as the implementation, target and specification language are discussed.     

Novell网络应用程序接口技术

简述了在网络环境下开发应用程序所存在的问题，提出设计一个介于用户和网络层之间的Ｎｏｖｅｌ网络应用程序接口软件包（ＡＰＩＳＰ）的新方法，并用ＢｏｒｌａｎｄＣ＋＋开发了ＡＰＩＳＰ，该软件包向用户提供Ｎｏｖｅｌ网络环境下标准的库函数。较好地解决了一般软件工程人员难于开发网络应用程序这一问题，且能用于其它类型的网络方面。     

Program entanglement,feature interaction and the feature language extensions

One of the most difficult tasks in software development is that the programmer must implement a feature going through a laborious and error prone process of modifying the programs of other features. The programs of the different features entangle in the same reusable program units of the programming language, making them also difficult to be verified, maintained and reused. We show that if (C1) the features interact, (C2) they are executed by the same process and (C3) they are implemented in a programming language that requires the programmer to specify execution flows, program entanglement is inevitable and the problem cannot be solved by software design alone. Applications with interacting features are common including those that require exception handling.The feature language extensions (FLX) is a set of programming language constructs designed to enable the programmer to develop interacting features as separate and reusable program modules even though the features interact. The programmer uses FLX to specify non-procedural program units, organize the program units into reusable features and integrate features into executable feature packages. He develops a feature based on a model instead of the code of other features. FLX supports an automatic procedure to detect the interaction condition among features; the programmer then resolve the interaction in a feature package without changing feature code. FLX features and feature packages are reusable; the programmer may package different combinations of them and resolve their interactions differently to meet different user needs. An FLX to Java compiler has been implemented; our experience of using it has been very positive.     

A language-independent prettyprinter

A general-purpose prettyprinting program is presented. The input to the prettyprinter is a linear stream composed of visible symbols and elementary formatting instructions. The user can specify a set of alternative formats and the precedence of the alternatives. The prettyprinter attempts to select automatically the ‘best’ layout that fits on the bounded horizontal space available on the output medium. The prettyprinter is implemented as a library module, which makes it more flexible than many traditional prettyprinters that are written as main programs. For instance, formatted expressions can be mixed with plain text or displayed interactively on the user's terminal, and the application program can use several prettyprinters simultaneously.     

Automated verification of design patterns: A case study

Representing design decisions for complex software systems, tracing them to code, and enforcing them throughout the lifecycle are pressing concerns for software architects and developers. To be of practical use, specification and modeling languages for software design need to combine rigor with abstraction and simplicity, and be supported by automated design verification tools that require minimal human intervention. This paper examines closely the use of the visual language of Codecharts for representing design decisions and demonstrate the process of verifying the conformance of a program to the chart. We explicate the abstract semantics of segments of the Java package java.awt as a finite structures, specify the Composite design pattern as a Codechart and unpack it as a set of formulas, and prove that the structure representing the program satisfies the formulas. We also describe a set of tools for modeling design patterns with Codecharts and for verifying the conformance of native (plain) Java programs to the charts.