SEARCH · PubMed Health

Results for “Software”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 325 records · Page 18Linked to original sources

PubMed2003

PROBEmer: A web-based software tool for selecting optimal DNA oligos.

PROBEmer (http://probemer.cs.loyola.edu) is a web-based software tool that enables a researcher to select optimal oligos for PCR applications and multiplex detection platforms including oligonucleotide microarrays and bead-based arrays. Given two groups of nucleic-acid sequences, a target group and a non-target group, the software identifies oligo sequences that occur in members of the target group, but not in the non-target group. To help predict potential cross hybridization, PROBEmer computes all near neighbors in the non-target group and displays their alignments. The software has been used to obtain genus-specific prokaryotic probes based on the 16S rRNA gene, gene-specific probes for expression analyses and PCR primers. In this paper, we describe how to use PROBEmer, the computational methods it employs, and experimental results for oligos identified by this software tool.

Algorithms↗

PubMed2005

metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella.

The metabolic SearcH And Reconstruction Kit (metaSHARK) is a new fully automated software package for the detection of enzyme-encoding genes within unannotated genome data and their visualization in the context of the surrounding metabolic network. The gene detection package (SHARKhunt) runs on a Linux system and requires only a set of raw DNA sequences (genomic, expressed sequence tag and/or genome survey sequence) as input. Its output may be uploaded to our web-based visualization tool (SHARKview) for exploring and comparing data from different organisms. We first demonstrate the utility of the software by comparing its results for the raw Plasmodium falciparum genome with the manual annotations available at the PlasmoDB and PlasmoCyc websites. We then apply SHARKhunt to the unannotated genome sequences of the coccidian parasite Eimeria tenella and observe that, at an E-value cut-off of 10(-20), our software makes 142 additional assertions of enzymatic function compared with a recent annotation package working with translated open reading frame sequences. The ability of the software to cope with low levels of sequence coverage is investigated by analyzing assemblies of the E.tenella genome at estimated coverages from 0.5x to 7.5x. Lastly, as an example of how metaSHARK can be used to evaluate the genomic evidence for specific metabolic pathways, we present a study of coenzyme A biosynthesis in P.falciparum and E.tenella.

Animals↗

PubMed1993

Features of commercial computer software systems for medical examiners and coroners.

There are many ways of automating medical examiner and coroner offices, one of which is to purchase commercial software products specifically designed for death investigation. We surveyed four companies that offer such products and requested information regarding each company and its hardware, software, operating systems, peripheral devices, applications, networking options, programming language, querying capability, coding systems, prices, customer support, and number and size of offices using the product. Although the four products (CME2, ForenCIS, InQuest, and Medical Examiner's Software System) are similar in many respects and each can be installed on personal computers, there are differences among the products with regard to cost, applications, and the other features. Death investigators interested in office automation should explore these products to determine the usefulness of each in comparison with the others and in comparison with general-purpose, off-the-shelf databases and software adaptable to death investigation needs.

Computers↗

PubMed2001

A longitudinal evaluation of an educational software program: a case study of Urinalysis-Tutor.

PURPOSE: To examine students' learning before and after revising an educational software program and to explore students' patterns of use of an interactive feature that compares images. METHOD: Study participants were 466 University of Washington School of Medicine students. Two cohorts of students (one in 1996 and one in 1997) used the original version of the software. Following analysis of the students' learning, the software program was modified based on instructional design principles pertaining to visual learning and concept acquisition. A 1998 cohort of students used the revised program and their performance was compared with that of the 1996 cohort. Analyses were based on pre- and post-test scores, data collected from the observation of students, and navigational pathways tracked by the program. RESULTS: There was very little difference in the overall performances of the students who used the original program and those who used the revised program. Error analysis focusing on 11 conceptual areas showed that reductions in errors occurred for six of 11 concepts, with statistically significant reductions of errors for two concepts. Additional navigational data collected in 1998 showed that students used an interactive feature for comparing images in different patterns. The data showed a positive association between performance and the anchored viewing mode of image display. CONCLUSIONS: While this study cannot point to specific design components that facilitated or hindered learning, it demonstrated a potential benefit of linking usage-pattern data and performance. Future studies should evaluate design factors that affect usage patterns and performances based on navigational data collected while students interact with software programs.

Cohort Studies↗

PubMedDate not supplied

Developing an evaluation tool for instructional software programs.

The use of instructional software is predominant in many nursing programs. The need for cost-effective, quality programs requires faculty to evaluate instructional software before its purchase and use. The purpose of this work was to develop a tool for evaluating instructional software programs. The tool was based on data from the literature, as well as input and feedback from nurse educators and multimedia specialists. The evaluation tool assists faculty to ensure proper evaluation and selection of instructional software.

Choice Behavior↗

PubMed2003

Coronary artery calcium scoring: diagnostic accuracy of different software implementations.

PURPOSE: To compare the diagnostic power of different software implementations for the quantification of coronary artery calcium. MATERIALS AND METHODS: Electron beam computed tomography was performed in 109 heart transplant recipients at the same time as catheter coronary angiography and intracoronary ultrasound. Electron beam computed tomography images were analyzed by 3 software packages marketed for the quantification of coronary calcifications using the same software settings, and the resultant calcium scores correlated with the invasive reference methods by Bland-Altman plots and analysis of the receiver operating characteristics. RESULTS: Although all scoring systems displayed close correlations upon regression analysis (r2=0.94-0.99), their ability to detect disease as per the invasive reference method varied significantly in some instances. The area under the ROC curve varied between Az=0.78 and 0.85 for the detection of coronary artery stenosis upon coronary angiography (P=0.05-0.13), and between Az=0.75 and 0.83 for the detection of accelerated intimal proliferation (P=0.03-0.18). CONCLUSIONS: Different software implementations for the quantification of coronary artery calcium load may display diagnostically relevant differences in spite of close direct correlation.

Adolescent↗

PubMed1998

A software system for data analysis in automated DNA sequencing.

Software for gel image analysis and base-calling in fluorescence-based sequencing consisting of two primary programs, BaseFinder and GelImager, is described. BaseFinder is a framework for trace processing, analysis, and base-calling. BaseFinder is highly extensible, allowing the addition of trace analysis and processing modules without recompilation. Powerful scripting capabilities combined with modularity and multilane handling allow the user to customize BaseFinder to virtually any type of trace processing. We have developed an extensive set of data processing and analysis modules for use with the program in fluorescence-based sequencing. GelImager is a framework for gel image manipulation. It can be used for gel visualization, lane retracking, and as a front end to the Washington University Getlanes program. The programs were designed using a cross-platform development environment, currently allowing them to run in Windows NT, Windows 95, Openstep/Mach, and Rhapsody. Work is ongoing to deploy the software on additional platforms, including Solaris, Linux, and MacOS. This software has been thoroughly tested and debugged in the analysis of >2 million bp of raw sequence data from human chromosome 19 region q13. Overall sequencing accuracy was measured using a significant subset of these data, consisting of approximately 600 sequences, by comparing the individual shotgun sequences against the final assembled contigs. Also, results are reported from experiments that analyzed the accuracy of the software and two other well-known base-calling programs for sequencing the M13mp18 vector sequence. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF025422]

Algorithms↗

PubMed2004

Practical aspects of the integration of different software in protein structure solution.

There is presently an increasing variety of choice in the software for macromolecular phasing and automated model building. In addition to its positive features, this variety poses the problem of which software to use in a specific crystallographic case. Moreover, it must be decided whether a sequence of programs should be used to achieve structure solution more accurately and more rapidly, taking into account the features of the different programs: some software is more suitable for dealing with low-symmetry rather than high-symmetry space groups in the detection of heavy-atom sites, while others can give better estimates of the figures of merit on phases in certain cases (which is crucial in dealing with maximum likelihood) and others are more suitable for chain tracing at low/medium-low resolution than at high resolution or vice versa. The 'integrated' choice of different software has become popular among crystallographers, especially when facing crystallographic cases that are not straightforward. A few examples will be presented on the use of different programs to achieve the goal of structure solution and the associated practicalities that can make the difference between solving or not solving a structure.

Bacillus subtilis↗

PubMed2004

SPIDER: software for protein identification from sequence tags with de novo sequencing error.

For the identification of novel proteins using MS/MS, de novo sequencing software computes one or several possible amino acid sequences (called sequence tags) for each MS/MS spectrum. Those tags are then used to match, accounting amino acid mutations, the sequences in a protein database. If the de novo sequencing gives correct tags, the homologs of the proteins can be identified by this approach and software such as MS-BLAST is available for the matching. However, de novo sequencing very often gives only partially correct tags. The most common error is that a segment of amino acids is replaced by another segment with approximately the same masses. We developed a new efficient algorithm to match sequence tags with errors to database sequences for the purpose of protein and peptide identification. A software package, SPIDER, was developed and made available on Internet for free public use. This paper describes the algorithms and features of the SPIDER software.

Algorithms↗

PubMed1999

Software error resulting in malfunction of an implantable cardioverter defibrillator.

Loss of ventricular output resulting from an unexpected software error in a dual chamber implantable cardioverter defibrillator (ICD) is reported. A 70-year-old man with a dual chamber ICD implanted for a history of cardiac arrest and infra-Hisian block presented with acute onset of dizziness. He was found to have loss of ventricular output due to an internal software problem. The problem was corrected by software reprogramming via the programmer. This malfunction exemplifies the potential ability to correct current-generation ICD software problems noninvasively, thus avoiding the need for replacement.

Aged↗

PubMed2000

The pros and cons of data analysis software for qualitative research.

PURPOSE: To explore the use of computer-based qualitative data analysis software packages. SCOPE: The advantages and capabilities of qualitative data analysis software are described and concerns about their effects on methods are discussed. FINDINGS: Advantages of using qualitative data analysis software include being freed from manual and clerical tasks, saving time, being able to deal with large amounts of qualitative data, having increased flexibility, and having improved validity and auditability of qualitative research. Concerns include increasingly deterministic and rigid processes, privileging of coding, and retrieval methods; reification of data, increased pressure on researchers to focus on volume and breadth rather than on depth and meaning, time and energy spent learning to use computer packages, increased commercialism, and distraction from the real work of analysis. CONCLUSIONS: We recommend that researchers consider the capabilities of the package, their own computer literacy and knowledge of the package, or the time required to gain these skills, and the suitability of the package for their research. The intelligence and integrity that a researcher brings to the research process must also be brought to the choice and use of tools and analytical processes. Researchers should be as critical of the methodological approaches to using qualitative data analysis software as they are about the fit between research question, methods, and research design.

Humans↗

PubMed2000

A software model to estimate zones of impact on marine mammals around anthropogenic noise.

Anthropogenic noise impacts marine mammals in a variety of ways. In order to estimate over which ranges this happens, we first need to understand the propagation of noise through the ocean away from the noise source, and, second, understand the relationship between received noise levels and impact thresholds. A software package combining both aspects is presented. (1) A sound propagation model based on ray theory was developed to calculate received noise levels as a function of range, depth, and frequency. (2) Current knowledge of noise impact thresholds for marine mammals was gathered and included in software routines predicting zones of impact on marine mammals around industrial underwater noise sources. As input parameters, this software package requires the source level and spectrum of the noise of interest; physical oceanography data about the local ocean environment such as bathymetry, bottom and surface loss data, and sound speed profiles; and bioacoustical information about the target species in the form of an audiogram, critical auditory bandwidths, spectra of typical animal vocalizations, reported sound levels of disturbance, and criteria for hearing damage. As output, the software produces data files and plots of the zones of audibility, masking, disturbance, and potential hearing damage around a noise source.

Animals↗

PubMed2005

SPIDER: software for protein identification from sequence tags with de novo sequencing error.

Algorithms↗

PubMed2006

Efficient algorithms and software for detection of full-length LTR retrotransposons.

LTR retrotransposons constitute one of the most abundant classes of repetitive elements in eukaryotic genomes. In this paper, we present a new algorithm for detection of full-length LTR retrotransposons in genomic sequences. The algorithm identifies regions in a genomic sequence that show structural characteristics of LTR retrotransposons. Three key components distinguish our algorithm from that of current software--(i) a novel method that preprocesses the entire genomic sequence in linear time and produces high quality pairs of LTR candidates in run-time that is constant per pair, (ii) a thorough alignment-based evaluation of candidate pairs to ensure high quality prediction, and (iii) a robust parameter set encompassing both structural constraints and quality controls providing users with a high degree of flexibility. We implemented our algorithm into a software program called LTR_par, which can be run on both serial and parallel computers. Validation of our software against the yeast genome indicates superior results in both quality and performance when compared to existing software. Additional validations are presented on rice BACs and chimpanzee genome.

Algorithms↗

PubMed1992

Software suite for image archiving and retrieval.

The efficient operation of a clinical picture archiving and communication system (PACS) requires a fully functional image archive. The archive should not only be able to store and retrieve images reliably but should also work in concert with software that optimizes the flow of image-related information throughout the PACS. The authors devised a software suite that serves to improve the flow and content of information and the integrity of the data. The software was developed by translating the functions performed by a conventional film library. Types of transactions possible with this system include scheduling, canceling, rescheduling, and prestaging examinations; changing demographic information; merging patient information; and generating reports. The authors believe such a software suite is essential for a clinically useful PACS.

Data Display↗

PubMed2003

Multi-detector row CT of left ventricular function with dedicated analysis software versus MR imaging: initial experience.

PURPOSE: To determine left ventricular (LV) volumetric and functional parameters from retrospectively electrocardiographically gated multi-detector row computed tomography (CT) by using semiautomated analysis software and to correlate results with those of magnetic resonance (MR) imaging. MATERIALS AND METHODS: In 30 patients (mean age, 59.2 years +/- 7.1 [SD]) known to have or suspected of having coronary artery disease, four-channel multi-detector row CT was performed with standard technique, and diastolic and systolic image reconstructions were generated. With commercially available analysis software capable of semiautomated contour detection, end diastolic and end systolic LV volumes were determined from short-axis secondary CT reformations. Steady-state free-precession cine MR images were acquired in short-axis orientation within 48 hours and analyzed by using dedicated software. Bland-Altman analysis was performed to calculate limits of agreement and systematic errors between CT and MR imaging. RESULTS: Mean end diastolic (138.8 mL +/- 31.9) and end systolic (53.9 mL +/- 21.2) LV volumes as determined with CT correlated well with MR imaging measurements (142.0 mL +/- 32.5 [r = 0.93] and 54.9 mL +/- 22.8 [r = 0.94], respectively [P <.001]). LV ejection fraction (61.6% +/- 10.6 for CT vs 62.3% +/- 10.1 for MR imaging; r = 0.89) and stroke volume (84.6 mL +/- 20.9 for CT vs 86.9 mL +/- 21.5 for MR imaging; r = 0.88) also showed good correlation (P <.001). Bland-Altman analysis showed acceptable limits of agreement (+/-9.8% for ejection fraction) without systematic errors. CONCLUSION: In selected patients, semiautomated analysis software enables LV volumetric and functional analysis based on multi-detector row CT data sets, the results of which correlate well with MR imaging findings.

Aged↗

PubMed2005

FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments.

BACKGROUND: Quantitative knowledge of intracellular fluxes is important for a comprehensive characterization of metabolic networks and their functional operation. In contrast to direct assessment of metabolite concentrations, in vivo metabolite fluxes must be inferred indirectly from measurable quantities in 13C experiments. The required experience, the complicated network models, large and heterogeneous data sets, and the time-consuming set-up of highly controlled experimental conditions largely restricted metabolic flux analysis to few expert groups. A conceptual simplification of flux analysis is the analytical determination of metabolic flux ratios exclusively from MS data, which can then be used in a second step to estimate absolute in vivo fluxes. RESULTS: Here we describe the user-friendly software package FiatFlux that supports flux analysis for non-expert users. In the first module, ratios of converging fluxes are automatically calculated from GC-MS-detected 13C-pattern in protein-bound amino acids. Predefined fragmentation patterns are automatically identified and appropriate statistical data treatment is based on the comparison of redundant information in the MS spectra. In the second module, absolute intracellular fluxes may be calculated by a 13C-constrained flux balancing procedure that combines experimentally determined fluxes in and out of the cell and the above flux ratios. The software is preconfigured to derive flux ratios and absolute in vivo fluxes from [1-13C] and [U-13C]glucose experiments and GC-MS analysis of amino acids for a variety of microorganisms. CONCLUSION: FiatFlux is an intuitive tool for quantitative investigations of intracellular metabolism by users that are not familiar with numerical methods or isotopic tracer experiments. The aim of this open source software is to enable non-specialists to adapt the software to their specific scientific interests, including other 13C-substrates, labeling mixtures, and organisms.

Bacteria↗

PubMed2006

Meta-DiSc: a software for meta-analysis of test accuracy data.

BACKGROUND: Systematic reviews and meta-analyses of test accuracy studies are increasingly being recognised as central in guiding clinical practice. However, there is currently no dedicated and comprehensive software for meta-analysis of diagnostic data. In this article, we present Meta-DiSc, a Windows-based, user-friendly, freely available (for academic use) software that we have developed, piloted, and validated to perform diagnostic meta-analysis. RESULTS: Meta-DiSc a) allows exploration of heterogeneity, with a variety of statistics including chi-square, I-squared and Spearman correlation tests, b) implements meta-regression techniques to explore the relationships between study characteristics and accuracy estimates, c) performs statistical pooling of sensitivities, specificities, likelihood ratios and diagnostic odds ratios using fixed and random effects models, both overall and in subgroups and d) produces high quality figures, including forest plots and summary receiver operating characteristic curves that can be exported for use in manuscripts for publication. All computational algorithms have been validated through comparison with different statistical tools and published meta-analyses. Meta-DiSc has a Graphical User Interface with roll-down menus, dialog boxes, and online help facilities. CONCLUSION: Meta-DiSc is a comprehensive and dedicated test accuracy meta-analysis software. It has already been used and cited in several meta-analyses published in high-ranking journals. The software is publicly available at http://www.hrc.es/investigacion/metadisc_en.htm.

Clinical Laboratory Techniques↗