UNIX Version Research Articles

Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies

TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate of the rate and also the associated date of the most recent common ancestor of the sequences, under a model which assumes a constant rate of substitution (molecular clock) but which accommodates the dates of isolation. Confidence intervals for these parameters are also estimated. The approach was applied to a sample of 17 dengue virus serotype 4 sequences, isolated at dates ranging from 1956 to 1994. The rate of substitution for this serotype was estimated to be 7.91 x 10(-4) substitutions per site per year (95% confidence intervals of 6.07 x 10(-4), 9.86 x 10(-4)). This is compatible with a date of 1922 (95% confidence intervals of 1900-1936) for the most recent common ancestor of these sequences. TipDate can be obtained by WWW from http://evolve.zoo. ox.ac.uk/software. The package includes the source code, manual and example files. Both UNIX and Apple Macintosh versions are available from the same site.

Web seismic Un ∗x: making seismic reflection processing more accessible

Web Seismic Un ∗x is a browser-based user interface for the Seismic Un ∗x freeware developed at Colorado School of Mines. The interface allows users to process and display seismic reflection data from any remote platform that runs a graphical Web browser. Users access data and create processing jobs on a remote server by completing form-based Web pages whose Common Gateway Interface scripts are written in Perl. These scripts supply parameters, manage files, call Seismic Un ∗x routines and return data plots. The interface was designed for undergraduate commuter students taking geophysics courses who need to: (a) process seismic data and other time series as a class using computers in campus teaching labs and (b) complete course assignments at home. Students from an undergraduate applied geophysics course tested the Web user interface while completing laboratory assignments in which they acquired and processed common-depth-point seismic reflection data into a subsurface image. This freeware, which will be publicly available by summer 1999, was developed and tested on a Solaris 2.5 server and will be ported to other versions of Unix, including Linux.

A procedure for generating bootstrap samples for the validation of nonlinear mixed-effects population models

A method is presented for automated preparation of bootstrap data samples and their presentation to NONMEM for use in the validation of population pharmacokinetic or pharmacodynamic models, which have been developed with relatively small numbers of subjects. The bootstrap sampling procedure involves the use of an MS-DOS batch file and a script file for use with the public-domain text processing program, AWK, which is a single EXE file (48k in size for the version used in this report). A UNIX version of AWK is also available and UNIX users can adapt the process to their needs. Its use obviates the need for expensive, high-end statistical packages and associated script files written using in-built programming languages. The method can easily be adapted to bootstrap sampling requirements in other biomedical modelling applications.

Associations Between Reported Dietary Practices of College Students and Sources of Nutrition Information

Nutrition research involving college students is common due to the availability of subjects. Most current studies examine either the reported eating behaviors of students or where they get their nutrition information. The purposes of this study were to (1) categorize students based on their reported nutrition-related practices, (2) to determine if these groups exhibit preferences for where they get their nutrition information, and (3) to determine if the introduction of computer technology into the classroom affects nutrition information sources. An attitudinal questionnaire was developed in 1995. The questionnaire was reviewed by a six-member panel, pilot-tested, and questions were eliminated through factor analysis. The final questionnaire contained 104 questions plus demographics. The survey was administered to fall semesters 1996 and 1997 of an introductory nutrition class in the first (pre-test, n=332, 367) and last (post-test, n=170, 373) weeks of the semester. SPSS (UNIX version 6.2) was used to analyze the data. Frequencies, crosstabulations with significant chi-squares, t-tests, factor analysis and ANOVA were used. Significant relationships were found between gender and the amount of calories, protein, and meat consumed. Television, magazines, and other people were the most often used sources for nutrition information. There was a significant relationship between gender and the use of magazines. The use of the Internet did not affect where students got their nutrition information.

Linux, open source, and software's future

Developed by Torvalds in 1991 from Minix, a simplified version of Unix intended for educational use, Linux has grown from a mere 10000-line kernel to a full-featured OS with more than 1.5 million lines of code. Once thought the exclusive province of hobbyists, students, and hard-core programmers, Linux has quietly, unassumingly slipped into the software mainstream. The paper discusses the advantages of Linux and considers massively parallel software development. It also discusses open source development.

Design of virtual-labo-system for metabolic engineering: Development of biochemical engineering system analyzing tool-kit (BEST KIT)

BEST-KIT is an efficient and user-friendly “biochemical engineering system analyzing tool-kit” integrated the following key modules: 1) mathematical modeling and editing of reaction-scheme, 2) automatic derivation of differential equations, 3) numerical calculation, 4) nonlinear optimization, 5) visualization, 6) retrieve the information on reaction mechanism and kinetic parameters from data-base of metabolic pathways. The users of this simulator are assumed to be unfamiliar with computer technology and with computer programming. The integrated interface (UNIX version) is based on Xlib, XToolkit and OSF/Motif Widget.

Asymmetric Methylation in the Hypermethylated CpG Promoter Region of the Human L1 Retrotransposon

We have investigated the function and sequence specificity of DNA methylation in the hypermethylated CpG island promoter region of the endogenous human LINE-1 (L1) retrotransposon family. In nontransformed human embryonic fibroblasts, inhibition of DNA methylation with 5-azadeoxycytidine induced a greater than 4-fold increase in transcription from potentially functional L1 elements without increasing the transcription level of the majority of degenerate elements, implicating hypermethylation in the repression of L1 activity. Using bisulfite genomic sequencing to assess the pattern of methylation in a subset of nondegenerate L1 elements, we found 29 sites within a 460-base pair region of the noncoding (top) DNA strand of the L1 promoter in which cytosine methylation was maintained with high efficiency. Of these, 25 were at CG dinucleotides and four were in non-CG sites. When the methylation sites were analyzed for the complementary (bottom) strand, the only highly conserved sites of methylation were in CG dinucleotides. Several of these sites of CG methylation in the bottom (coding) strand were at positions where top (noncoding) strand-derived sequences were unmethylated, suggesting that these sites might be maintained in a hemi-methylated state. Hence, there is a subset of human L1 elements in which methylation is efficiently maintained in asymmetric non-CG sites and further that this non-CG methylation may be part of a wider phenomenon involving hemi-methylation at CG dinucleotides. Maintenance of asymmetric methylation at non-CG sites (and possibly at hemi-methylated CG dinucleotides) could be through a novel DNA methyltransferase activity. Alternatively, the promoter region of L1 elements may be induced by factor binding to form some type of secondary structure that presents as a highly efficient substrate for de novo methylation.

An evaluation of the real-time performances of SVR4.0 and SVR4.2

UNIX is one of the most widely used operating systems on current workstations. However, UNIX was originally designed as a multitasking and time-sharing system with little concern for supporting real-time applications. Recent versions of UNIX have incorporated real-time features and the designers of these systems claim to provide better response times than the standard UNIX kernel. In order to assess the benefits of these new features and verify these claims, this paper compares the real-time performances of two popular versions of UNIX namely System V Release 4.0 and System V Release 4.2 for the Intel platform.

EGS4 dosimetry calculations for cylindrically symmetric brachytherapy sources.

Computer algorithms for electron binding correction to Compton scattering and for detailed simulation of K-edge characteristic x-ray production were incorporated into EGS4 unix version 2.0. Based on detailed modelling of the internal structures of sources, the modified version was used to calculate dose rate constants, radial dose functions, and anisotropy functions on the long axis for an 125I model 6711 source, 169Yb Type 5 and Type 8 sources, and a stainless steel clad (SS) 192Ir source. The geometry of these sources is cylindrically symmetric. Calculated results are generally in good agreement with corresponding values recommended by TG-43 and Monte Carlo results published by other authors. The influence of electron binding in Compton scattering on the calculated dose distribution for an 125I model 6711 source in water, and of different characteristic x-ray production models for 125I model 6711 and 192Ir SS sources, were also studied.

Computer-assisted analysis of singlet-triplet rotational spectra: application to case (A), case (B) and case (AB) coupling cases in polyatomic molecules

A non-graphical, character-based computer program for the least-squares analysis of the high-resolution rotational spectra of singlet-triplet transitions in orthorhombic molecules has been developed under the ANSI C programming language. The program is applicable to molecules which show either Hund's case (A) or case (B) or case (AB) type splittings. Up to 22 rotational, spin, centrifugal distortion and spin-centrifugal distortion constants may be varied. Only constants of the excited state may be fitted. The program has been tested under the HP-UX and DOS/Windows environments. J-values up to 255 can be accommodated in the UNIX version of the program while the DOS/Windows version is limited to J = 50. A compiled and linked executable file is available for the DOS/Windows version for those without access to a C compiler. A limited band contour capability is provided through the production of an ASCII file of frequency versus intensity for the calculated spectrum.

The EM Program Package: A Platform for Image Processing in Biological Electron Microscopy

EM is a software package developed for image processing in the field of biological electron microscopy. After a brief summary of its history, an outline of the package is given, by describing some characteristic features rather than by a complete report of all facilities. New developments, connected with the introduction of a UNIX version and the advent of automated electron microscopy, are described in more detail.

Machine learning and planning for data management in forestry

The Seidam project uses an AI planning-based approach that combines three problem-solving methods-transformational analogy, derivational analogy and goal regression-to automatically answer forest-management queries. The project is conducted under NASA's Applied Information Systems Research Program. Seidam, which runs on a Sun Sparcstation using the Solaris 2.3 version of Unix, is a complex system that relies on extensive cooperation between expert systems and processing agents.

Making the Figaro Data Reduction System Portable

AbstractThe Figaro data reduction system was originally written for DEC VAXes running VMS, and little attention was paid to making it portable. Recently, however, a cooperative effort between the AAO, MSSSO, UNSW, the UK Starlink network and Caltech has resulted in a version for UNIX. This new version has been run under VMS and three different versions of UNIX. The files produced by any version may be read directly by any other version, although Figaro has a particularly complex file format which contains an extensible, self-defining, hierarchical structure of data items. This complexity has allowed the addition of error and quality data, as well as specific structures used, for example, for echelle data. Figaro is written mainly in Fortran (with numerous DEC extensions) but there is also a significant use of C. While C and Fortran are reasonably portable, the way one is called from the other is less portable and needs careful handling. Ports to other systems are possible, with effort; a Macintosh version is being considered.

Resources for networks in less-industrialized nations

True global connectivity is years away. Countries must first have an internal network, no matter how small, before linking electronically to the rest of the world's networks. The article considers the evolution of the Relcom (Reliable Communications) network in the ex Soviet Union. Relcom is a spin off of the Demos Cooperative, which in 1982 began distributing a version of Unix in the Soviet Union. (Demos is a Russian acronym for interactive portable operating system.) Network related resources-communication infrastructure, software, hardware, people, and sponsorship and applications-differ from one LIN to the next. For example, Relcom and the much smaller Cuban networks use similar technology and both lack capital, but the communication infrastructures, user and technician pools, and applications are quite different. Furthermore, all computer networks, regardless of nation, are shaped and constrained by communication, economic, and education policies. >

BEST-KIT; Development of Biochemical Engineering System Analyzing Tool-KIT

The final goal of this study is the implementation of an efficient and user-friendly “biochemical engineering system analyzing tool (BEST-KIT)” integrated the following key modules: 1) mathematical modeling and editing of reaction scheme, 2) aulomatic derivation of simultaneous nonlinear differential equations of reaction scheme, 3)numcrical simulation of reaction scheme, 4)visualizalion of the numerical results, S)cvaluation of kinetic parameters and estimation of unknown parameters, 6)estimation of control variable for artificial control of reactor system. This paper mainly deals with the development of integrated interface (UNIX version) of these key modules and with the algorithm of automatic derivation of simultaneous nonlinear differential equations.

Memory system performance of UNIX on CC-NUMA multiprocessors

This study characterizes the performance of a variant of UNIX SVR4 on a large shared-memory multiprocessor and analyzes the effects of possible OS and architectural changes. We use a nonintrusive cache miss monitor to trace the execution of an OS-intensive multiprogrammed workload on the Stanford DASH, a 32-CPU CC-NUMA multiprocessor (CC-NUMA multiprocessors have cache-coherent shared memory that is physically distributed across the machine). We find that our version of UNIX accounts for 24% of the workload's total execution time. A surprisingly large fraction of OS time (79%) is spent on memory system stalls, divided equally between instruction and data cache miss time. In analyzing techniques to reduce instruction cache miss stall time, we find that replication of only 7% of the OS code would allow 80% of instruction cache misses to be serviced locally on a CC-NUMA machine. For data cache misses, we find that a small number of routines account for 96% of OS data cache stall time. We find that most of these misses are coherence (communication) misses, and larger caches will not necessarily help. After presenting detailed performance data, we analyze the benefits of several OS changes and predict the effects of altering the cache configuration, degree of clustering, and cache coherence mechanism of the machine. (This paper is available via http://wwwflash.stanford.edu.)

Gnome--an Internet-based sequence analysis tool.

Gnome (GenomeNet Open Mail-service Environment) is a sequence analysis tool that enables an end-user to make use of several Internet- (mainly e-mail) based services with an easy-to-use graphical user interface. Users can conduct homology and motif searches, and database-entry retrieval against the latest databases by emitting search requests to and receiving their results form a search-server by e-mail. The search results are viewed and managed efficiently with this system. The Macintosh and X (Motif) versions of the Gnome client and the UNIX version of the Gnome server are available to academic users free of charge.

Securing UNIX-Based Networks

For many users and organizations, UNIX has become the operating system of choice for distributed systems, because of its networking capabilities and the availability of UNIX-based network protocols (e.g., TCP/IP). UNIX networks typically consist of workstations and one or more file servers linked together to form a local area network (LAN); these LANs may in turn be connected to other widely dispersed networks, thereby forming a wide area network (WAN). Protection of information on such networks can pose a serious challenge to security professionals. This article addresses the basic network security features available with most current versions of UNIX.

A hypertext-like approach to navigating through the GCG sequence analysis package.

Programs of the recently released Unix version of the Genetics Computing Group (GCG) sequence analysis package can now be accessed via a user-friendly hypertext-like navigation system, HYGCG. The resultant system organizes the diverse suite of programs into logical groups, and provides a guide and explanation of commands. In addition, for users unfamiliar with the Unix operating system, the program also provides a similar interface to commonly used Unix commands. Options for personal customization and expansion to accommodate GCG extensions and other software are also provided. This system should be useful especially to the inexperienced or infrequent user as context-sensitive on-line help is provided within this simple and consistent approach. Written in the C language and using the curses and termcap libraries, the system is easily portable to most Unix environments and has been made freely available via anonymous file transfer protocol (FTP) through the Internet global computer network. No modification of the GCG package is needed.

Software for information storage and retrieval tested, evaluated and compared Part IV — Indexing and full‐text retrieval programs

In this article, the fourth in a series on microcomputer software for information storage and retrieval, test results of six indexing and full‐text retrieval programs are presented and various properties and qualities of these programs are discussed. The common feature of programs in these categories is that they are primarily meant to retrieve words (or combinations of them) in large text files. To do this they either simply index existing text files in one or more formats (indexing programs), or they store and index them in their own database format (full‐text retrieval programs). The programs reviewed in this issue are the indexing programs Ask‐It, Texplore and ZYindex and the full‐text retrieval programs KAware, TextMaster and WordCruncher. All programs run under MS‐DOS. In addition ZYindex has a Windows and a Unix version and TextMaster is also available for Unix. For each of the six programs almost 100 facts and test results are tabulated. The programs are also discussed individually.