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At least 541 records · Page 30Linked to original sources

PubMed1990

Commercial software as the basis for an augmentative communication system on a personal computer.

Many severely speech-impaired individuals have a need or desire to maintain the capability for computerized speech generation while performing a variety of other computer-supported tasks such as word processing, financial analysis, or database management. Criteria are presented for augmentative communication systems that both incorporate a personal computer (PC) and provide capabilities for voice output to satisfy this requirement. Current approaches to such systems are categorized and reviewed in light of these criteria. A new method is then described in which word processing or other appropriate PC software is used for speech production, providing a natural integration of written and spoken communication. The approach separates the computer access and voice output functions to allow great flexibility in the choice of an alternative access system. This flexibility combined with appropriate exploitation of PC software features has the potential to yield a high communication rate as well as maximum compatibility with application software.

Communication Devices for People with Disabilities↗

PubMed1999

A review of the FDA draft guidance document for software validation: guidance for industry.

A Draft Guidance Document (Version 1.1) was issued by the United States Food and Drug Administration (FDA) to address the software validation requirement of the Quality System Regulation, 21 CFR Part 820, effective June 1, 1997. The guidance document outlines validation considerations that the FDA regards as applicable to both medical device software and software used to "design, develop or manufacture" medical devices. The Draft Guidance is available at the FDA web site http:@www.fda.gov/cdrh/comps/swareval++ +.html. Presented here is a review of the main features of the FDA document for Quality System Regulation (QSR), and some guidance for its implementation in industry.

Guidelines as Topic↗

PubMed2002

Hip-Op: an innovative software to plan total hip replacement surgery.

This paper describes an innovative surgical simulation software environment for the pre-operative planning of total hip replacement surgery. The software is a CT-based three-dimensional planning environment, with a user-friendly graphic user interface based on the multimodal display visualization paradigm. Although it relies on a fully three dimensional internal representation, this approach represents the relevant anatomical objects by means of multiple views, each simulating a different medical imaging modality familiar to the medical professional. In the Hip-Op program the multimodal display interface integrates four different display modalities: orthogonal radiographs, Blended slices, CT slices, and arbitrary slices. A conventional surface rendering view is also available. The user 'navigates' the prosthetic components, which are dynamically selected from a library of available parts, within the CT volume while the implant and the patient anatomy are simultaneously rendered in each specialized view. Beside a consideration of anatomical compatibility, the surgeon may evaluate the planned implant type, size and position, also on the basis of two analysis modules that compute the achieved level of implant fitting and filling. After being evaluated in an internal clinical trial, the software is currently made available as freeware at http:// www.ior.it/hipop/.

Algorithms↗

PubMed1998

A computer software application for managing occupational exposure data.

The Health Hazard Information Module is the U.S. Army's computer software application for managing occupational exposure data. The project mission is to utilize automated information systems technology to improve the overall effectiveness of industrial hygiene programs. Field industrial hygiene professionals document their survey methods, findings, conclusions, and recommendations with a portable, pen-based computer. Back at the office, the data are electronically transferred to a desktop workstation. Users can generate standard or customized reports in hard copy or electronic formats. Annually, users transfer their data to a corporate mainframe computer. The software incorporates appropriate information and represents an excellent template worth examining during the ongoing international effort to standardize occupational exposure data. Planned refinements include distributing the software to other Department of Defense agencies and making it commercially available for a nominal fee through the National Technical Information Service in the near future.

Computer Systems↗

PubMed2005

A software tool for 2D/3D visualization and analysis of phase-space data generated by Monte Carlo modelling of medical linear accelerators.

A computer program has been developed for novel 2D/3D visualization and analysis of the phase-space parameters of Monte Carlo simulations of medical accelerator radiation beams. The software is written in the IDL language and reads the phase-space data generated in the BEAMnrc/BEAM Monte Carlo code format. Contour and colour-wash plots of the fluence, mean energy, energy fluence, mean angle, spectra distribution, energy fluence distribution, angular distribution, and slices and projections of the 3D ZLAST distribution can be calculated and displayed. Based on our experience of using it at Massachusetts General Hospital, the software has proven to be a useful tool for analysis and verification of the Monte Carlo generated phase-space files. The software is in the public domain.

Computer Graphics↗

PubMed2003

Research use of the AIDA www.2aida.org diabetes software simulation program: a review--part 2. Generating simulated blood glucose data for prototype validation.

The purpose of this review is to describe research applications of the AIDA diabetes software simulator. AIDA is a computer program that permits the interactive simulation of insulin and glucose profiles for teaching, demonstration, and self-learning purposes. Since March/April 1996 it has been made freely available on the Internet as a noncommercial contribution to continuing diabetes education. Up to May 2003 well over 320,000 visits have been logged at the main AIDA Website--www.2aida.org--and over 65,000 copies of the AIDA program have been downloaded free-of-charge. This review (the second of two parts) overviews research projects and ventures, undertaken for the most part by other research workers in the diabetes computing field, that have made use of the freeware AIDA program. As with Part 1 of the review (Diabetes Technol Ther 2003;5:425-438) relevant research work was identified in three main ways: (i) by personal (e-mail/written) communications from researchers, (ii) via the ISI Web of Science citation database to identify published articles which referred to AIDA-related papers, and (iii) via searches on the Internet. Also, in a number of cases research students who had sought advice about AIDA, and diabetes computing in general, provided copies of their research dissertations/theses upon the completion of their projects. Part 2 of this review highlights some more of the research projects that have made use of the AIDA diabetes simulation program to date. A wide variety of diabetes computing topics are addressed. These range from learning about parameter interactions using simulated blood glucose data, to considerations of dietary assessments, developing new diabetes models, and performance monitoring of closed-loop insulin delivery devices. Other topics include evaluation/validation research usage of such software, applying simulated blood glucose data for prototype training/validation, and other research uses of placing technical information on the Web. This review confirms an unexpected but useful benefit of distributing a medical program, like AIDA, for free via the Internet--demonstrating how it is possible to have a synergistic benefit with other researchers--facilitating their own research projects in related medical fields. A common theme that emerges from the research ventures that have been reviewed is the use of simulated blood glucose data from the AIDA software for preliminary computer lab-based testing of other decision support prototypes. Issues surrounding such use of simulated data for separate computer prototype testing are considered further.

Blood Glucose↗

PubMed2004

Adaptive user displays for intelligent tutoring software.

Intelligent tutoring software (ITS) holds great promise for K-12 instruction. Yet it is difficult to obtain rich information about users that can be used in realistic educational delivery settings--public school classrooms--in which eye tracking and other user sensing technologies are not suitable. We are pursuing three "cheap and cheerful" strategies to meet this challenge in the context of an ITS for high school math instruction. First, we use detailed representations of student cognitive skills, including tasks to assess individual users' proficiency with abstract reasoning, proficiency with simple math facts and computational skill, and spatial ability. Second, we are using data mining and machine learning algorithms to identify instructional sequences that have been effective with previous students, and to use these patterns to make decisions about current students. Third, we are integrating a simple focus-of-attention tracking system into the software, using inexpensive, web cameras. This coarse-grained information can be used to time the display of multimedia hints, explanations, and examples when the user is actually looking at the screen, and to diagnose causes of problem-solving errors. The ultimate goal is to create non-intrusive software that can adapt the display of instructional information in real time to the user's cognitive strengths, motivation, and attention.

Algorithms↗

PubMed1991

Considerations for selecting nutrient-calculation software: evaluation of the nutrient database.

With the growing number of nutrient-calculation software packages on the market, potential users are faced with the increasingly difficult task of determining which system best meets their needs. Most published reviews of nutrient-calculation software focus on program features rather than on the quality of the nutrient database on which all calculations are based. This is unfortunate because program features are of little consequence if the nutrients calculated are not of acceptable quality. The purpose of this paper is to focus on the evaluation of the nutrient database as the foremost consideration in selecting nutrient-calculation software. Six questions that may be used as a guide for evaluating a nutrient database are presented and discussed.

Databases, Factual↗

PubMed2000

Comparing the success of different prediction software in sequence analysis: a review.

The abundance of computer software for different types of prediction in DNA and protein sequence analyses raises the problem of adequate ranking of prediction program quality. A single measure of success of predictor software, which adequately ranks the predictors, does not exist. A typical example of such an incomplete measure is the so-called correlation coefficient. This paper provides an overview and short analysis of several different measures of prediction quality. Frequently, some of these measures give results contradictory to each other even when they relate to the same prediction scores. This may lead to confusion. In order to overcome some of the problems, a few new measures are proposed including some variants of a 'generalised distance from the ideal predictor score'; these are based on topological properties, rather than on statistics. In order to provide a sort of a balanced ranking, the averaged score measure (ASM) is introduced. The ASM provides a possibility for the selection of the predictor that probably has the best overall performance. The method presented in the paper applies to the ranking problem of any prediction software whose results can be properly represented in a true positive-false positive framework, thus providing a natural set-up for linear biological sequence analysis.

Computational Biology↗

PubMed2005

Software agents in molecular computational biology.

Progress made in applying agent systems to molecular computational biology is reviewed and strategies by which to exploit agent technology to greater advantage are investigated. Communities of software agents could play an important role in helping genome scientists design reagents for future research. The advent of genome sequencing in cattle and swine increases the complexity of data analysis required to conduct research in livestock genomics. Databases are always expanding and semantic differences among data are common. Agent platforms have been developed to deal with generic issues such as agent communication, life cycle management and advertisement of services (white and yellow pages). This frees computational biologists from the drudgery of having to re-invent the wheel on these common chores, giving them more time to focus on biology and bioinformatics. Agent platforms that comply with the Foundation for Intelligent Physical Agents (FIPA) standards are able to interoperate. In other words, agents developed on different platforms can communicate and cooperate with one another if domain-specific higher-level communication protocol details are agreed upon between different agent developers. Many software agent platforms are peer-to-peer, which means that even if some of the agents and data repositories are temporarily unavailable, a subset of the goals of the system can still be met. Past use of software agents in bioinformatics indicates that an agent approach should prove fruitful. Examination of current problems in bioinformatics indicates that existing agent platforms should be adaptable to novel situations.

Algorithms↗

PubMed1995

Object-oriented data handler for sequence analysis software development.

We report an object-oriented data handler and supplementary tools for the development of molecular genetics application software for various sequence analyses. Our data handler has a flexible and expandable format that supports the most common data types for molecular genetic software. New data types can be constructed in an object-oriented manner from the basic units. The data handler includes an object library, a format-converting program and a viewer that can visualize simultaneously the data contained in several files to construct a general picture from separate data. This software has been implemented on an IBM PC-compatible personal computer.

Atrial Natriuretic Factor↗

PubMed1999

E-CELL: software environment for whole-cell simulation.

MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://e-cell.org/.

Adenosine Triphosphate↗

PubMed1999

Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences.

MOTIVATION: The annotation of the Arabidopsis thaliana genome remains a problem in terms of time and quality. To improve the annotation process, we want to choose the most appropriate tools to use inside a computer-assisted annotation platform. We therefore need evaluation of prediction programs with Arabidopsis sequences containing multiple genes. RESULTS: We have developed AraSet, a data set of contigs of validated genes, enabling the evaluation of multi-gene models for the Arabidopsis genome. Besides conventional metrics to evaluate gene prediction at the site and the exon levels, new measures were introduced for the prediction at the protein sequence level as well as for the evaluation of gene models. This evaluation method is of general interest and could apply to any new gene prediction software and to any eukaryotic genome. The GeneMark.hmm program appears to be the most accurate software at all three levels for the Arabidopsis genomic sequences. Gene modeling could be further improved by combination of prediction software. AVAILABILITY: The AraSet sequence set, the Perl programs and complementary results and notes are available at http://sphinx.rug.ac.be:8080/biocomp/napav/. CONTACT: Pierre.Rouze@gengenp.rug.ac.be.

Alternative Splicing↗

PubMed1990

Free molecular biological software available from the EMBL file server.

A new service provided by EMBL (EMBL Software File Server) is described that will make free molecular biology software available to anyone with computer network access. MS-DOS, Apple Macintosh and VAX/VMX are supported at the moment. The programs will be delivered by normal electronic mail; conversion mechanisms will transform binary files to ASCII to allow mail transfer. This service will also help authors to distribute their software conveniently.

Computer Communication Networks↗

PubMed1991

CAMBIO: software for modelling and simulation of bioprocesses.

CAMBIO, a software package devoted to bioprocess modelling, which runs on Apollo computers, is described. This software enables bioengineers to easily and interactively design appropriate mathematical models directly from their perception of the process. CAMBIO provides the user with a set of design symbols and mnemonic icons in order to interactively design a functional diagram. This diagram has to exhibit the most relevant components with their related interactions through biological and physico-chemical reactions. Then, CAMBIO automatically generates the dynamical material balance equations of the process in the form of an algebraic-differential system by taking advantage of the knowledge involved in the functional diagram. The model may be used for control design purpose or completed by kinetics expressions with a view to simulation. CAMBIO offers facilities to generate a simulation model (for coding of kinetics, introducing auxiliary variables, etc.). This model is automatically interfaced with a specialized simulation software which allows an immediate visualization of the process dynamical behaviour under various operational conditions (possibly involving feedback control strategies). An example of an application dealing with yeast fermentation is given.

Algorithms↗

PubMed2026

MultiDMPcaller: a one-stop software for detection and visualization of differentially methylated positions and regions.

MOTIVATION: Whole-genome bisulfite sequencing (WGBS/BS-Seq) is the gold standard for single-base resolution DNA methylome profiling. However, the diverse statistical models of existing computational methods lead to limited overlap between their results, highlighting the need for novel methods to detect differentially methylated positions (DMPs) and differentially methylated regions (DMRs). RESULTS: We developed MultiDMPcaller, an automated downstream methylome analysis software. It processes upstream outputs to profile DMPs, non-DMPs, DMRs, and context-specific (CpG/CHG/CHH) methylation status, alongside visualizing their chromosomal distribution and enrichment. The software features two key innovations: (i) an adaptive two-step P-value adjustment strategy based on organism-specific methylation patterns, with raw P-value ≤0.05 pre-filtering followed by false discovery rate (FDR) correction, to recover potential DMPs usually missed by standard FDR correction in plant CHG/CHH and animal CpG contexts; and (ii) a multiple pairwise comparison approach, which performs m × n pairwise comparisons for m control and n experimental replicates, followed by a voting system supporting both user-defined majority thresholds and model-based adaptive thresholds, to identify robust and reliable DMPs (with a stricter voting threshold exclusively for loci with low methylation differences) and DMRs. On real datasets from Arabidopsis, apple, and mouse, as well as simulated human datasets, MultiDMPcaller's results showed good agreement with those of other software, exhibiting high conservativeness and superior precision, which suggested a low false discovery proportion. AVAILABILITY AND IMPLEMENTATION: MultiDMPcaller is available at GitHub (https://github.com/jiantaoyuNWAFU/MultiDMPcaller) and via a web server (https://ciebioinfo.nwafu.edu.cn).

Software↗

PubMed2004

SNPbox: a modular software package for large-scale primer design.

UNLABELLED: We developed a modular software package SNPbox that automates and standardizes the generation of PCR primers and is used in the strategy for constructing single nucleotide polymorphisms (SNPs) maps. In this strategy, the focus of primer design can be either on the validation of annotated public SNPs or on the SNP discovery in exon regions or extended genomic regions, both by resequencing. SNPbox relies on Primer3 for the primer design and combines this program with other publicly available software tools such as BLAST, Spidey and RepeatMasker, and newly developed algorithms. Primer conditions were chosen such that PCR amplifications are uniform for each PCR amplicon facilitating the use of high-throughput genetic platforms. SNPbox can also be used for the design of primer sets for mutation analysis, STR marker genotyping and microarray oligo design. Of the 2500 primer sets designed by SNPbox, 95% successfully amplified genomic DNA under uniform PCR conditions. AVAILABILITY: The software is available from the authors upon request. SUPPLEMENTARY INFORMATION: SNPbox_supplement.

Algorithms↗

PubMed2005

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry.

SUMMARY: Research in proteomics requires powerful database-searching software to automatically identify protein sequences in a complex protein mixture via tandem mass spectrometry. In this paper, we describe a novel database-searching software system called pFind (peptide/protein Finder), which employs an effective peptide-scoring algorithm that we reported earlier. The pFind server is implemented with the C++ STL, .Net and XML technologies. As a result, high speed and good usability of the software are achieved.

Algorithms↗