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Software

About: Software is a research topic. Over the lifetime, 130577 publications have been published within this topic receiving 2028987 citations. The topic is also known as: computer software & computational tool.


Papers
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Journal ArticleDOI
TL;DR: DIYABC v2.0 implements a number of new features and analytical methods, including efficient Bayesian model choice using linear discriminant analysis on summary statistics and the serial launching of multiple post-processing analyses.
Abstract: DIYABC is a software package for a comprehensive analysis of population history using approximate Bayesian computation on DNA polymorphism data. Version 2.0 implements a number of new features and analytical methods. It allows (i) the analysis of single nucleotide polymorphism data at large number of loci, apart from microsatellite and DNA sequence data, (ii) efficient Bayesian model choice using linear discriminant analysis on summary statistics and (iii) the serial launching of multiple post-processing analyses. DIYABC v2.0 also includes a user-friendly graphical interface with various new options. It can be run on three operating systems: GNU/Linux, Microsoft Windows and Apple Os X. Freely available with a detailed notice document and example projects to academic users at http://www1.montpellier.inra.fr/CBGP/diyabc CONTACT: estoup@supagro.inra.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

897 citations

Journal ArticleDOI
TL;DR: The tools needed for analysis and visualization of three‐dimensional human brain functional magnetic resonance image results are outlined, covering the processing categories of data storage, interactive vs batch mode operations, visualization, spatial normalization, analysis of functional activation, integration of multiple datasets, and interface standards.
Abstract: The tools needed for analysis and visualization of three-dimensional human brain functional magnetic resonance image results are outlined, covering the processing categories of data storage, interactive vs batch mode operations, visualization, spatial normalization (Talairach coordinates, etc.), analysis of functional activation, integration of multiple datasets, and interface standards. One freely available software package is described in some detail. The features and scope that a generally useful and extensible fMRI toolset should have are contrasted with what is available today. The article ends with a discussion of how the fMRI research community can cooperate to create standards and develop software that meets the community's needs.

894 citations

Journal ArticleDOI
TL;DR: This paper calculated the object-oriented metrics given by Chidamber and Kemerer to illustrate how fault-proneness detection of the source code of the open source Web and e-mail suite called Mozilla can be carried out and checked the values obtained against the number of bugs found in its bug database to validate the usefulness of these metrics for fault- proneness prediction.
Abstract: Open source software systems are becoming increasingly important these days. Many companies are investing in open source projects and lots of them are also using such software in their own work. But, because open source software is often developed with a different management style than the industrial ones, the quality and reliability of the code needs to be studied. Hence, the characteristics of the source code of these projects need to be measured to obtain more information about it. This paper describes how we calculated the object-oriented metrics given by Chidamber and Kemerer to illustrate how fault-proneness detection of the source code of the open source Web and e-mail suite called Mozilla can be carried out. We checked the values obtained against the number of bugs found in its bug database - called Bugzilla - using regression and machine learning methods to validate the usefulness of these metrics for fault-proneness prediction. We also compared the metrics of several versions of Mozilla to see how the predicted fault-proneness of the software system changed during its development cycle.

894 citations

Journal ArticleDOI
TL;DR: A comprehensive but simple‐to‐use software package called DPS (Data Processing System) has been developed to execute a range of standard numerical analyses and operations used in experimental design, statistics and data mining in entomology.
Abstract: A comprehensive but simple-to-use software package called DPS (Data Processing System) has been developed to execute a range of standard numerical analyses and operations used in experimental design, statistics and data mining. This program runs on standard Windows computers. Many of the functions are specific to entomological and other biological research and are not found in standard statistical software. This paper presents applications of DPS to experimental design, statistical analysis and data mining in entomology.

892 citations

Journal ArticleDOI
TL;DR: MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data, is developed.
Abstract: The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity. We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The advantages of this program over other software are that it is open-source freeware, can analyze a large number of sequences simultaneously, can visualize both sequence alignment and similarity/identity values concurrently, employs global alignment in calculations, and has been formatted to run under both the Unix and the Microsoft Windows Operating Systems. We are presently completing the Macintosh-based version of the program.

892 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20246
20235,523
202213,625
20213,455
20205,268
20195,982