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PubMed2000

Expression profile viewer (ExProView): a software tool for transcriptome analysis.

A software tool, Expression Profile Viewer (ExProView), for analysis of gene expression profiles derived from expressed sequence tags (ESTs) and SAGE (serial analysis of gene expression) is presented. The software visualizes a complete set of classified transcript data in a two-dimensional array of dots, a "virtual chip," in which each dot represents a known gene as characterized in the transcript databases Expressed Gene Anatomy Database or UniGene. The virtual chip display can be changed between representations of different conceptual systems for gene/protein classification and grouping. Four alternative projections are currently available: (i) cellular role, (ii) subcellular compartment, (iii) chromosome localization, and (iv) total UniGene display. However, the chip can be adapted to any other desired layout. By selecting dots, further information about the represented genes is obtained from the local database and WWW links. The software thus provides a visualization of global mRNA expression at the descriptive level and guides in the exploration of patterns of functional expression, while maintaining direct access to detailed information on each individual gene. To evaluate the software, public EST and SAGE gene expression data obtained from the Cancer Genome Anatomy Project at the National Center for Biotechnology Information were analyzed and visualized. A demonstration of the software is available at http://www.biochem.kth. se/exproview/.

Data Display↗

PubMed1998

Balancing needs, efficiency, and functionality in the provision of modeling software: a perspective of the NIH WinSAAM Project.

The development of new software or the refinement of existing software for new operating environments each calls for judicious balancing. On the one hand, we strive for simplicity, predictability, and operational protection as it is well recognized that software with these attributes will attract an audience of satisfied users. But, on the other hand, these attributes do not conjure a sense of power, efficiency, or flexibility, and these other properties are also appreciated by users, albeit a somewhat different group of users. The goal is to achieve a blend which isolates critical functionality, flexible control, and user support while meeting the needs of the broadest collection of serious users. In this chapter, we discuss the issues impacting the migration of SAAM to the Windows environment, the NIH WinSAAM Project, and we outline the steps taken to ensure its feasibility. In addition, we describe a new paradigm for software development and use which ensures the durability of the software for modeling.

Computer Simulation↗

PubMed1986

The current situation, aspects, and projects concerning nuclear medicine software in Europe.

Since the 1984 Congress of the Society of Nuclear Medicine-Europe in Helsinki, the "Task Group for European Nuclear Medicine Software Cooperation", which became the "Joint ENMS/SNME Nuclear Medicine Software Task Group" in London in 1985, has focused attention on establishing a new COST project (European Cooperation in the Field of Scientific and Technical Research) (COST 1981) in the field of nuclear medicine Software. On 20 March 1986, the mandate was finally approved officially by the COST Committee of Senior Officials in Brussels (see Editorial in this issue). The problems, content, and objectives of specific items and ideas regarding NM software that have been publicized at the European level are dealt with here. The reader actively interested in NM software is encouraged to participate in the COST framework and forum, in order to avoid duplication of effort and to utilize resources more efficiently by coordinating activities in nuclear medicine in Europe.

Artificial Intelligence↗

PubMed1995

Hologic QDR 2000 whole-body scans: a comparison of three combinations of scan modes and analysis software.

This study reports on the short-term in vivo precision and absolute measurements of three combinations of whole-body scan modes and analysis software using a Hologic QDR 2000 dual-energy X-ray densitometer. A group of 21 normal, healthy volunteers (11 male and 10 female) were scanned six times, receiving one pencil-beam and one array whole-body scan on three occasions approximately 1 week apart. The following combinations of scan modes and analysis software were used: pencil-beam scans analyzed with Hologic's standard whole-body software (PB scans); the same pencil-beam analyzed with Hologic's newer "enhanced" software (EPB scans); and array scans analyzed with the enhanced software (EA scans). Precision values (% coefficient of variation, %CV) were calculated for whole-body and regional bone mineral content (BMC), bone mineral density (BMD), fat mass, lean mass, %fat and total mass. In general, there was no significant difference among the three scan types with respect to short-term precision of BMD and only slight differences in the precision of BMC. Precision of BMC and BMD for all three scan types was excellent: < 1% CV for whole-body values, with most regional values in the 1%-2% range. Pencil-beam scans demonstrated significantly better soft tissue precision than did array scans. Precision errors for whole-body lean mass were: 0.9% (PB), 1.1% (EPB) and 1.9% (EA). Precision errors for whole-body fat mass were: 1.7% (PB), 2.4% (EPB) and 5.6% (EA). EPB precision errors were slightly higher than PB precision errors for lean, fat and %fat measurements of all regions except the head, although these differences were significant only for the fat and % fat of the arms and legs. In addition EPB precision values exhibited greater individual variability than PB precision values. Finally, absolute values of bone and soft tissue were compared among the three combinations of scan and analysis modes. BMC, BMD, fat mass, %fat and lean mass were significantly different between PB scans and either of the EPB or EA scans. Differences were as large as 20%-25% for certain regional fat and BMD measurements. Additional work may be needed to examine the relative accuracy of the scan mode/software combinations and to identify reasons for the differences in soft tissue precision with the array whole-body scan mode.

Absorptiometry, Photon↗

PubMed1994

Native American youths and cancer risk reduction. Effects of software intervention.

PURPOSE: Toward developing attractive and effective means to reduce cancer risks faced by Native American people, this study developed and tested interactive computer software to improve dietary choices and prevent tobacco use among Native American adolescents. METHODS: Based on a legend of the Seneca Nation, a cancer prevention lesson was developed and programmed for software. A sample of 368 Native American adolescents were divided randomly into intervention and control arms. Youths in both arms were pre-tested, youths in the intervention arm interacted with the software, and all youths were post-tested. Pre-test and post-test measures covered information and attitudes about cancer risks from dietary practices and tobacco use. RESULTS: Pre-test scores differed between the two arms on youths' age and on one outcome variable. Relative to their counterparts in the control arm, youths in the intervention arm increased their post-test scores on 8 of 12 outcome measurement variables. Process data gathered during intervention delivery indicated that nearly all youths were involved with the interactive software and lesson. CONCLUSION: Interactive computer software holds promise for delivering cancer risk reduction intervention aimed at modifying dietary habits and preventing tobacco use among Native American youth.

Adolescent↗

PubMed1996

Prism: a new approach to radiotherapy planning software.

PURPOSE: We describe the capabilities and performance of Prism, an innovative new radiotherapy planning system with unusual features and design. The design and implementation strategies are intended to assure high quality and clinical acceptability. The features include Artificial Intelligence tools and special support for multileaf collimator (MLC) systems. The design provides unusual flexibility of operation and ease of expansion. METHODS AND MATERIALS: We have implemented Prism, a three-dimensional (3D) radiotherapy treatment-planning system on standard commercial workstations with the widely available X window system. The design and implementation use ideas taken from recent software engineering research, for example, the use of behavioral entity-relationship modeling and the "Mediator Method" instead of ad-hoc programming. The Prism system includes the usual features of a 3D planning system, including Beam's Eye View and the ability to simulate any treatment geometry possible with any standard radiotherapy accelerator. It includes a rule-based expert system for automated generation of the planning target volume as defined in ICRU Report 50. In addition, it provides special support for planning treatments with a multileaf collimator (MLC). We also implemented a Radiotherapy Treatment Planning Tools Foundation for Prism, so that we are able to use software tools form other institutions without any source code modification. RESULTS: The Prism system has been in clinical operation at the University of Washington since July 1994 and has been installed at several other clinics. The system is run simultaneously by several users, each with their own workstation operating from a common networked database and software. In addition to the dosimetrists, the system is used by radiation oncologists to define tumor and target volumes and by radiation therapists to select treatment setups to load into a computer controlled accelerator. CONCLUSIONS: Experience with the installation and operation has shown the design to be effective as both a clinical and research tool. Integration of software tools has eased the development and significantly enhanced the clinical usability of the system. The design has been shown to be a sound basis for further innovation in radiation treatment planning software and for research in the treatment planning process.

Computer Communication Networks↗

PubMed2000

Clinical and practical requirements of online software for anesthesia documentation an experience report.

The aim of this paper is the presentation of a new version of the anesthesia documentation software, NarkoData, that has been used in routine clinical work in our department as part of an anesthesia information management system (AIMS) since 1995. The performance of this software is presented along with requirements for future development of such a system. The originally used version, NarkoData 3.0, is an online anesthesia documentation software established by the software company ProLogic GmbH. It was primarily developed as a disk-based system for the MacOS operating system (Apple Computer Inc.). Based on our routine experience with the system, a catalogue of requirements was developed that concentrated on improvement in the sequence of work, administration and data management. In 1996, the concepts developed in our department, in close co-operation with medical personnel and the software company, led to a considerable enlargement of the program functions and the subsequent release of a new version of NarkoData. Since 1997, more than 20 000 anesthesia procedures have been recorded annually with this new version at 115 decentralized work stations at our university hospital.

Anesthesiology↗

PubMed1997

Approaches for certification of electronic prescription software.

The proper management of drug treatment is essential, since adverse drug reactions are common reasons of hospitalisations. Expenditure on drug therapy has also been growing faster than any other aspect of health care in many countries. Savings and quality improvements in drug treatment could be achieved with computerised prescribing. In this paper, the architecture of an electronic prescription system is described in the light of software certification and registration. An electronic prescription system is an example of a system supporting shared care and therefore it should be person based, integrated, secure and confidential and data should be shared among health care institutions. The system architecture shares the idea of a virtual patient record and a smart card will be used as a key to prescription data located on the network. The certification and registration of medical software is a difficult and costly procedure. Ensuring the quality of software can be based on; certification of development process, voluntary evaluation, and post-market surveillance. Voluntary evaluation practice would be a precious tool for both the customers and software developers, and it would also be an invaluable source of information in terms of developing new software.

Certification↗

PubMed2000

Software sensors to monitor the dynamics of microbial communities: application to anaerobic digestion.

A mass balance based model has been derived to represent the dynamical behavior of the ecosystem contained in an anaerobic digester. The model considers two bacterial populations: acidogenic and methanogenic bacteria. It forms the basis for the design of a software sensor considering both a model of the biological system and on-line gaseous measurements. The software sensor computes the concentration of inorganic carbon and volatile fatty acids (VFA) in the digester. Another software sensor is dedicated to the estimation of the bacterial biomasses. The predictions of the software sensors for a real experiment are very close to the actual off-line measurements. The software sensors monitor the accumulation of VFA and thus very early detect a destabilization of the digester due to overloading. The presented methodology demonstrates the usefulness of advanced monitoring techniques for an improved understanding of the internal working of a biological system.

Bacteria, Anaerobic↗

PubMed2001

The effects of different image file formats and image-analysis software programs on dental radiometric digital evaluations.

OBJECTIVES: To determine if variations in radiodensity data are introduced by lossy Joint Photographic Experts Group (JPEG) compression and/or the use of three software programs. METHODS: An occlusal film with an aluminium step wedge was exposed, processed and digitized under standard conditions. Before the image was saved, the coordinates and the gray-scale value for each pixel in a 20 x 20 pixel area near the middle of the thickest step were recorded. These pixel coordinates and gray-scale values served as Truth 1. In addition, a digital simulated-radiographic image with assigned gray-scale values for each pixel was created and served as Truth 2. The digital data for the scanned radiograph and the simulated radiograph were saved as Tagged Image File Format (TIFF) and lossy JPEG files. Each file was opened with three software programs and the gray-scale values of homologous pixels were recorded. For these pixels in each image type, the mean gray-scale values and standard deviations were calculated. The pixel gray-scale values for each homologous pixel were also individually compared. RESULTS: When the TIFF images were opened with the three software programs, one program resulted in gray-scale values that were not concordant with truth. All JPEG images resulted in gray-scale values that were not concordant with truth. CONCLUSIONS: One software program added a column of 0s to data files. Lossy JPEG compression introduced potentially deleterious variations to radiodensity data, and at least two of the software programs performed JPEG image decompression differently.

Absorptiometry, Photon↗

PubMedDate not supplied

[Software and system-induced errors in isokinetic force measurements].

In the literature a good reliability of isokinetic measurements is reported. In spite of these reports high variations of the peak torque and work values were registered when testing 24 patients with low back pain, using a CYBEX TR isokinetic trunk rotation apparatus. After a 3 week's training the patients force (peak torque) increased in the average between 10.7 p.c. (SD +/- 26.4) and 23.2 p.c. (SD +/- 63.8), corresponding to the test-velocity. Seven of the 24 patients improved or deteriorated more than 30 p.c. Analysing the parameters which could interfere with the results there was found a discrepancy between the original CYBEX software and the German Iso-Kin 4.0 software. The Isokin 4.0 does not warm up and calibrate the isokinetic apparatus daily. Investigations with definite weights showed that the values for peak torque are 40-50 m higher when using the Iso-Kin 4.0 software in comparison to the original CYBEX software. Furthermore there are a lot of other parameters such as acceleration of the body, psychological alterations, pain, motivation, learning effects, and artificial oscillations of the registered curve, which can affect the results even when using the original CYBEX software.

Adult↗

PubMedDate not supplied

Development of a software for the design of custom-made hip prostheses using an open-source rapid application development environment.

The present work describes a technology transfer project called HIPCOM devoted to the re-engineering of the process used by a medical devices manufacturer to design custom-made hip prostheses. Although it started with insufficient support from the end-user management, a very tight scheduling and a moderate budget, the project developed into what is considered by all partners a success story. In particular, the development of the design software, called HIPCOM Interactive Design Environment (HIDE) was completed in a time shorter than any optimistic expectation. The software was quite stable since its first beta version, and once introduced at the user site it fully replaced the original procedure in less than two months. One year after the early adoption, more than 80 custom-made prostheses had been designed with HIDE and the user had reported only two bugs, both cosmetics. The scope of the present work was to report the development experience and to investigate the reasons for these positive results, with particular reference to the development procedure and the software architecture. The choice of TCL/TK as development language and the adoption of well-defined software architecture were found to be the success key factors. Other important determinants were found to be the adoption of an incremental software engineering strategy, well suited for small to medium projects and the presence in the development staff of a technology transfer expert.

Computer-Aided Design↗

PubMed1997

Q-RT-PCR: data analysis software for measurement of gene expression by competitive RT-PCR.

MOTIVATION: We have developed software to assist in the computation of gene expression from data obtained in competitive reverse transcription-polymerase chain reaction (RT-PCR). This report describes the mathematical basis of competitive RT-PCR and discusses the criteria which must be met to permit accurate estimations of gene expression to be obtained using this technique. RESULTS: The software that has been developed assists in both the assessment of assay performance (specifically in establishing the equality of amplification efficiency of the native and competitor templates) and in the routine analysis of data obtained in quantitation of gene expression by competitive RT-PCR. The software is a 100 kb module which functions as a Microsoft Excel add-in. It is compatible with both Windows and Mac versions of Excel 5 and Excel 7 on the Windows 95 platform, and employs the spreadsheet, statistical and graphing capabilities incorporated into Excel. AVAILABILITY: The software can be downloaded from http://www.grad.ttuhsc.edu/archive/. A brief summary in both HTML and Microsoft Word 6 format of the installation and use of the software is also located at this website.

Algorithms↗

PubMed1996

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and the lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations in the human p53 gene, the human hprt gene and the rodent transgenic lacZ locus. The databases themselves are stand-alone dBase files and the software for analysis of the databases runs on IBM- compatible computers. The software created for these databases permits filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open home page http://sunsite.unc.edu/dnam/mainpage.ht ml with a WWW browser. Alternatively, the databases and programs are available via public ftp from anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found in subdirectory pub/academic/biology/dna-mutations. Two other programs are available at the WWW site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.

Animals↗

PubMed1992

[Workload in software development work. A consideration based on work-characteristics and analysis on workload factors of each working group].

To clarify workload factors in software developing work, we designed questionnaires composed of questions of work-content based on the interview survey. For the analysis of workload, Cumulative Fatigue Symptom Index (CFSI) and the stress-rating-method by 7-likert-scale were used. With the cooperation of the Japanese Software Engineers' Association (SEA) responses were obtained from 270 out of 1,100 members and from 553 non-member software engineers in 18 companies in Japan. The CFSI score obtained was higher than those of other groups of other industries obtained in our previous studies. The stress-rating showed that "time-pressure," "too much amount of work, and "ambiguity in job specification" were the highest stressors. The work groups were categorized by the results of CFSI profile into 4 types. The results of stress-ratings were significantly different between the 4 type groups. Based on the multiple comparison analysis, the workload factors of each group could be specified. Out of the foregoing 4 types, the work groups which showed the deviation in F1B (depression) in CFSI and the work groups which showed high scores in every category in CFSI were higher in "ambiguity of specification" in stress-ratings. This result indicates that "ambiguity in specification" is a significant stressor in software engineers. This stressor is caused by the complicated communication process between users and engineers and by the shortage of tools or rules in this process. This stressor is considered to be the most typical workload which characterizes the software developing work.

Adult↗

PubMed1999

Software for population pharmacokinetics and pharmacodynamics.

Pharmacokinetic-pharmacodynamic modelling is being used increasingly as a tool in drug development because often in phase III clinical trials only sparse data are available for analysis and so a nonlinear mixed effects modelling approach has to be adopted. Specialist data analytical techniques and software are required to analyse such data. This article reviews some of the software currently available for performing nonlinear mixed effects modelling. A questionnaire was devised and sent to a number of software producers and the findings are presented and discussed in this paper. The programs could be grouped into 3 main categories: parametric and nonparametric maximum likelihood and Bayesian. It was apparent from the questionnaire that software development for population data analysis is a very active area of investigation. The implementation of methodologies varied widely between the packages: some were self-contained programs, whereas others were written within another application, usually a statistical package. They also varied with respect to their ease of use and level of support offered by the software producers. Although robustness and reliability are important concerns, they were not addressed in the present review. Most of the programs surveyed are in continual development.

Animals↗

PubMedDate not supplied

A general software package for the handling of medical images.

PICS (portable imaging computer software), is a software system designed for handling and processing a variety of types of medical image. It has been designed to satisfy the following criteria: (a) the software should be portable between different items of hardware with minimal alteration; (b) there should be a simple operator interface to enable use by inexperienced users, while avoiding the need for experienced users to be directed through tedious menu trees; (c) the programming environment should enable simple integration of new data handling protocols. To meet these requirements the software was written in FORTRAN using structured subroutine organization. The software has basic image handling and processing facilities and contains a comprehensive set of nuclear medicine clinical protocols. Other facilities include alignment of images from different modalities with display of superimposed images and ability to handle, analyse and display three-dimensional data sets. Data transfer programs have been written to capture data from gamma camera, CT, MRI, ultrasound and radiographs by converting the images to a common data format. The system provides a hospital with a central digital image handling resource, enabling investigation of the value of digital image processing in potential clinical applications.

Diagnostic Imaging↗

PubMedDate not supplied

Medical imaging workstation: a software environment.

In a study to set up an experimental simple imaging workstation with facilities for image input, storage, presentation and manipulation, BAZIS developed a software package called FRACTALS (Filmless Radiology And Computerized Task Analysis Lab Software). The investment in the development of effective software for digital radiological workstations is of great importance in picture archiving and communication systems (PACS) research. General purpose workstations are becoming less expensive and more powerful. They are an important tool for performing radiological research and developing an adequate human interface. The software should provide the tools and flexibility for modifications that turn out to be required for interaction with the radiologists. The software package FRACTALS is presented in this paper and its applications and future developments are discussed.

Computer Systems↗