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At least 19 recordsLinked to original sources
PubMed2005

Improving the reliability of medical software by predicting the dangerous software modules.

Software reliability analysis is inevitable for modern medical systems, since a large amount of medical system functionality is now dependent on software, and software does contribute to system failures. Most software reliability models are based on software failure data collected from the project. This creates a problem for the designers since, during the early stage, software failure data are not available. However, a valuable knowledge can be learned from the analysis of previous projects and applied to the new ones. This paper presents the approach that predicts the potentially dangerous software modules under development based on the analysis of the already finished modules using the machine-learning techniques. On the basis of the prediction given by our method software designers are able to devote more testing effort to the dangerous parts of the system, which results in a more reliable medical software system.

Algorithms↗
PubMed2006

The Gaggle: an open-source software system for integrating bioinformatics software and data sources.

BACKGROUND: Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing. RESULTS: In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment. We demonstrate that four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools. CONCLUSION: We have integrated diverse databases (for example, KEGG, BioCyc, String) and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer). Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and Pubmed abstracts (STRING web resource), creating an exploratory environment useful to 'web browser and spreadsheet biologists', to statistically savvy computational biologists, and those in between. The Gaggle uses Java RMI and Java Web Start technologies and can be found at http://gaggle.systemsbiology.net.

Computational Biology↗
PubMed2001

Combining speech recognition software with Digital Imaging and Communications in Medicine (DICOM) workstation software on a Microsoft Windows platform.

This presentation describes our experience in combining speech recognition software, clinical review software, and other software products on a single computer. Different processor speeds, random access memory (RAM), and computer costs were evaluated. We found that combining continuous speech recognition software with Digital Imaging and Communications in Medicine (DICOM) workstation software on the same platform is feasible and can lead to substantial savings of hardware cost. This combination optimizes use of limited workspace and can improve radiology workflow.

Humans↗
PubMedDate not supplied

Buying software off the rack. Packages can be the solution to the software shortage.

The rapid pace of the computer revolution may well be slowed by the lack of suitable software. Though computers should be increasing business efficiency and productivity, many companies do not have the software that would enable them to enjoy these benefits. Packaged software can close the gap for both large and small companies. Here are some guidelines for making the decision whether to buy a package and for avoiding trouble once the package is installed. The article also describes the features a company should look for in packaged software and the optimal provisions of a software contract.

Computers↗
PubMed2003

Software systems as complex networks: structure, function, and evolvability of software collaboration graphs.

Software systems emerge from mere keystrokes to form intricate functional networks connecting many collaborating modules, objects, classes, methods, and subroutines. Building on recent advances in the study of complex networks, I have examined software collaboration graphs contained within several open-source software systems, and have found them to reveal scale-free, small-world networks similar to those identified in other technological, sociological, and biological systems. I present several measures of these network topologies, and discuss their relationship to software engineering practices. I also present a simple model of software system evolution based on refactoring processes which captures some of the salient features of the observed systems. Some implications of object-oriented design for questions about network robustness, evolvability, degeneracy, and organization are discussed in the wake of these findings.

Journal Article↗
PubMed1991

Distribution and communication in software engineering environments. Application to the HELIOS Software Bus.

Modularity, distribution and integration are current trends in Software Engineering. To reach these goals HELIOS, a distributive Software Engineering Environment dedicated to the medical field, has been conceived and a prototype implemented. This environment is made by the collaboration of several, well encapsulated Software Components. This paper presents the architecture retained to allow communication between the different components and focus on the implementation details of the Software Bus, the communication and integration vector of the currently running prototype.

Computer Communication Networks↗
PubMed1986

The maintenance, distribution and development of biomedical computer software: an exercise in software engineering.

The growing reliance of biomedical investigations on computer software in almost all facets of their work places considerable emphasis on the need for the integrated management of the software. In order to efficiently develop, distribute, and maintain the software, tools are required which not only automate these tasks but also, wherever possible, 'semi-intelligently', alert their user to irregular situation. We describe an assortment of such tools routinely used in the management of the SAAM/CONSAM biokinetic software and illustrate their application. Furthermore, using these techniques we have presented some comparative performances of numerical integrators and of computer processors.

Computers↗
PubMed2002

UK audit of single photon emission computed tomography reconstruction software using software generated phantoms.

The purpose of this study was to undertake an audit of the quantitative characteristics of single photon emission computed tomography software using projection data from an analytically generated software phantom and a measured line source. The phantom consisted of three structures. A uniformly filled cylinder, a series of cylindrical rods of various diameters in a background activity with a rod to background ratio of 2:1 and lastly, a set of three concentric rings of activity in the ratio 1:0:1. The phantom contained no added statistical noise. No attenuation was imposed on the data. The phantom was generated analytically and projections were distributed at six different count densities. A single set of projections from a thin line source was also distributed. These data were distributed to centres throughout the UK. Centres were asked to reconstruct the data using a 'ramp only' reconstruction with no additional smoothing function applied. Data were requested for mean and standard deviation in the uniform cylinder, the maximum counts for each cylindrical rod and the mean counts in regions placed within the concentric rings. For the measured line source, centres were asked to measure the full width at half maximum and peak pixel counts for a profile through the reconstructed line. Results from 115 systems were obtained from 100 centres throughout the UK. These provided data from 12 software providers, 11 of these being commercial companies. Data were compared with the known input values and histograms of the distribution of results obtained. Significant differences in quantitative parameters were noted for the different input count densities as well as between suppliers and revisions of software from single suppliers.

Computer Simulation↗
PubMed1991

Software quality regulation under the Safe Medical Devices Act of 1990: hospitals are now the canaries in the software mine.

The 1990 Medical Device Amendments to the Food and Drug Act have caused a significant change in the regulation of medical software. The 1990 Act replaces the prior emphasis on premarket approvals with an emphasis on postmarket surveillance. Hospitals and other institutional users are now required to report to the FDA product defects that cause injuries or death. They are also required to report product defects to the manufacturer. The Act provides for rapid suspensions of device approval, recalls of defective products and civil penalties for violators. The combination of these factors may lead to enhanced FDA supervision of the purchase and use of medical software, and particularly an emphasis on finding unregistered producers. In addition, the new Act will have a direct effect on the regulation of software, because it is much better suited to addressing the problem of software quality than the 1976 Act.

Equipment Safety↗
PubMedDate not supplied

Presentation of the SIGMA software: Software of Imagery and Graphics for Molecular Architecture.

Sigma (Software of Imagery and Graphics for Molecular Architecture) is a software package designed for visualization and exploration of three-dimensional (3D) molecular electron microscopy data. It comprises a text and two graphic modes. In the text mode, a language allows the writing of scripts for repetitive tasks. The two graphic modes are based on the multiwindow environment with a mouse as pointer. The first graphic mode is dedicated to vectorial objects and the second to pixel/voxel objects. The data imported by SIGMA have various origins such as 3D reconstruction volumes, Protein Data Bank data, or geometrical objects like spheres, cubes, or cylinders. These 3D objects are interactively rotated, translated, and rendered with SIGMA. This software, written in C language, runs on Silicon Graphics workstations using the X-Window plus Motif environment. The specific 3D routines are based on the Silicon Graphics GL library.

Animals↗
PubMed2001

Software and speech--a review of software in phonology therapy.

A review of software was carried out to evaluate to what extent particular titles could be used within a phonological therapy programme using a psycholinguistic approach for children aged between four and seven years. Some of the software had been developed specifically for speech and language therapists working with children's phonological impairments. Other titles were from the education market and aimed at developing children's literacy skills. This paper describes how these software programmes could be used to address phonological impairments through developing the sub-skills described within the psycholinguistic framework.

Humans↗
PubMedDate not supplied

Software safety for every phase of software development.

Where does risk management belong, at the beginning of a project or at the end? Many managers choose one or the other, or both. The correct answer is that risk management needs to be considered throughout the software development life cycle. When the risks include the safety of patients or the users of the software, the methods need to be more formal. This article will explain why, and then will provide the how and the how much.

Biomedical Engineering↗
PubMed2006

Integrating software into PRA: a software-related failure mode taxonomy.

Probabilistic risk assessment is a methodology to assess the probability of failure or success of a mission. Results provided by the risk assessment methodology are used to make decisions concerning choice of upgrades, scheduling of maintenance, decision to launch, etc. However, current PRA neglects the contribution of software to the risk of failure of the mission. Our research has developed a methodology to account for the impact of software to system failure. This article focuses on an element of the approach: a comprehensive taxonomy of software-related failure modes. Application of the taxonomy is discussed in this article. A validation of the taxonomy and conclusions drawn from this validation effort are described. Future research is also summarized.

Journal Article↗
PubMed1989

Drug interaction microcomputer software evaluation: Therapeutic Software's Adverse Interactions.

Therapeutic Software's Adverse Interactions was evaluated using general and specific criteria. The installation process, ease of learning, and technical support were rated as excellent. The ease of use and documentation for use were rated as good. The program received an excellent rating for the quality of the clinical documentation and good ratings for the scope of coverage and overall clinical performance. The frequency of updates is fair. The program is an excellent value because of its comprehensiveness, sources of the data base, and relatively low cost. It may be one of the better buys for drug interaction softwares.

Drug Interactions↗
PubMed1999

[Software package for self-constructed CCD-ICP-OES. 1. Software system and design idealogy].

A software package and its design idealogy for the self-constructed CCD-ICP-OES are described. The MS Windows 95TR was used as the operating platform. The Software package written in MS Visual C + + TR V 4.2 included the control of grating and CCD, the dynamic monitoring, the treatment of spectral signal, the fixing of wavelength position, the automatic fixing of spectral line, the quantitative analysis, the stripping method, the Kalman filter and the artificial neural network.

English Abstract↗
PubMed2005

Beamline Scheduling Software: administration software for automatic operation of the RIKEN structural genomics beamlines at SPring-8.

Beamline Scheduling Software (BSS) has been developed for the schedule management and equipment control of the RIKEN Structural Genomics Beamlines I and II (BL26B1 and BL26B2 at SPring-8). The beamline operation is automated with a sample-changer robot and a database system. The experimental schedule is registered to BSS as a list of diffraction measurements for numbers of protein crystals. BSS implements the beamline operation communicating with beamline instruments through the computer network. The RIKEN Structural Genomics Beamline I (BL26B1) opened for users using BSS in October 2002, and the automatic operation was implemented at BL26B2 in October 2003.

Automation↗