Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “software tools”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources
PubMed2002

A direct measure of facial similarity and its relation to human similarity perceptions.

Research is reported on a measure of facial similarity in which the similarity of 2 faces is defined as the Euclidean distance between them in a principal-component space. Five studies were conducted in which participants rated sets of facial images, and in which the measure was applied to 2 problems in the eyewitness literature. Comparisons of ratings with distances derived from the principal-component analysis suggest that the measure corresponds reasonably well to perceptions of facial similarity. In addition, the measure correlates strongly with empirical measures of lineup fairness and is related to eyewitness identification performance. Further potential applications include a software tool for constructing arrays of faces of varying similarity, and a software tool for reconstructing facial images from memory.

Adolescent↗
PubMed2002

ARROGANT: an application to manipulate large gene collections.

ARROGANT (ARRay OrGANizing Tool) is a software tool developed to facilitate the identification, annotation and comparison of large collections of genes or clones. The objective is to enable users to compile gene/clone collections from different databases, allowing them to design experiments and analyze the collections as well as associated experimental data efficiently. ARROGANT can relate different sequence identifiers to their common reference sequence using the UniGene database, allowing for the comparison of data from two different microarray experiments. ARROGANT has been successfully used to analyze microarray expression data for colon cancer, to compile genes potentially related to cardiac diseases for subsequent resequencing (to identify single nucleotide polymorphisms, SNPs), to design a new comprehensive human cDNA microarray for cancer, to combine and compare expression data generated by different microarrays and to provide annotation for genes on custom and Affymetrix chips.

Base Sequence↗
PubMed2002

Trabecular microstructure and surface changes in the greater tuberosity in rotator cuff tears.

OBJECTIVE: When planning surgery in patients with rotator cuff tear, strength of bone at the tendon insertion and trabecular bone structure in the greater tuberosity are usually taken into consideration. We investigated radiographic changes in bone structure of the greater tuberosity in rotator cuff tears. DESIGN: Twenty-two human cadaveric shoulders from subjects ranging from 55 to 75 years of age were obtained. The integrity of the rotator cuff was examined by sonography to determine if it is intact without any tear, or torn partially or completely. The humeral head was sectioned in 3 mm thick coronal slab sections and microradiographed. After digitization of the microradiographs and imaging processing with in-house semi-automated image processing software tools developed using software interfaces on a Sun workstation, the trabecular histomorphometrical structural parameters and connectivity in the greater tuberosity were quantified. The degenerative changes on the surface of the greater tuberosity were interpreted blindly by 2 independent readers. RESULTS: Among the 22 shoulder specimens, the rotator cuff was found intact in 10 shoulders, partially in 7 and fully torn in 5. Statistically significant loss in apparent trabecular bone volume fraction, number of trabecular nodes, and number of trabecular branches, and a statistically significant increase in apparent trabecular separation and number of trabecular free ends were found in the greater tuberosity of the shoulders with tears. The loss was greater in association with full tear than in partial tear. Thickening of the cortical margin of the enthesis, irregularity of its surface, and calcification beyond the tidemark were observed in 2 (20%) shoulders with intact rotator cuff, in 6 (86%) shoulders with partial tear, and in 5 (100%) shoulders with full tear. CONCLUSIONS: Rotator cuff tears are associated with degenerative changes on the bone surface and with disuse osteopenia of the greater tuberosity. Aging, degenerative enthesopathy of the supraspinatus tendon, and rotator cuff tears appear closely related.

Aged↗
PubMed2004

A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry.

We present a software tool for visualizing data obtained from analyzing complex peptide mixtures by liquid chromatography (LC) electrospray ionization (ESI) mass spectrometry (MS). The data are represented as a two-dimensional density plot. For experiments employing collision-induced dissociation (CID), links are embedded in the image to the CID spectra and the corresponding peptide sequences that are represented by the respective feature. The image provides an intuitive method to evaluate sample quality and the performance of an LC-ESI-MS system and can be used to optimize experimental conditions. Local patterns of the image can also be used to identify chemical contaminants and specific peptide features. Therefore, this software tool may have broad application in MS-based proteomics.

Chromatography, Liquid↗
PubMed2007

Three-dimensional CT angiography: a new technique for imaging microvascular anatomy.

To date there has been no satisfactory research method for imaging microvascular anatomy in three dimensions (3D). In this article we present a new technique that allows both qualitative and quantitative examination of the microvasculature in 3D. In 10 fresh cadavers (7 females, 3 males, mean age 68 years), selected arteries supplying the abdominal wall and back were injected with a lead oxide/gelatin contrast mixture. From these regions, 30 specimens were dissected free and imaged with a 16-slice spiral computed tomographic (CT) scanner. Using three-dimensional CT (3D-CT) angiography, reconstructions of the microvasculature of each specimen were produced and examined for their qualitative content. Two calibration tools were constructed to determine (1) the accuracy of linear measurements made with CT software tools, and (2) the smallest caliber blood vessel that is reliably represented on 3D-CT reconstructions. Three-dimensional CT angiography produced versatile, high quality angiograms of the microvasculature. Correlation between measurements made with electronic calipers and CT software tools was very high (Lin's concordance coefficient, 0.99 (95% CI 0.99-0.99)). The finest caliber of vessel reliably represented on the 3D-CT reconstructions was 0.4 mm internal diameter. In summary, 3D-CT angiography is a simple, accurate, and reproducible method that imparts a much improved perception of anatomy when compared with existing research methods. Measurement tools provide accurate quantitative data to aid vessel mapping and preoperative planning. Further work will be needed to explore the full utility of 3D-CT angiography in a clinical setting.

Abdominal Wall↗
PubMed2005

A novel approach for clustering proteomics data using Bayesian fast Fourier transform.

MOTIVATION: Bioinformatics clustering tools are useful at all levels of proteomic data analysis. Proteomics studies can provide a wealth of information and rapidly generate large quantities of data from the analysis of biological specimens. The high dimensionality of data generated from these studies requires the development of improved bioinformatics tools for efficient and accurate data analyses. For proteome profiling of a particular system or organism, a number of specialized software tools are needed. Indeed, significant advances in the informatics and software tools necessary to support the analysis and management of these massive amounts of data are needed. Clustering algorithms based on probabilistic and Bayesian models provide an alternative to heuristic algorithms. The number of clusters (diseased and non-diseased groups) is reduced to the choice of the number of components of a mixture of underlying probability. The Bayesian approach is a tool for including information from the data to the analysis. It offers an estimation of the uncertainties of the data and the parameters involved. RESULTS: We present novel algorithms that can organize, cluster and derive meaningful patterns of expression from large-scaled proteomics experiments. We processed raw data using a graphical-based algorithm by transforming it from a real space data-expression to a complex space data-expression using discrete Fourier transformation; then we used a thresholding approach to denoise and reduce the length of each spectrum. Bayesian clustering was applied to the reconstructed data. In comparison with several other algorithms used in this study including K-means, (Kohonen self-organizing map (SOM), and linear discriminant analysis, the Bayesian-Fourier model-based approach displayed superior performances consistently, in selecting the correct model and the number of clusters, thus providing a novel approach for accurate diagnosis of the disease. Using this approach, we were able to successfully denoise proteomic spectra and reach up to a 99% total reduction of the number of peaks compared to the original data. In addition, the Bayesian-based approach generated a better classification rate in comparison with other classification algorithms. This new finding will allow us to apply the Fourier transformation for the selection of the protein profile for each sample, and to develop a novel bioinformatic strategy based on Bayesian clustering for biomarker discovery and optimal diagnosis.

Algorithms↗
PubMed2006

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.

BACKGROUND: The Gene Ontology has become an extremely useful tool for the analysis of genomic data and structuring of biological knowledge. Several excellent software tools for navigating the gene ontology have been developed. However, no existing system provides an interactively expandable graph-based view of the gene ontology hierarchy. Furthermore, most existing tools are web-based or require an Internet connection, will not load local annotations files, and provide either analysis or visualization functionality, but not both. RESULTS: To address the above limitations, we have developed GOLEM (Gene Ontology Local Exploration Map), a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet at http://function.princeton.edu/GOLEM.

Computer Graphics↗
PubMed2000

PSG-EXPERT. An expert system for the diagnosis of sleep disorders.

This paper describes PSG-EXPERT, an expert system in the domain of sleep disorders exploring polysomnographic data. The developed software tool is addressed from two points of view: (1)--as an integrated environment for the development of diagnosis-oriented expert systems; (2)--as an auxiliary diagnosis tool in the particular domain of sleep disorders. Developed over a Windows platform, this software tool extends one of the most popular shells--CLIPS (C Language Integrated Production System) with the following features: backward chaining engine; graph-based explanation facilities; knowledge editor including a fuzzy fact editor and a rules editor, with facts-rules integrity checking; belief revision mechanism; built-in case generator and validation module. It therefore provides graphical support for knowledge acquisition, edition, explanation and validation. From an application domain point of view, PSG-Expert is an auxiliary diagnosis system for sleep disorders based on polysomnographic data, that aims at assisting the medical expert in his diagnosis task by providing automatic analysis of polysomnographic data, summarising the results of this analysis in terms of a report of major findings and possible diagnosis consistent with the polysomnographic data. Sleep disorders classification follows the International Classification of Sleep Disorders. Major features of the system include: browsing on patients data records; structured navigation on Sleep Disorders descriptions according to ASDA definitions; internet links to related pages; diagnosis consistent with polysomnographic data; graphical user-interface including graph-based explanatory facilities; uncertainty modelling and belief revision; production of reports; connection to remote databases.

Computer Systems↗
PubMed2003

A visual approach for the accurate determination of echocardiographic left ventricular ejection fraction by medical students.

BACKGROUND: Previously published reports show that there is significant intraobserver, interobserver, and interinstitutional variability in the determination of left ventricular (LV) ejection fraction (EF) by echocardiography. With the increased deployment of echocardiography (eg, handheld devices), there exists a need for developing a simple, intuitive approach for evaluating LVEF that allows a wider range of physicians to accurately and rapidly determine LVEF. OBJECTIVE: We sought to create a system for assessing LVEF that relies on recognition and matching of patterns, rather than on mathematic calculations and geometric assumptions. METHODS: A library of videoclips of cardiac function was compiled from 54 patients who spanned the spectrum of LVEF. LVEFs were calculated for these patients using standard echocardiographic methods, with further validation of a subsample using cardiac magnetic resonance imaging measurement of LVEF. The library of images was used to create a software tool for assessing LVEF on the basis of a "template-matching" approach. The software tool was then tested on medical students (N=13) to determine whether it enabled relatively untrained individuals to make accurate LVEF estimates. RESULTS: Using a template-matching approach for interpretation of echocardiograms, medical students were able to accurately estimate LVEF after only a limited introduction to echocardiography. Their LVEF estimates showed good correlation and agreement with gold standard (r = 0.88, standard square of the estimate = 6.0, limits of agreement = +12.0%, -15.6%). CONCLUSIONS: A new visual approach for assessing cardiac function using template matching can accurately estimate LVEF. With minimal training, medical students can make LVEF estimates that correlate well with gold standard. The application of this new approach includes allowing for the interpretation of LVEF from echocardiograms to be performed by a broader spectrum of physicians.

Adult↗
PubMed2000

Computer-aided ergonomics: a case study of incorporating ergonomics analyses into workplace design.

One of the primary goals of computer-aided ergonomics is to develop software tools that allow ergonomics information to be accessed at the earliest stages of design. This case study discusses a PC-based software program that allows a designer to quantify a worker's biomechanical risk for injury based on a proposed workplace design. The program couples an established software tool for biomechanical analysis, the Three-Dimensional Static Strength Prediction Program (3DSSPP), with a widely used computer-aided design software package, AutoCAD. The use of this "3DSSPP/AutoCAD interface" in the proactive analysis of an automotive assembly task is described and the results compared with an independent assessment using observations of workers performing the same task. Both studies yield similar conclusions, suggesting that proactive use of software such as the 3DSSPP/AutoCAD interface may be a valid tool in evaluating proposed workplace designs. In this context, issues in the analysis of workplace designs regarding the use of supporting ergonomic tools, assumptions, and posture selection are discussed.

Accidents, Occupational↗
PubMedDate not supplied

[Measurement technics].

Aim of the research has been the evaluation of an image processing technique suggested for measuring procedures in the field of dental materials and devices studies. An analysis of measurement systems and largest employment's equipments in the biotechnologies field has been performed. Particularly, digital and image processing technologies have been considered and, between them, an evaluation of "Image Tool" software, made by UTHSCSA and available freeware on Internet has been carried out. The "Image Tool" software showed to be easy in handling and reliable on this results. Since it is based on image processing, the measuring precision is related to subject to be evaluated dimensions and always in the 1/1000 tolerance. This software also allow the direct surfaces measuring and comparing. The process accuracy is at the same level of mechanical regulation's measuring instruments (calipers, micrometres, surface probes) but it is not comparable to the laser controlled equipments, like CAD-CAM systems, micrometres and surface explores, precision which are much more sophisticated and expensives.

Biotechnology↗
PubMed2004

Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry.

MOTIVATION: The correlation among fragment ions in a tandem mass spectrum is crucial in reducing stochastic mismatches for peptide identification by database searching. Until now, an efficient scoring algorithm that considers the correlative information in a tunable and comprehensive manner has been lacking. RESULTS: This paper provides a promising approach to utilizing the correlative information for improving the peptide identification accuracy. The kernel trick, rooted in the statistical learning theory, is exploited to address this issue with low computational effort. The common scoring method, the tandem mass spectral dot product (SDP), is extended to the kernel SDP (KSDP). Experiments on a dataset reported previously demonstrate the effectiveness of the KSDP. The implementation on consecutive fragments shows a decrease of 10% in the error rate compared with the SDP. Our software tool, pFind, using a simple scoring function based on the KSDP, outperforms two SDP-based software tools, SEQUEST and Sonar MS/MS, in terms of identification accuracy. SUPPLEMENTARY INFORMATION: http://www.jdl.ac.cn/user/yfu/pfind/index.html

Algorithms↗
PubMed2002

Efficient multiple genome alignment.

MOTIVATION: To allow a direct comparison of the genomic DNA sequences of sufficiently similar organisms, there is an urgent need for software tools that can align more than two genomic sequences. RESULTS: We developed new algorithms and a software tool 'Multiple Genome Aligner' (MGA for short) that efficiently computes multiple genome alignments of large, closely related DNA sequences. For example, it can align 85% percent of the complete genomes of six human adenoviruses (average length 35305 bp.) in 159 seconds. An alignment of 74% of the complete genomes of three of strains of E. coli (lengths: 5528445; 5498450; 4639221 approximately bp.) is produced in 30 minutes.

Algorithms↗
PubMed2006

ProMAT: protein microarray analysis tool.

SUMMARY: ProMAT is a software tool for statistically analyzing data from enzyme-linked immunosorbent assay microarray experiments. The software estimates standard curves, sample protein concentrations and their uncertainties for multiple assays. ProMAT generates a set of comprehensive figures for assessing results and diagnosing process quality. The tool is available for Windows or Mac, and is distributed as open-source Java and R code. AVAILABILITY: ProMAT is available at http://www.pnl.gov/statistics/ProMAT. ProMAT requires Java version 1.5.0 and R version 1.9.1 (or more recent versions). ProMAT requires either Windows XP or Mac OS 10.4 or newer versions.

Algorithms↗
PubMed2001

Balancing flexibility for the employer and the employee: a case study of the development of annualized hours employment contracts.

As with many forms of flexible working, Annualized Hours (AH) systems offer potential benefits to both the employer and the employee. However, the flexibility requirements of employers and employees often conflict. Therefore, when a large food manufacturing organization decided to redesign its AH system, it employed an independent consultancy to act as neutral third party. The consultancy provided technical expertise and assistance in developing an AH system that optimised productivity and was acceptable to the workforce. Data are presented, obtained from focus groups conducted throughout the organization, describing some of the potential difficulties of implementing an AH system. Drawing upon these data, a number of new AH systems were proposed and modelled using specialist software tools. The design process is described, together with the advantages and difficulties associated with use of the software tools. It is concluded that the key elements in the process of designing AH systems are centred around issues of trust and communication; the involvement of a broad range of interested parties, through a process of carefully managed group facilitation; and the need for adequate technical support in the development and evaluation of AH systems.

Computer Simulation↗
PubMed2006

GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.

MOTIVATION: Analyzing the networks of interactions between genes and proteins has become a central theme in systems biology. Versatile software tools for interactively displaying and analyzing these networks are therefore very much in demand. The public-domain open software environment Cytoscape has been developed with the goal of facilitating the design and development of such software tools by the scientific community. RESULTS: We present GenePro, a plugin to Cytoscape featuring a set of versatile tools that greatly facilitates the visualization and analysis of protein networks derived from high-throughput interactions data and the validation of various methods for parsing these networks into meaningful functional modules. AVAILABILITY: The GenePro plugin is available at the website http://genepro.ccb.sickkids.ca.

Algorithms↗
PubMed1987

Managing research data with self-documenting files.

Processing biomedical research data is frequently complex due to the evolutionary nature of experiments and the requisite modification of analysis software. For the past several years we have been evolving a set of software tools designed to improve our ability to respond to evolving experimental designs. These tools allow the investigator to easily manipulate the research data and specify desired data transformations at run time. Coupling of analysis software to research data files is dependent on data files that are commented in a manner similar to that used in programming languages. The resulting annotated data files are self-documenting, and their use facilitates visual interpretation of displayed data as well as automatic processing of subsets of data. Here we present a formal description of a self-documenting file and describe several software tools that facilitate processing of biomedical research data.

Electronic Data Processing↗
PubMedDate not supplied

GFSWeb: a web tool for genome-based identification of proteins from mass spectrometric samples.

The interpretation of mass spectrometry data for protein identification has become a vital component of proteomics research. However, since most existing software tools rely on protein databases, their success is limited, especially as the pace of annotation efforts fails to keep pace with sequencing. We present a publicly available, web-based version of a software tool that maps peptide mass fingerprint data directly to their genomic origin, allowing for genome-based, annotation-independent protein identification.

Databases, Protein↗