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At least 1,621 records · Page 90Linked to original sources

PubMed2004

GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.

Genome sequence data can be used to analyze genome plasticity by whole genome PCR scanning. Small sized chromosomes can indeed be fully amplified by long-range PCR with a set of primers designed using a reference strain and applied to several other strains. Analysis of the resulting patterns can reveal the genome plasticity. To facilitate such analysis, we have developed GenoFrag, a software package for the design of primers optimized for whole genome scanning by long-range PCR. GenoFrag was developed for the analysis of Staphylococcus aureus genome plasticity by whole genome amplification in approximately 10 kb-long fragments. A set of primers was generated from the genome sequence of S.aureus N315, employed here as a reference strain. Two subsets of primers were successfully used to amplify two portions of the N315 chromosome. This experimental validation demonstrates that GenoFrag is a robust and reliable tool for primer design and that whole genome PCR scanning can be envisaged for the analysis of genome diversity in S.aureus, one of the major public health concerns worldwide.

Base Pairing↗

PubMed2004

ARB: a software environment for sequence data.

The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.

Data Display↗

PubMed2004

IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis.

IMGT/V-QUEST, for 'V-QUEry and STandardization', is an integrated software program which analyses the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. The extraordinary diversity of the IG and TR repertoires (10(12) antibodies and 10(12) TR per individual) results from several mechanisms at the DNA level: the combinatorial diversity of the variable (V), diversity (D) and joining (J) genes, the N-diversity and, for IG, the somatic mutations. IMGT/V-QUEST identifies the V, D and J genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. IMGT/V-QUEST delimits the structurally important features, frameworks and complementarity-determining regions (the last of these forming the antigen binding site), on the basis of the IMGT unique numbering. The tool localizes the somatic mutations of the IG rearranged sequences. IMGT/V-QUEST also dynamically displays a graphical two-dimensional representation, or IMGT Collier de Perles, of the IG and TR variable regions. Moreover, IMGT/V-QUEST can interact with IMGT/JunctionAnalysis for the detailed description of the V-J and V-D-J junctions, and with IMGT/PhyloGene for the construction of phylogenetic trees. IMGT/V-QUEST is currently available for human and mouse, and partly for non-human primates, sheep, chondrichthyes and teleostei. IMGT/V-QUEST is freely available at http://imgt.cines.fr.

Animals↗

PubMed2005

MINER: software for phylogenetic motif identification.

MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM sequence analysis and structural visualization. The web implementation of MINER is freely available at http://www.pmap.csupomona.edu/MINER/. Source code is available to the academic community on request.

Amino Acid Motifs↗

PubMed2006

WormBase: better software, richer content.

WormBase (http://wormbase.org), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the Genome Browser highly customizable in how it views and exports genomic subsequences. Arbitrarily complex, user-specified queries are now possible through Textpresso (for all available literature) and through WormMart (for most genomic data). Biological content was enriched by reconciling all available cDNA and expressed sequence tag data with gene predictions, clarifying single nucleotide polymorphism and RNAi sites, and summarizing known functions for most genes studied in this organism.

Animals↗

PubMed2006

The Stanford Microarray Database: implementation of new analysis tools and open source release of software.

The Stanford Microarray Database (SMD; http://smd.stanford.edu/) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release.

Animals↗

PubMed2006

siVirus: web-based antiviral siRNA design software for highly divergent viral sequences.

siVirus (http://siVirus.RNAi.jp/) is a web-based online software system that provides efficient short interfering RNA (siRNA) design for antiviral RNA interference (RNAi). siVirus searches for functional, off-target minimized siRNAs targeting highly conserved regions of divergent viral sequences. These siRNAs are expected to resist viral mutational escape, since their highly conserved targets likely contain structurally/functionally constrained elements. siVirus will be a useful tool for designing optimal siRNAs targeting highly divergent pathogens, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), influenza virus and SARS coronavirus, all of which pose enormous threats to global human health.

Anti-HIV Agents↗

PubMed2006

Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins.

We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of 2-3 helices and strands with known tertiary structures. For each of these proteins, a structure within 3-6 A RMSD (root mean square deviation) of the native has been obtained in the 10 lowest energy structures. The protocol has been web enabled and is accessible at http://www.scfbio-iitd.res.in/bhageerath.

Computational Biology↗

PubMed2004

Transposon Express, a software application to report the identity of insertions obtained by comprehensive transposon mutagenesis of sequenced genomes: analysis of the preference for in vitro Tn5 transposition into GC-rich DNA.

Comprehensive mutant libraries can be readily constructed by transposon mutagenesis. To systematically mutagenise the genome of the Gram-positive bacterium Streptomyces coelicolor A3(2), we have employed high-throughput shuttle transposon mutagenesis of a cosmid library prepared in Escherichia coli. The location of transposon insertions is determined using automated procedures for cosmid isolation and DNA sequencing. However, a major bottleneck was the subsequent analysis of DNA sequence files. To overcome this limitation, a software application, Transposon Express, was written to allow the rapid location of transposon insertions in a sequenced genome (available at http://www.swan.ac.uk/genetics/dyson/InstallTE). Transposon Express determines the identity both of a disrupted open reading frame (ORF), and the short target site duplication created by transposition. Transposon Express also reports the orientation of the transposon and can therefore predict transcriptional coupling between an upstream promoter and a promoter-less reporter gene carried by the transposon. Analysis of a large dataset of independent insertions created using a Tn5-based transposon revealed an insertional preference for GC-rich streptomycete DNA compared to E.coli vector DNA. In addition to demonstrating the value of Transposon Express as a generic tool supporting genome-wide transposon mutagenesis programs, these data provide insight into target site selection by Tn5.

Computational Biology↗

PubMed2002

On the possibility of using commercial software packages for thermoluminescence glow curve deconvolution analysis.

This paper explores the possibility of using commercial software for thermoluminescence glow curve deconvolution (GCD) analysis. The program PEAKFIT has been used to perform GCD analysis of complex glow curves of quartz and dosimetric materials. First-order TL peaks were represented successfully using the Weibull distribution function. Second-order and general-order TL peaks were represented accurately by using the Logistic asymmetric functions with varying symmetry parameters. Analytical expressions were derived for determining the energy E from the parameters of the Logistic asymmetric functions. The accuracy of these analytical expressions for E was tested for a wide variety of kinetic parameters and was found to be comparable to the commonly used expressions in the TL literature. The effectiveness of fit of the analytical functions used here was tested using the figure of merit (FOM) and was found to be comparable to the accuracy of recently published GCD expressions for first- and general-order kinetics.

Kinetics↗

PubMed1999

Evaluating computerized health information systems: hardware, software and human ware: experiences from the Northern Province, South Africa.

Despite enormous investment world-wide in computerized health information systems their overall benefits and costs have rarely been fully assessed. A major new initiative in South Africa provides the opportunity to evaluate the introduction of information technology from a global perspective and assess its impact on public health. The Northern Province is implementing a comprehensive integrated hospital information system (HIS) in all of its 42 hospitals. These include two mental health institutions, eight regional hospitals (two acting as a tertiary complex with teaching responsibilities) and 32 district hospitals. The overall goal of the HIS is to improve the efficiency and effectiveness of health (and welfare) services through the creation and use of information, for clinical, administrative and monitoring purposes. This multi-site implementation is being undertaken as a single project at a cost of R130 million (which represents 2.5 per cent of the health and welfare budget on an annual basis). The implementation process commenced on 1 September 1998 with the introduction of the system into Mankweng Hospital as the pilot site and is to be completed in the year 2001. An evaluation programme has been designed to maximize the likelihood of success of the implementation phase (formative evaluation) as well as providing an overall assessment of its benefits and costs (summative evaluation). The evaluation was designed as a form of health technology assessment; the system will have to prove its worth (in terms of cost-effectiveness) relative to other interventions. This is more extensive than the traditional form of technical assessment of hardware and software functionality, and moves into assessing the day-to-day utility of the system, the clinical and managerial environment in which it is situated (humanware), and ultimately its effects on the quality of patient care and public health. In keeping with new South African legislation the evaluation process sought to involve as many stakeholders as possible at the same time as creating a methodologically rigorous study that lived within realistic resource limits. The design chosen for the summative assessment was a randomized controlled trial (RCT) in which 24 district hospitals will receive the HIS either early or late. This is the first attempt to carry out an RCT evaluation of a multi-site implementation of an HIS in the world. Within this design the evaluation will utilize a range of qualitative and quantitative techniques over varying time scales, each addressing specific aims of the evaluation programme. In addition, it will attempt to provide an overview of the general impact on people and organizations of introducing high-technology solutions into a relatively unprepared environment. The study should help to stimulate an evaluation culture in the health and welfare services in the Northern Province as well as building the capacity to undertake such evaluations in the future.

Computers↗

PubMed2005

PRDC--a software package for personnel radiation dose calculation.

To determine effective dose, we usually need to use a very complicated human body model and a sophisticated computer code to transport radiations in the body model and surrounding medium, which is not very easy to practicing health physicists in the field. This study develops and tests a software package, called PRDC (Personnel Radiation Dose Calculation), which calculates effective dose and radiation doses to various organs/tissues and personal dosemeters based on a series of interpolations.

Algorithms↗

PubMed2006

Dose imaging with gel-dosemeter layers: optical analysis and dedicated software.

In radiotherapy involving thermal and epithermal neutrons, the knowledge of dose distributions, with separation of the contribution of each secondary radiation component, is of utmost importance. Layers of Fricke-Xylenol-Orange-infused gel dosemeters give the possibility of achieving such requirements because, owing to the layer-geometry, enriching or depleting the gel matrix of suitable isotopes does not sensibly alter neutron transport. The dosimetry method has been critically re-examined with the aim of improving its suitability to boron neutron capture therapy (BNCT) requirements, as it applies to the protocol of measurement and analysis, the sensitivity of the method and the range of the linearity of the dosemeters. Software has been developed and studied to obtain automatically the images of the various dose components with the established separation procedure.

Algorithms↗

PubMed1987

Computer software program to plot locations of death.

A BASIC computer software program that plots the occurrence of various types of death on a grid map is described. The capabilities, requirements, and potential uses of the program are discussed.

Coroners and Medical Examiners↗

PubMed2006

Nonlinear changes in brain dynamics during emergence from sevoflurane anesthesia: preliminary exploration using new software.

BACKGROUND: New software was used during a pilot study of nonlinear changes in the electroencephalogram during emergence from sevoflurane anesthesia. METHODS: Digitized electroencephalographic signals were recorded from bipolar forehead electrodes between 1.2 and 40 k s/sec. Trajectories derived from underlying attractors were displayed continuously, and attractor dimensions were estimated. Observations are reported from 13 patients emerging from sevoflurane anesthesia. RESULTS: Qualitative observations and quantitative analysis of the data demonstrated four dynamical stages during emergence from deep anesthesia to consciousness. CONCLUSIONS: The dynamical stages of emergence from sevoflurane anesthesia into consciousness demonstrate a classic route toward chaos, but the presence of chaos in the conscious state remains unproven. These stages are apparent both pictorially and analytically. Pre-emergent attractor patterns are usually distinctive; their real-time display could be a useful adjunct to depth of anesthesia monitors because they may provide warning of an imminent return to consciousness.

Adult↗

PubMed1992

Facial video image processing: standard facial image capturing, software modification, development of a surgical plan, and comparison of presurgical and postsurgical results.

Video imaging is a maturing technology that will challenge the 35-mm photograph in its usefulness to the plastic surgeon. Computer modification of a patient image communicates to the patient a reconstructive plan. A comparison of the presurgical and postsurgical images keenly sensitizes the surgeon to the results of surgical technique. The equipment required for video imaging also provides a powerful tool for creation of presentation graphic prints (for publication), 35-mm slides, and, with additional software, educational video tapes. I describe here a video method for standard alignment of patients. The preoperative and modified patient image (surgical plan) is compared with the postoperative image to determine the degree of success in achieving the reconstructive goals. Comparison of standardized presurgical and postsurgical images offers the surgeon greater objectivity in his analysis of the surgical technique than is possible by comparison of clinical photographs. The value of video imaging to the reconstructive surgeon magnifies the success (or disappointment) of surgical technique.

Computer Graphics↗

PubMedDate not supplied

Development and solution of finite-difference equations for burn injury with spreadsheet software.

This article presents a brief description of a set of equations by which the thermal burn process may be modeled, a formulation of the differential equations into a finite-difference format, and a simple method of solution using a standard commercial spreadsheet software application. A companion article provides a discussion of results that can be obtained with the modeling techniques presented here. A short version of the spreadsheet program is available from the author.

Burns↗

PubMedDate not supplied

Simulation software: engineer processes before reengineering.

People make decisions all the time using intuition. But what happens when you are asked: "Are you sure your predictions are accurate? How much will a mistake cost? What are the risks associated with this change?" Once a new process is engineered, it is difficult to analyze what would have been different if other options had been chosen. Simulating a process can help senior clinical officers solve complex patient flow problems and avoid wasted efforts. Simulation software can give you the data you need to make decisions. The author introduces concepts, methodologies, and applications of computer aided simulation to illustrate their use in making decisions to improve workflow design.

Computer Simulation↗