MOLECULAR DESIGNER: an interactive program for the display of protein structure on the IBM-PC

A BASIC interactive graphics program has been developed for the IBM-PC which utilizes the graphics capabilities of that computer to display and manipulate protein structure from coordinates. Structures may be generated from typed files, or from Brookhaven National Laboratories' Protein Data Bank data tapes. Once displayed, images may be rotated, translated and expanded to any desired size. Figures may be viewed as ball-and-stick or space-filling models. Calculated multiple-point perspective may also be added to the display. Docking manipulations are possible since more than a single figure may be displayed and manipulated simultaneously. Further, stereo images and red/blue three-dimensional images may be generated using the accompanying DESIPLOT program and an HP-7475A plotter. A version of the program is also currently available for the Apple Macintosh. Full implementation on the Macintosh requires 512 K and at least one disk drive. Otherwise this version is essentially identical to the IBM-PC version described herein.     

Computer program to predict the gas exchange process of a diesel engine

Ruston Paxman Diesels Ltd has made much use of computer programs in the development of diesel engines, in particular for the prediction of thermodynamic performance. The original program for this purpose has undergone considerable change, both to improve the accuracy and extend the application. These changes have resulted in the program becoming unnecessarily complicated for the designer to use.By returning to first principles a new program has been written that is considerably more versatile than the old one, and which is far simpler to use because data preparation is now governed solely by the complexity of the problem being tackled. This program is described.     

Pascal-P,program structure and program behaviour

This note describes some interesting results observed during the implementation of Pascal-P upon a Data General NOVA computer. A significant performance improvement was obtained by altering the program structure of the Pascal-P compiler to reflect the dynamic behaviour of the program. Some implications of this behaviour for the design of computer architectures are discussed.     

VEGA: a versatile program to convert,handle and visualize molecular structure on Windows-based PCs

We here propose the program VEGA, that was developed to create a bridge between the most popular molecular software packages. In this tool some features are implemented some features to analyze, display and manage the three dimensional (3D) structure of the molecules. The most important features are (1) file format conversion (with assignment of the atom types and atomic charges), (2) surface calculation and (3) trajectory analysis. The executable and the source code can be free downloaded from [URL: see text].     

A data acquisition, display and plotting program for the IBM PC

A program, AQ, has been developed to perform analog-to-digital (A/D) conversions on IBM PC products using the Data Translation DT2801-A or DT2801 boards. This program provides support for all of the triggered and continuous A/D modes of these boards. Additional subroutines for management of data files and display of acquired data have also been developed. These programs have been written so that a minimum number of keystrokes are required for their operation. Parameter files are used to simplify reconfiguration of this program for various data acquisition tasks.     

Palmagfisheranal, a computer program using fisher's analysis to analyze paleomagnetic directions—Or other directions distributed on a sphere

The computer program PALMAGFISHERANAL was written in WATFIV to analyze paleomagnetic directions. It is based on the method of Fisher, and has been extended to assess whether the population of directions is distributed randomly. Limitations of Fisher's technique are obvious in results of the analysis of artificial test data. The tabulated output lists all directions, mean directions and statistics and results of the randomness test in a cumulative fashion. Any directional data distributed on a sphere can be analyzed using PALMAGFISHERANAL, which is useful in both research and teaching.     

Scalability analysis of Dalton,a molecular structure program

Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.     

分子局部图形绘制及电势分析软件设计与实现

随着计算机技术的迅速发展,分子图形学在研究分子结构、计算机辅助分子设计中发挥着日益显著的作用.本文作者利用Visual C#呈序设计语言,结合已有的Raswin和WaferPainter两个开源软件,通过对.PDB(蛋白质数据库)文件、原子电量数据文件的读取、分析和计算,改进了原有软件仅限于观看分子的整体结构、绘制整体三维静电势、无法根据用户需要显示局部细节及二维静电势图的缺陷,实现了在用户定制的坐标范围内完成局部分子图、分子的平面静电势图的绘制等功能,这在蛋白质分子结构研究、分析原子间的作用力以及辅助分子设计方面有着重要意义.     

Using the k-core decomposition to analyze the static structure of large-scale software systems

The structures of large-scale software systems are complex and difficult to understand for designers and developers. Traditional software metrics can hardly describe the structural complexity in modern software, and finding a quantitative method to depict and analyze large-scale software is still a challenge. In this paper we use complex networks theory to study software structure; in particular, we visualize the software graph and use the k-core to study it based on a recursive pruning of the least connected vertices. Different types of software are analyzed and some new noticeable properties are found, such as similar coreness, the vital highest core, high-core connecting tendency, and evolution stability. These features suggest that software is organized in a defined hierarchy of increasing centrality from outside to inside. The k-core analysis can help developers to improve software understanding, instruction test, and measurement and evaluation of the system in development.     

Batch RNAi selector: a standalone program to predict specific siRNA candidates in batches with enhanced sensitivity

RNA interference (RNAi) is a popular and effective method for silencing gene expression. siRNAs should be gene-specific and effective to achieve specific and potent gene silencing. However, most currently available siRNA design programs are web-based programs that either require each sequence be submitted individually, making large-batch analyses difficult to conduct, or only provide limited options for searching off-target candidates (e.g. NCBI-BLAST). We have developed a stand-alone, enhanced RNAi design program that overcomes these shortcomings. We have implemented WU-BLAST, FASTA and SSEARCH homology searches for siRNA candidates to improve gene specific siRNA selection and to identity siRNA candidates that could lead to off-target gene silencing. We also included many new features such as siRNA score calculation and calculation of siRNA internal stability to help select highly potent siRNAs. This program is freely available for academic and commercial use (), and can be installed and run on any Linux machine. Our program automates the search for siRNAs and the resulting data files including a list of siRNA primers with scores and database search results for each siRNA candidate are stored locally for easy retrieval and inspection when needed.     

MOSBY: a molecular structure viewer program with portability and extensibility

A molecular structure viewer program, MOSBY has been developed for studies that use atomic coordinates to understand the structures of protein molecules. The program is designed to be portable with a comprehensive user interface by our high-throughput graphics library. In addition, it cooperates with extension modules customized for individual research topics and analysis. For example, an electron density module loads and displays electron density maps derived in X-ray crystallographic analysis superimposed to an atomic model. A molecular dynamics module reads a trajectory file of the results of molecular dynamics calculations and animates the structure. These plug-in modules are devised to function without modification to the MOSBY program. For variations of analysis and calculations with atomic coordinates, the portability and extensibility illustrated by MOSBY play an important rule in scientific computational tools with active software development.     

The mapping method as a toolbox to analyze,design, and optimize micromixers

The mapping method is employed as an efficient toolbox to analyze, design, and optimize micromixers. A new and simplified formulation of this technique is introduced here and applied to three micromixers: the staggered herringbone micromixer (SHM), the barrier-embedded micromixer (BEM), and the three-dimensional serpentine channel (3D-SC). The mapping method computes a distribution matrix that maps the color concentration distribution from inlet to outlet of a micromixer to characterize mixing in a quantitative way. Once the necessary distribution matrices are obtained, computations are fast and numerous layouts of the mixer are easily evaluated, resulting in an optimal design. This approach is demonstrated using the SHM and the BEM as typical examples. Mixing analysis in the 3D-SC illustrates that also complex flows, for example in the presence of back-flows, can be efficiently dealt with by using the new formulation of the mapping method.     

Constructing a theory of a data structure as an aid to program development

Summary This paper illustrates an extension to the method of developing programs via abstract data types. In order to make the proofs shorter and more intuitive a collection of lemmas (theory) is constructed for the main data types (trees). The problem used as an example is the recording of equivalence relations, one of the programs given is based on the Fischer-Galler algorithm.     

Graphical program to display a testbed block diagram with real-time data on an IBM personal computer

A graphical program called TESTBED was written in Pascal in summer 1985 for NASA Lewis Research Center, Cleveland, Ohio. TESTBED displays on an IBM Personal Computer/XT a block diagram of the DC testbed for the power management and distribution system for the space station. When the testbed, which will contain photovoltaic arrays, batteries, and loads, is deployed in the field, it will be permanently connected to the IBM PC/XT via direct memory access. Sensors attached to the testbed in the field will continually collect and updata data in real time. The program will superimpose the real-time data on the block diagram of the testbed displayed on the screen of the IBM PC/XT. The program uses procedures contained in Metawindow, a software package of graphics utilities written by Metagraphics Corp., Mountain View, California.     

Mathematical model and FORTRAN IV program to predict flow, bed topography and grain size in open-channel bends

A mathematical model is presented to calculate steady, nonuniform flow, bed topography, and bed-sediment size in noncircular open-channel bends. Bed topography and grain size are predicted by consideration of the balance of fluid, frictional, and gravity forces acting on sediment particles traveling over the bed. Local mean flow velocity and effective bed shear acting on sediment particles are calculated using Engelund's method. A FORTRAN IV computer program which calculates and plots values of grain size, depth and various flow parameters on a series of maps is given. Details of input requirements and an illustrative sample run are included.     

A simulation program to display specific digestion products of predicted RNA foldings.

A parameterizable program in Pascal was developed for VAX/VMS computers to simulate the autoradiograms of gel-separated RNA fragments generated by partial cleavage of a folded RNA molecule using five specific RNases. Each screen displays the results of cleavage by either one enzyme or all five, with the RNA molecule labeled at either of its ends (5' or 3'); each run is performed with three different lengths and against a ladder containing alkaline hydrolysis products of the same RNA molecule as size markers. The program should be useful for comparing actual results with predicted functional foldings of RNA molecules.