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At least 1,027 records · Page 57Linked to original sources
PubMed1997

Visuvalve software: an aid to the diagnosis of shunt failure.

Software designed to help the neurosurgeon in the diagnosis of shunt malfunction is presented. This software allows the possibility to record on a 3.5 diskette a patient's clinical information and four views of a CT scan performed when the patient was doing perfectly well with his shunt. This diskette, operated by MS-DOS on any IBM-compatible personal computer, can be read at any time, anywhere. The evaluation of the system demonstrated it was safe, with an excellent adhesion of the patients and of their families.

Cerebral Ventriculography↗
PubMedDate not supplied

Newly developed software for capillary blood pressure analysis in microcirculatory research.

The introduction of the servonulling technique by Wiederhielm in 1963 allowed for the first time continuous and dynamic recording of capillary blood pressure (CP). In 1979 Mahler used this technique for the first measurements in humans. Data analysis was limited to manual analysis of chart recordings. Nowadays fast analog-digital converters with ay high sampling frequency are used for data recordings, and consequently there is a need for an easy-to-use software for data analysis of CP data. The presented newly developed computer software allows analysis of mean CP, taking into account the zero pressure measured before and after capillary cannulation. The simultaneously recorded electrocardiogram R wave is used as a marker for the calculation of the mean capillary pulse pressure waves and of their characteristic data. This may help determine the significance of the capillary pulse waveform for microvascular function. Changes in the pulse waveform may be the only detectable difference between patients and healthy controls. Analysis of simultaneously recorded temperature, the display of markers for valid readings, and the possibility of excluding nonvalid data or artefacts from analysis are additional features.

Adult↗
PubMed1984

Computer software design for pediatric practice. A modular approach.

Practical applications for using computers in everyday medical practice have not kept pace with the technical developments that now make this tool available to the pediatric practitioner. A modular approach to user-developed applications software is presented as a model for computerizing the pediatric office. Benefits have included lower cost, greater data reliability and validity, standardization of office and medical procedures, and automation of jobs formerly requiring much personnel time. Some patient services have improved, and other new services have become possible, through the application of computer software designed in accordance with our practice philosophy.

Computers↗
PubMed1999

Criteria for software evaluation: legal issues.

The maintenance of electronic health records in the school setting requires knowledge of the legal standards of both electronic records and health records. School nurses are responsible for the selection of software and hardware that meet federal and state legal standards. Software capabilities that enhance the legal value of the student health record are: overwrite protection, multi-user passwords, multi-level access, auditability, rejection, automatic back-up, and the ability to enter and process dates for the year 2000.

Computer Security↗
PubMed1997

Developing sexual health software incorporating user feedback: a British experience.

This article describes an interactive prototyping model for development of four computer software modules for British youth on sexual issues. An iterative cycle of development, user review and feedback, and subsequent modification and retesting was used with approximately 150 young adults, with particular attention to presentation style, screen design, usability, relevance of material, enjoyment, and learning. The software was designed to be realistically accommodated in school settings, to be used as a reference tool by students working alone or in a group teaching situation. Feedback from youth and adults attests to the feasibility of development, implementation, and instructional usefulness. Interactive prototyping proved essential in the face of skepticism from teachers concerning young people's information needs and acceptance of a computerized educational approach.

Adolescent↗
PubMed2006

Clinical, information and business process modeling to promote development of safe and flexible software.

Using a factorial vignette survey and modeling methodology, we developed clinical and information models - incorporating evidence base, key concepts, relevant terms, decision-making and workflow needed to practice safely and effectively - to guide the development of an integrated rule-based knowledge module to support prescribing decisions in asthma. We identified workflows, decision-making factors, factor use, and clinician information requirements. The Unified Modeling Language (UML) and public domain software and knowledge engineering tools (e.g. Protégé) were used, with the Australian GP Data Model as the starting point for expressing information needs. A Web Services service-oriented architecture approach was adopted within which to express functional needs, and clinical processes and workflows were expressed in the Business Process Execution Language (BPEL). This formal analysis and modeling methodology to define and capture the process and logic of prescribing best practice in a reference implementation is fundamental to tackling deficiencies in prescribing decision support software.

Asthma↗
PubMed2004

ABC: software for interactive browsing of genomic multiple sequence alignment data.

BACKGROUND: Alignment and comparison of related genome sequences is a powerful method to identify regions likely to contain functional elements. Such analyses are data intensive, requiring the inclusion of genomic multiple sequence alignments, sequence annotations, and scores describing regional attributes of columns in the alignment. Visualization and browsing of results can be difficult, and there are currently limited software options for performing this task. RESULTS: The Application for Browsing Constraints (ABC) is interactive Java software for intuitive and efficient exploration of multiple sequence alignments and data typically associated with alignments. It is used to move quickly from a summary view of the entire alignment via arbitrary levels of resolution to individual alignment columns. It allows for the simultaneous display of quantitative data, (e.g., sequence similarity or evolutionary rates) and annotation data (e.g. the locations of genes, repeats, and constrained elements). It can be used to facilitate basic comparative sequence tasks, such as export of data in plain-text formats, visualization of phylogenetic trees, and generation of alignment summary graphics. CONCLUSIONS: The ABC is a lightweight, stand-alone, and flexible graphical user interface for browsing genomic multiple sequence alignments of specific loci, up to hundreds of kilobases or a few megabases in length. It is coded in Java for cross-platform use and the program and source code are freely available under the General Public License. Documentation and a sample data set are also available http://mendel.stanford.edu/sidowlab/downloads.html.

Animals↗
PubMed2005

SplitTester: software to identify domains responsible for functional divergence in protein family.

BACKGROUND: Many protein families have undergone functional divergence after gene duplications such that current subgroups of the family carry out overlapping but distinct biological roles. For the protein families with known functional subtypes (a functional split), we developed the software, SplitTester, to identify potential regions that are responsible for the observed distinct functional subtypes within the same protein family. RESULTS: Our software, SplitTester, takes a multiple protein sequences alignment as input, generated from protein members of two subgroups with known functional divergence. SplitTester was designed to construct the neighbor joining tree (a split cluster) from variable-sized sliding windows across the alignment in a process called split-clustering. SplitTester identifies the regions, whose split cluster is consistent with the functional split, but may be inconsistent with the phylogeny of the protein family. We hypothesize that at least some number of these identified regions, which are not following a random mutation process, are responsible for the observed functional split. To test our method, we used reverse transcriptase from a group of Pseudoviridae retrotransposons: to identify residues specific for diverged primer recognition. Candidate regions were then mapped onto the three dimensional structures of reverse transcriptase. The locations of these amino acids within the enzyme are consistent with their biological roles. CONCLUSION: SplitTester aims to identify specific domain sequences responsible for functional divergence of subgroups within a protein family. From the analysis of retroelements reverse transcriptase family, we successfully identified the regions splitting this family according to the primer specificity, implying their functions in the specific primer selection.

Algorithms↗
PubMed2005

A software tool for creating simulated outbreaks to benchmark surveillance systems.

BACKGROUND: Evaluating surveillance systems for the early detection of bioterrorism is particularly challenging when systems are designed to detect events for which there are few or no historical examples. One approach to benchmarking outbreak detection performance is to create semi-synthetic datasets containing authentic baseline patient data (noise) and injected artificial patient clusters, as signal. METHODS: We describe a software tool, the AEGIS Cluster Creation Tool (AEGIS-CCT), that enables users to create simulated clusters with controlled feature sets, varying the desired cluster radius, density, distance, relative location from a reference point, and temporal epidemiological growth pattern. AEGIS-CCT does not require the use of an external geographical information system program for cluster creation. The cluster creation tool is an open source program, implemented in Java and is freely available under the Lesser GNU Public License at its Sourceforge website. Cluster data are written to files or can be appended to existing files so that the resulting file will include both existing baseline and artificially added cases. Multiple cluster file creation is an automated process in which multiple cluster files are created by varying a single parameter within a user-specified range. To evaluate the output of this software tool, sets of test clusters were created and graphically rendered. RESULTS: Based on user-specified parameters describing the location, properties, and temporal pattern of simulated clusters, AEGIS-CCT created clusters accurately and uniformly. CONCLUSION: AEGIS-CCT enables the ready creation of datasets for benchmarking outbreak detection systems. It may be useful for automating the testing and validation of spatial and temporal cluster detection algorithms.

Algorithms↗
PubMed2006

Utilizing FEM-Software to quantify pre- and post-interventional cardiac reconstruction data based on modelling data sets from surgical ventricular repair therapy (SVRT) and cardiac resynchronisation therapy (CRT).

BACKGROUND: Left ventricle (LV) 3D structural data can be easily obtained using standard transesophageal echocardiography (TEE) devices but quantitative pre- and intraoperative volumetry and geometry analysis of the LV is presently not feasible in the cardiac operation room (OR). Finite element method (FEM) modelling is necessary to carry out precise and individual volume analysis and in the future will form the basis for simulation of cardiac interventions. METHOD: A Philips/HP Sonos 5500 ultrasound device stores volume data as time-resolved 4D volume data sets. In this prospective study TomTec LV Analysis TEE Software was used for semi-automatic endocardial border detection, reconstruction, and volume-rendering of the clinical 3D echocardiographic data. With the software FemCoGen a quantification of partial volumes and surface directions of the LV was carried out for two patients data sets. One patient underwent surgical ventricular repair therapy (SVR) and the other a cardiac resynchronisation therapy (CRT). RESULTS: For both patients a detailed volume and surface direction analysis is provided. Partial volumes as well as normal directions to the LV surface are pre- and post-interventionally compared. CONCLUSION: The operation results for both patients are quantified. The quantification shows treatment details for both interventions (e.g. the elimination of the discontinuities for CRT intervention and the segments treated for SVR intervention). The LV quantification is feasible in the cardiac OR and it gives a detailed and immediate quantitative feedback of the quality of the intervention to the medical.

Arrhythmias, Cardiac↗
PubMed2004

A survey of current software for haplotype phase inference.

In the past two years, tracking the explosion in data due to ever-improving single nucleotide polymorphism (SNP) maps and cheaper high-throughput genotyping technologies, a bewildering array of new algorithms and relevant software have appeared for haplotype phase inference. The alternatives to haplotype inference are to resolve haplotypes completely, either by in vitro methods or by typing close pedigrees, which is expensive and is not guaranteed in pedigrees, or to ignore haplotype-level analysis in favour of genotype-level analysis, which avoids the danger of treating inferred haplotypes as real but denies the researcher, potentially, any valuable analytic insights. This review attempts a snapshot of this rapidly moving field as it stands at present, and is mainly restricted, given the current predominance of SNP genotyping, to the consideration of diallelic data. For completeness, the review will occasionally refer to algorithms for which no software exists.

Algorithms↗
PubMed2004

A review of the 'Statistical Analysis for Genetic Epidemiology' (S.A.G.E.) software package.

The 'Statistical Analysis for Genetic Epidemiology' (S.A.G.E.) software package is an integrated, comprehensive package of computer programs designed to perform many of the different analyses required in the study of genetic epidemiology. It offers a graphical user interface for most platforms and, unlike many programs available in the public domain, is flexible in both receiving many types of input files and in allowing the user to choose among output files. All of the programs accept the same data files and together provide the means to perform familial correlation, segregation, linkage and association analyses, as well as many of the ancillary analyses that help achieve these goals. Many, but not all, of the same or similar analyses can be performed (with more difficulty) using publicly available freeware. The primary limitations of S.A.G.E. at present are the lack of software for estimating haplotypes or for identifying probable double recombinants in linkage analysis. S.A.G.E. is continually being extended and upgraded, however, with automatic downloading of the latest version always available to users.

Databases, Genetic↗
PubMed2007

Counting colonies of clonogenic assays by using densitometric software.

Clonogenic assays are a useful tool to test whether a given cancer therapy can reduce the clonogenic survival of tumour cells. A colony is defined as a cluster of at least 50 cells which can often only be determined microscopically. The process of counting colonies is very extensive work and so we developed software that is able to count the colonies automatically from scanned flasks. This software is made freely available by us with a detailed description how to use and install the necessary features.

Algorithms↗
PubMed2002

BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data.

The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the hybridization images and their extracted data matrices, and information about the physical array, the features and reporter molecules. We present a web-based customizable bioinformatics solution called BioArray Software Environment (BASE) for the management and analysis of all areas of microarray experimentation. All software necessary to run a local server is freely available.

Database Management Systems↗
PubMed2004

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

Computational Biology↗
PubMed1998

Test rig and software for recording force and muscle activity.

OBJECTIVE: To design a test rig for measuring isometric quadriceps' force which is easily adjustable, dismountable, transportable, relatively lightweight and inexpensive. Also to produce a data-acquisition software program that enables real-time feedback of the force signal, automatic analysis of maximal voluntary contraction (MVC) force, and submaximal target levels to be displayed on a computer screen, as well as acquisition of other signals such as electromyographic (EMG) activity. METHODOLOGY: A test rig was constructed using an aluminium tubing system which was fully adjustable and could be flat-packed for transportation. The data acquisition software program was written in Borland C++ and is suitable for use with an IBM-compatible PC. The interface is user friendly, and the entire testing system is relatively inexpensive compared to commercially available systems. CONCLUSIONS: The equipment is suitable for various applications in rehabilitation research and clinical testing, and is suitable for examining different muscles. Further technical details are freely available from the authors.

Electromyography↗
PubMed1993

Relationship between molecular connectivity and carcinogenic activity: a confirmation with a new software program based on graph theory.

For a database of 826 chemicals tested for carcinogenicity, we fragmented the structural formula of the chemicals into all possible contiguous-atom fragments with size between two and eight (nonhydrogen) atoms. The fragmentation was obtained using a new software program based on graph theory. We used 80% of the chemicals as a training set and 20% as a test set. The two sets were obtained by random sorting. From the training sets, an average (8 computer runs with independently sorted chemicals) of 315 different fragments were significantly (p < 0.125) associated with carcinogenicity or lack thereof. Even using this relatively low level of statistical significance, 23% of the molecules of the test sets lacked significant fragments. For 77% of the molecules of the test sets, we used the presence of significant fragments to predict carcinogenicity. The average level of accuracy of the predictions in the test sets was 67.5%. Chemicals containing only positive fragments were predicted with an accuracy of 78.7%. The level of accuracy was around 60% for chemicals characterized by contradictory fragments or only negative fragments. In a parallel manner, we performed eight paired runs in which carcinogenicity was attributed randomly to the molecules of the training sets. The fragments generated by these pseudo-training sets were devoid of any predictivity in the corresponding test sets. Using an independent software program, we confirmed (for the complex biological endpoint of carcinogenicity) the validity of a structure-activity relationship approach of the type proposed by Klopman and Rosenkranz with their CASE program.

Carcinogens↗