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 1,801 records · Page 100Linked to original sources
PubMed2002

[Current perspectives of orthogonal polarization spectral imaging in plastic surgery].

The technology of Orthogonal Polarization Spectral Imaging (OPSI), patented in the United States in 1999, has been heralded as an alternative to conventional intravital microscopy for several reasons, including ease of application and ability to perform continued observations. In the following examples, OPSI was applied to reconstructive plastic surgery. Two experimental and one clinical model are presented. Currently, the image quality does not allow a qualitative analysis of the microvasculature. The data analysis of images remains inconclusive. However, a technically modified version with improved image resolution and software could become a valuable experimental as well as clinical tool in the field of reconstructive plastic surgery in the future.

Animals↗
PubMed2005

Intelligent Data Analysis of clinical trials.

We describe the software architecture of DART, an Intelligent Data-Analysis (IDA) tool for clinical trials data. This tool, which is coupled with COATI, a generic clinical trials database, embodies rule-based systems for data extraction and preparation, and algorithm-driven statistical analysis for the creation of fully ICH-compliant study reports.

Algorithms↗
PubMed2004

VisANT: an online visualization and analysis tool for biological interaction data.

BACKGROUND: New techniques for determining relationships between biomolecules of all types--genes, proteins, noncoding DNA, metabolites and small molecules--are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems. RESULTS: We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology. CONCLUSION: VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at http://visant.bu.edu.

Animals↗
PubMedDate not supplied

BrainImageJ: a Java-based framework for interoperability in neuroscience, with specific application to neuroimaging.

The Human Brain Project consortium continues to struggle with effective sharing of tools. To facilitate reuse of its tools, the Stanford Psychiatry Neuroimaging Laboratory (SPNL) has developed BrainImageJ, a new software framework in Java. The framework consists of two components-a set of four programming interfaces and an application front end. The four interfaces define extension pathways for new data models, file loaders and savers, algorithms, and visualization tools. Any Java class that implements one of these interfaces qualifies as a BrainImageJ plug-in-a self-contained tool. After automatically detecting and incorporating new plug-ins, the application front end transparently generates graphical user interfaces that provide access to plug-in functionality. New plug-ins interoperate with existing ones immediately through the front end. BrainImageJ is used at the Stanford Psychiatry Neuroimaging Laboratory to develop image-analysis algorithms and three-dimensional visualization tools. It is the goal of our development group that, once the framework is placed in the public domain, it will serve as an interlaboratory platform for designing, distributing, and using interoperable tools.

Algorithms↗
PubMed2003

Challenges in using geographic information systems (GIS) to understand and control malaria in Indonesia.

Malaria is a mosquito-borne disease of global concern with 1.5 to 2.7 million people dying each year and many more suffering from it. In Indonesia, malaria is a major public health issue with around six million clinical cases and 700 deaths each year. Malaria is most prevalent in the developing countries of the world. Aid agencies have provided financial and technical assistance to malaria-prone countries in an effort to battle the disease. Over the past decade, the focus of some of this assistance has been in the provision of geographic information systems (GIS) hardware, software and training. In theory, GIS can be a very effective tool in combating malaria, however, in practice there have been a host of challenges to its successful use.This review is based, in part, on the literature but also on our experience working with the Indonesian Ministry of Health. The review identifies three broad problem areas. The first of these relates to data concerns. Without adequate data, GIS is not very useful. Specific problem areas include: accurate data on the disease and how it is reported; basic environmental data on vegetation, land uses, topography, rainfall, etc.; and demographic data on the movement of people. The second problem area involves technology - specifically computer hardware, GIS software and training. The third problem area concerns methods - assuming the previous data and technological problems have been resolved - how can GIS be used to improve our understanding of malaria? One of the main methodological tools is spatial statistical analysis, however, this is a newly developing field, is not easy to understand and suffers from the fact that there is no agreement on standard methods of analysis.The paper concludes with a discussion of strategies that can be used to overcome some of these problems. One of these strategies involves using ArcView GIS software in combination with ArcExplorer (a public domain program that can read ArcView files) to deal with the problem of needing multiple copies of GIS software. Another strategy involves the development of a self-paced training package that can be used to train individuals

Journal Article↗
PubMed1997

Family physicians' preferences for computerized decision-support hardware and software.

BACKGROUND: While computers are now widely used by family physicians for billing and patient registration purposes, their use as decision-support tools is still quite limited. The purpose of this study was to determine the current use of computer hardware and software by family physicians, and the characteristics these physicians desire in computerized decision-support hardware and software. METHODS: A cross-sectional survey of a random sample of 250 Michigan family physicians was undertaken in mid-1995. These physicians were asked about their current use of a variety of computer hardware and software. They were also asked to rate the value of different kinds of decision-support information potentially available by computer. The survey instrument also gathered the family physicians' preferences for design factors (both hardware and software), such as the size of a computer, the time needed to access information, and the frequency of updates. RESULTS: Word processing on desktop computers and hospital information systems are the most widely used computer applications by family physicians. Physicians are most interested in computer-based information on drugs, storage and generation of patient education materials, and accessing treatment recommendations. Most feel that semiannual or annual updates of information are adequate, and would like a uniform interface. A high percentage of physicians (84.5% of all physicians and 94.1% of younger physicians) stated that they would consider carrying a handheld computer. CONCLUSIONS: There is significant interest in several types of clinical decision-support software. Based on the results of this study, such software should have following characteristics: (1) be available for handheld as well as networked and desktop computers, (2) include drug information (particularly warnings, interactions, and side effects), (3) include overviews of treatment recommendations, (4) include patient education materials, and (5) have a uniform user interface and be updated at least annually.

Adult↗
PubMed1993

SURVIVAL--an integrated software package for survival curve estimation and statistical comparison of survival rates of two groups of patients or experimental animals.

SURVIVAL, a new integrated software package for survival curve estimation and statistical comparison of survival rates of two censored or uncensored groups of patients or experimental animals, is described and demonstrated. The software is based on the calculation of the Kaplan-Meier estimates of survival curves and utilizes the Mantel-Haenszel and/or Fisher's test for the statistical comparison of the corresponding survival rates. SURVIVAL can be used for statistical evaluation of survival data obtained either on sequentially created or fixed size groups. The software is menu driven to provide a very user friendly tool for analyzing survival data. It may be of great value mainly in clinical use because it automatically enables evaluation of a large set of survival data, sequentially collected in SURVIVAL's own database during a long survival study, with entry and evaluation possible at any time during the study.

Animals↗
PubMed1995

Application of computer graphics for assessment of spinal deformities.

A graphical portrayal system to assess spinal deformities is described. The system is based on software to display and manipulate three-dimensional images of the spine and trunk surface. Qualitative measurements of internal spinal alignment and trunk appearance are provided. The graphics display is developed using graPHIGS routines in conjunction with the C programming language and the UNIX operating system. This software provides clinicians with a computer-aided measurement tool that rapidly conveys clear and concise information about the deformities associated with abnormal spinal curvatures.

Computer Graphics↗
PubMed1994

Application of a bi-directional associative memory (BAM) network in computer assisted learning in chemistry.

A computer assisted learning software based on a bi-directional associative memory (BAM) network was developed. The software was implemented to assist students in associating the names of the elements in the periodic table with their chemical symbols. The use of the BAM facilitates the analysis and interpretation of students' responses. The software package can be modified easily as an educational tool for other disciplines.

Algorithms↗
PubMed1994

Low-cost data acquisition and analysis programs for electrophysiology.

In the laboratory, powerful personal computers are invaluable tools for data acquisition and analysis. The commercially available software for these purposes is often very expensive and does not always conform to the experimenter's needs. In our laboratory, we have developed two programs for acquisition and analysis of electrophysiological data from retinal neurons, although they can be used for many other types of data acquisition and analysis as well. These programs were written for IBM PC-compatible computer systems and are being distributed as shareware. Thus they are available for users to try out free of charge; if they are found to be of use, they can be purchased for a minimal cost. PATCHIT, the data-acquisition program can use one of several popular data-acquisition boards to simultaneously stimulate and record from an experimental preparation. TACK, the data analysis program was developed to analyze data recorded by PATCHIT and other data-acquisition programs. PATCHIT and TACK are powerful programs which are competitive with similar commercially available programs, but are sold at a much lower cost. Details on the development and operation of these programs are presented in this paper.

Computer Graphics↗
PubMed2006

Accuracy of digital and analogue cephalometric measurements assessed with the sandwich technique.

INTRODUCTION: The purpose of the study was to evaluate the accuracy of cephalometric measurements obtained with digital tracing software compared with equivalent hand-traced measurements. In the sandwich technique, a storage phosphor plate and a conventional radiographic film are placed in the same cassette and exposed simultaneously. The method eliminates positioning errors and potential differences associated with multiple radiographic exposures that affected previous studies. It was used to ensure the equivalence of the digital images to the hard copy radiographs. Cephalometric measurements instead of landmarks were the focus of this investigation in order to acquire data with direct clinical applications. METHODS: The sample consisted of digital and analog radiographic images from 47 patients after orthodontic treatment. Nine cephalometric landmarks were identified and 13 measurements calculated by 1 operator, both manually and with digital tracing software. Measurement error was assessed for each method by duplicating measurements of 25 randomly selected radiographs and by using Pearson's correlation coefficient. A paired t test was used to detect differences between the manual and digital methods. RESULTS: An overall greater variability in the digital cephalometric measurements was found. Differences between the 2 methods for SNA, ANB, S-Go:N-Me, U1/L1, L1-GoGn, and N-ANS:ANS-Me were statistically significant (P < .05). However, only the U1/L1 and S-Go:N-Me measurements showed differences greater than 2 SE (P < .0001). CONCLUSIONS: The 2 tracing methods provide similar clinical results; therefore, efficient digital cephalometric software can be reliably chosen as a routine diagnostic tool. The user-friendly sandwich technique was effective as an option for interoffice communications.

Adolescent↗
PubMed2006

The probable structure of the protamine-DNA complex.

A detailed molecular structure is proposed for the human protamine-DNA complex, which has hitherto been largely a mystery. The structure was created with virtual modeling software (AmiraMol), employing logical deduction as the primary investigative tool. A beta-sheet structure for the protein component is essentially mandated, as the alternatives can be decisively excluded. A dimeric structure too is essentially mandated, since the cysteine residues of protamines P1 and P2 are invariably aligned in all species having both chains. The cross-sectional and axial spacings of arginine guanidinium groups in this protein structure can be perfectly aligned with those of phosphate groups in DNA according to the DNA structure proposed by Wu. This is a non-helical structure, whose possible occurrence in certain plasmids has been suggested by experimental observations. The unit cell of this protamine-DNA complex is essentially devoid of steric hindrances, and heavily favored by a multitude of ionic and hydrogen bonds. The packing of adjacent "unit cells" of the protamine-DNA structure is based on a complex array of salt bridges, the mere existence of which is so fortuitous that it is virtually inconceivable that it comes about through a mere modeling "coincidence". The possible significance of the structure beyond the sperm cell is discussed.

Amino Acid Sequence↗
PubMed2002

A method for spatial analysis of risk in a population-based case-control study.

Spatial distributions of disease occurrence and risk have traditionally served as a tool for identifying exposures of public health concern. Current software for manipulating geographic data (GIS) now allows many kinds of analyses not feasible before. This paper presents a method for producing a "picture" of disease risks based on residential history data from a population based case-control study. We illustrate the method using geographically coded data on individual-level risk factors, such as age and smoking, from a cancer study of the Upper Cape Cod region of Massachusetts for 1983-1986. Our results show the association between lung cancer and residential location as an indicator of exposure. Crude and adjusted odds ratios were estimated by adaptive rate stabilization and mapped using kriging as an interpolation method to examine the risk of lung cancer in the region. The crude and adjusted surfaces for various smoothing parameters were compared to identify areas of increased lung cancer not explained by standard risk factors. Such spatial patterns of disease risk may provide clues to exposures of importance or confirm associations with previously suspected exposures.

Adult↗
PubMed2004

Automatic construction of gene relation networks using text mining and gene expression data.

Microarray gene expression analysis is a powerful high-throughput technique that enables researchers to monitor the expression of thousands of genes simultaneously. Using this methodology huge amounts of data are produced which have to be analysed. Clustering algorithms are used to group genes together based on a predefined distance measure. However, clustering algorithms do not necessarily group the genes in a biological meaningful way. Additional information is needed to improve the identification of disease relevant genes. The primary objective of our project is to support the analysis of microarray gene expression data by construction of gene relation networks (GRNs). Required information can not be found in a structured representation like a database. In contrast, a large number of relations are described in biomedical literature. The main outcome of this project is the implementation of a software system that provides clinicians and researchers with a tool that supports the analysis of microarray gene expression data by mapping known relationships from the biomedical literature to local gene expression experiments.

Abbreviations as Topic↗
PubMed2000

POWER_SAGE: comparing statistical tests for SAGE experiments.

MOTIVATION: The Serial Analysis of Gene Expression (SAGE) technology determines the expression level of a gene by measuring the frequency of a sequence tag derived from the corresponding mRNA transcript. Several statistical tests have been developed to detect significant differences in tag frequency between two samples. However, which one of these tests has the greatest power to detect real changes remains undetermined. RESULTS: This paper compares three statistical tests for detecting significant changes of gene expression in SAGE experiments. The comparison makes use of Monte Carlo simulation that, in essence, generates "virtual" SAGE experiments. Our analysis shows that the Chi-square test has the best power and robustness. Since the POWER_ SAGE program can easily run "virtual" SAGE studies with different combinations of sample size and tag frequency and determine the power for each combination, it can serve as a useful tool for planning SAGE experiments. AVAILABILITY: The POWER_ SAGE software is available upon request from the authors. CONTACT: michael.man@pfizer.com

Algorithms↗
PubMed2004

ReDiT: Repeat Discrepancy Tagger--a shotgun assembly finishing aid.

UNLABELLED: Finishing, i.e. gap closure and editing, is the most time-consuming part of genome sequencing. Repeated sequences together with sequencing errors complicate the assembly and often result in misassemblies that are difficult to correct. Repeat Discrepancy Tagger (ReDiT) is a tool designed to aid in the finishing step. This software processes assembly results produced by any fragment assembly program that outputs ace files. The input sequences are analyzed to determine possible differences between repeated sequences. The output is written as tags in an ace file that can be viewed by, e.g. the Consed sequence editor. AVAILABILITY: The ReDiT program is freely available at http://web.cgb.ki.se/redit

Algorithms↗
PubMed2005

PatMatch: a program for finding patterns in peptide and nucleotide sequences.

Here, we present PatMatch, an efficient, web-based pattern-matching program that enables searches for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences. The program can be used to find matches to a user-specified sequence pattern that can be described using ambiguous sequence codes and a powerful and flexible pattern syntax based on regular expressions. A recent upgrade has improved performance and now supports both mismatches and wildcards in a single pattern. This enhancement has been achieved by replacing the previous searching algorithm, scan_for_matches [D'Souza et al. (1997), Trends in Genetics, 13, 497-498], with nondeterministic-reverse grep (NR-grep), a general pattern matching tool that allows for approximate string matching [Navarro (2001), Software Practice and Experience, 31, 1265-1312]. We have tailored NR-grep to be used for DNA and protein searches with PatMatch. The stand-alone version of the software can be adapted for use with any sequence dataset and is available for download at The Arabidopsis Information Resource (TAIR) at ftp://ftp.arabidopsis.org/home/tair/Software/Patmatch/. The PatMatch server is available on the web at http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl for searching Arabidopsis thaliana sequences.

Arabidopsis↗
PubMed1997

Value of automatic processing and reliability of stored data in an implanted pacemaker: initial results in 59 patients.

Stored data in implantable pacemakers have rarely been used as a diagnostic tool because of the complexity. Our group has developed software called AIDA, providing an automatic interpretation of data stored in memories of the Chorus (ELA medical) pacemaker. We compared the results of AIDA analysis to surface ECG Holter interpretation in 59 patients (age 75 +/- 9 years). In 33 cases, neither AIDA nor the Holter found any anomaly. Eleven patients demonstrated episodes of supraventricular tachycardia (SVT), confirmed by AIDA in ten patients; AIDA failure was due to nonsustained episodes of SVT not inducing mode switch. Loss of atrial sensing, pacemaker-mediated tachycardia, and ventricular extrasystoles were detected by AIDA in ten patients. Traditional Holter missed three cases. This initial study confirms that stored pacemaker data, automatically interpreted can provide reliable information over a 24-hour period.

Aged↗

Refine your search to explore more results.