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Proceedings of the 2006 symposium on Eye tracking research & applications

作者： Hidetake Uwano Masahide Nakamura Akito Monden Ken-ichi Matsumoto Nara Institute of Science and Technology

ISBN: (纸本)9781595933058

This paper proposes to use eye movements to characterize the performance of individuals in reviewing source code of computer programs. We first present an integrated environment to measure and record the eye movements of the code reviewers. Based on the fixation data, the environment computes the line number of the source code that the reviewer is currently looking at. The environment can also record and play back how the eyes moved during the review process. We conducted an experiment to analyze 30 review processes (6 programs, 5 subjects) using the environment. As a result, we have identified a particular pattern, called scan, in the subjects' eye movements. Quantitative analysis showed that reviewers who did not spend enough time for the scan tend to take more time for finding defects.

关键词： human factor eye movement computer program source code review

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BuildQSAR: A New computer program for QSAR Analysis

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Molecular Informatics 2003年第6期19卷

作者： Daniel Barbosa de Oliveira Anderson Coser Gaudio Departamento de Física – CCE – Universidade Federal do Espírito Santo Campus de Goiabeiras Vitória ES 29060–900 Brazil

A new computer program called BuildQSAR has been designed to help the QSAR practitioner on the task of building and analyzing quantitative models through regression analysis. The main part of the program is a spreadsheet, in which the user can enter with the data set composed by the structure definition of the compounds, one or more types of biological activity values and many physicochemical properties. The program has an external data bank, which includes the values of many known substituent parameters. The common tasks that can be performed by the program are: (a) linear, quadratic and bilinear models; (b) graphics analysis; (c) correlation analysis and; (d) hypothesis testing. BuildQSAR can also: (e) build subsets of the data set that include groups of compounds chosen by the user; (f) create new variables, derived from the existing ones, and create many types of indicator variables; (g) build data sets directly from the data bank by selecting the substituents and the variables therein; (h) perform variable selection by systematic search and genetic algorithm; (i) perform cross-validation of specific models; (j) eliminate outliers and analyze the resulting model; and others. The program was coded in Delphi 5 and runs in Windows 95/98/00/NT environments.

关键词： Quantitative structure-activity relationships multiple linear regression QSAR data set computer program regression analysis variable selection Hansch analysis linear parabolic and bilinear models

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SIMQUADNMR: a program for simulation and interpretation of multiple quantum-filtered NMR spectra of quadrupolar nuclei

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JOURNAL OF MAGNETIC RESONANCE 2005年第1期172卷 142-151页

作者： D'Amelio, N Gaggelli, E Molteni, E Valensin, G Univ Siena Dept Chem I-53100 Siena Italy Univ Siena NMR Ctr I-53100 Siena Italy

In this paper, we present a computer program which simulates NMR multiple quantum-filtered spectra of quadrupolar nuclei as a function of physical parameters, of the type of experiment and experimental conditions. The program works by solving relaxation theory equations for the given system, and it can be useful in order to plan the ideal conditions to set up specific experiments or to give a physical interpretation of experimental results. The program allows to independently follow the dependence of individual coherences and relaxation rates as a function of up to 50 parameters regarding the physical properties of the system under investigation, sample conditions and instrumental setup making it an helpful tool also for teaching purposes. (C) 2004 Elsevier Inc. All rights reserved.

关键词： quadrupolar NMR computer program simulation multiple quantum-filtered spectra

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Software news and updates -: Zori 1.0:: A parallel quantum Monte Carlo electronic structure package

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JOURNAL OF COMPUTATIONAL CHEMISTRY 2005年第8期26卷 856-862页

作者： Aspuru-Guzik, A Salomón-Ferrer, R Austin, B Perusquía-Flores, R Griffin, MA Oliva, RA Skinner, D Domin, D Lester, WA Univ Calif Berkeley Dept Chem Kenneth S Pitzer Ctr Theoret Chem Berkeley CA 94720 USA Lawrence Berkeley Natl Lab Div Chem Sci Berkeley CA 94720 USA Lawrence Berkeley Natl Lab ERULF Program 2001 Berkeley CA 94720 USA Lawrence Berkeley Natl Lab High Performance Comp Res Berkeley CA 94720 USA Lawrence Berkeley Natl Lab Natl Energy Res Sci Comp Ctr Berkeley CA 94720 USA

The Zori 1.0 package for electronic structure computations is described. Zori performs variational and diffusion Monte Carlo computations as well as correlated wave function optimization. This article presents an over... 详细信息

关键词： electronic structure quantum Monte Carlo linear diffusion Monte Carlo quantum chemistry computer program computational chemistry

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Concepts in sediment budgets

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JOURNAL OF COASTAL RESEARCH 2005年第2期21卷 307-322页

作者： Rosati, JD USA Corps Engineers Engineer Res Dev Ctr Coastal & Hydraul Lab Vicksburg MS 39180 USA

The sediment budget is fundamental in coastal science and engineering. Budgets allow estimates to be made of the volume or volume rate of sediment entering and exiting a defined region of the coast and the surplus or deficit 01 remaining in that region. Sediment budgets have been regularly employed with variations in approaches to determine the sources and sinks through application of the primary conservation of mass equation. Historically, sediment budgets have been constructed and displayed on paper or maps. Challenges in constructing a sediment budget include determining the appropriate boundaries of the budget and interior cells;defining the possible range of sediment transport pathways, and the relative magnitude of each;representing the uncertainty associated with values and assumptions in the budget;and testing the sensitivity of the series of budgets to variations in the unknown and temporally-changing values. These challenges are usually addressed by representing a series of budget alternatives that are ultimately drawn on paper, maps, or graphs. Applications of the methodology include detailed local-scale sediment budgets, such as for an inlet or beach fill project, and large-scale sediment budgets for the region surrounding the study area. The local-scale budget has calculation cells representing features on the order of 10s to 100s of meters, and it must be shown separately from the regional sediment budget, with cells ranging from 100s of meters to kilometers. This paper reviews commonly applied sediment budget concepts and introduces new considerations intended to make the sediment budget process more reliable, streamlined, and understandable. The need for both local and regional sediment budgets is discussed, and the utility of combining, or collapsing, cells is shown to be beneficial for local budgets within a regional system. Collapsing all cells within the budget creates a "macrobudget," which can be applied to check for overall balance of values.

关键词： uncertainty sensitivity testing Long Island New York Ocean City Inlet Maryland regional scale computer program beaches

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The EpiLink record linkage software - Presentation and results of linkage test on cancer registry files

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METHODS OF INFORMATION IN MEDICINE 2005年第1期44卷 66-71页

作者： Contiero, P Tittarelli, A Tagliabue, G Maghini, A Fabiano, S Crosignani, P Tessandori, R Ist Nazl Studio & Cura Tumori Canc Registry Div I-20133 Milan Italy Azienda Sanit Locale Prov Sondrio Sondrio Italy

Objectives: Record linkage, the process of bringing together separately compiled but related records from different databases, is essential in many area's of biomedical research. We developed a, record linkage program (EpiLink), which employs a simple mathematical approach. We describe the program and present results obtained testing it in a linkage task. Methods: EpiLink was designed to be flexible with user-friendly settings to tailor linkage and operating parameters to specific linkage tasks, and employ deterministic, probabilistic or sequential deterministic-probabilistic linkage strategies as required. The user con also standardize data format, examine linkage results and accept of discard them. We used EpiLink to link a subset of cases of the Lombardy Cancer Registry (20,724 records) with the Social Security file of the population (1,021,846 records) covered by the registry. I The linkage strategy was deterministic, followed by several probabilistic linkage steps. Results: Manual inspection of the-results showed that EpiLink achieved 98.8% specificity and 96.5% sensitivity. Conclusions. EpiLink is a practical and accurate means of linking records from different databases that con be used by non-statisticians and is efficient in terms of human and financial resources.

关键词： cancer registry record linkage computer program follow-up methods

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MoCalc: A new graphical user interface for molecular calculations

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JOURNAL OF COMPUTATIONAL CHEMISTRY 2005年第2期26卷 142-144页

作者： Depizzol, DB Paiva, MHM dos Santos, TO Gaudio, AC Fed Univ Espirito Santo Dept Phys BR-29075910 Vitoria ES Brazil

A new computer program called MoCalc (Molecular Calculations) has been designed to help the computational chemistry practitioner in the task of performing and analyzing molecular calculations. MoCalc is a graphical user interface for the MO calculation programs Gamess and Mopac, and uses Rasmol and Babel for molecule display and file conversion, respectively. In its initial version, MoCalc can execute the following operations: (a) create and handle Gamess and Mopac input files;(b) import any kind of molecular geometry supported by Babel and paste it as Cartesian, internal, or Gaussian-type coordinates on the input file;(c) convert Gamess and Mopac output files to inputs of both programs;(d) edit and validate the keywords that control the Gamess and Mopac calculation procedure;(e) display the input (Mopac) and output (Gamess and Mopac) molecular geometries;(f) run single or multiple (batch) calculations, either interactively or in background;(g) automatically open the output files as soon as the calculation finishes;(h) extract results from the output files, such as energy, charges, dipole, population analysis, wave function, bond orders, and valence analysis, and display them in spreadsheets;(i) calculate reactivity indices derived from the frontier orbital theory and the root-mean-square (rms) deviation of input and output geometries. All the results generated by MoCalc can be promptly transferred to text editors and electronic spreadsheets, which facilitate a detailed subsequent analysis and the publication of the results. MoCalc can also perforin graphical and numerical comparative analysis of the some results when more than one output file is loaded. The program was coded in Visual Basic and runs in Windows 95/98/NT4/ME/2000/XP environments. (C) 2004 Wiley Periodicals, Inc.

关键词： computer program graphical user interface molecular orbital calculation Gamess Mopac Rasmol Babel

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Virtual MRI:: A PC-based simulation of a clinical MR scanner

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ACADEMIC RADIOLOGY 2005年第1期12卷 85-96页

作者： Hackländer, T Mertens, H Hosp Univ Witten Herdecke HELIOS Klinikum Wuppertal Dept Radiol D-42283 Wuppertal Germany

Rationale and Objective. The aim of this project was to simulate the features and functions of a clinical or real-world MR scanner on a personal computer by means of a computer program. The users should be able to change all relevant settings of the virtual scanner and adapt them to the expected pathology. Materials and Methods. The algorithms of the simulation are based on parameter images of the three physical basic properties T1, T2, and proton density. From this, the synthetic images are calculated pixel by pixel on the basis of the well-known formulas of the pulse sequences chosen and modified by the user. The graphical user inter-face is oriented to a real-world MR scanner. The software is programmed in pure Java and is freely available under the GPL license. Results. Besides spin echo pulse sequence, 6 other pulse sequence classes are implemented. Parameters like repetition time and echo time can be adjusted. The choice of parameters like matrix size, slice-thickness, and number of acquisitions has an impact on the signal-to-noise ratio of the images. In a first step, the simulation calculates the signal intensity in k-space. Wraparound and motion artifacts are simulated by modifying the data of k-space. In a last step, a 2D-Fourier transform of k-space data is performed. As the image calculation takes only a few seconds, an interactive manner of working is possible. Conclusion. The simulation has been used in the education of medical students and interns for more than 1 year and has gained widespread acceptance.

关键词： MRI simulation computer program education image synthesis

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Organization and potential function of the mrjp3 locus in four honeybee species

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JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2005年第20期53卷 8075-8081页

作者： Albertová, V Su, SK Brockmann, A Gadau, J Albert, T Univ Wurzburg MSZ D-97078 Wurzburg Germany Zhejiang Univ Coll Anim Sci Hangzhou 310029 Peoples R China Univ Wurzburg Biozentrum Inst Verhaltensphysiol & Soziobiol D-97074 Wurzburg Germany

Royal jelly is a nutritious secretion produced by nurse honeybees to provision queens and growing larvae. Major proteins of royal jelly are mutually similar, and they all belong to the MRJP/yellow protein family (pfam03022). The mrjp3 loci in four traditional honeybee species (Apis mellifera, Apis cerana, Apis dorsata, and Apis florea) were sequenced and found to share high sequence and structural similarities. PCR analyses confirmed the presence of an extensive repetitive region, which showed size and sequence polymorphisms in all species. The evolutionary history of mrjp genes and their repetitive regions was reconstructed from their nucleotide sequences. The analyses proved that the repeat region appeared early in the evolution of the mrjp gene family and that the extreme elongation of the repeat is mrjp3 specific. In the MRJPs was documented a correlation between nitrogen content and repeat length. Therefore, it is argued that the repeat occurred due to a selection for an increase in nitrogen storage for a more efficient nutrition of queens and larvae.

关键词： royal jelly honeybee nutrition nitrogen storage protein MRJP evolution genomic sequence computer program

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PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database

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NUCLEIC ACIDS RESEARCH 2002年第15期30卷 3481-3489页

作者： Ashelford, KE Weightman, AJ Fry, JC Univ Wales Coll Cardiff Cardiff Sch Biosci Cardiff CF10 3TL S Glam Wales

We describe PRIMROSE, a computer program for identifying 16S rRNa probes and PCR primers for use as phylogenetic and ecological tools in the identification and enumeration of bacteria. PRIMROSE is designed to use data from the Ribosomal Database Project (RDP) to find potentially useful oligonucleotides with up to two degenerate positions. The taxonomic range of these, and other existing oligonucleotides, can then be explored, allowing for the rapid identification of suitable oligonucleotides. PRIMROSE includes features to allow user-defined sequence databases to be used. An in silico trial of the program using the RDP database identified oligonucleotides that described their target taxa with a degree of accuracy far greater than that of equivalent currently used oligonucleotides. We identify oligonucleotides for subdivisions of the Proteobacteria and for the Cytophaga-Flexibacter-Bacteroides (CFB) division. These oligonucleotides describe up to 94.7% of their target taxon with fewer than 50 non-target hits, and the authors recommend that they be investigated further. A comparison with PROBE DESIGN within the ARB software package shows that PRIMROSE is capable of identifying oligonucleotides with a higher specificity. PRIMROSE has an intuitive graphical user interface and runs on the Microsoft Windows 95/NT/2000 operating systems. It is open source and is freely available from the authors.

关键词： .oligonucleotides Degenerate computer program RDP probes and primers Ashelford

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