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PubMed2001

Selection of bioprocess simulation software for industrial applications.

Two commercially available, process-simulation software packages (Aspen Batch Plus v1.2, Aspen Technology, Inc., Cambridge, Massachusetts, and Intelligen SuperPro v3.0, INTELLIGEN, INC., Scotch Plains, Ner Jersey) are evaluated for use in modeling industrial, biotechnology processes. Software is quantitatively evaluated by Kepner-Tregoe Decision Analysis (Kepner and Tregoe, 1981). This evaluation shows that Aspen Batch Plus v1.2 (ABP) and Intelligen SuperPro v3.0 (ISP) can successfully perform specific simulation tasks but do not provide a complete model of all phenomena occurring within a biotechnology process. Software is best suited to provide a format for process management, using material and energy balances to answer scheduling questions, explore equipment change-outs, and calculate cost data. The ability of simulation software to accurately predict unit operation scale-up and optimize bioprocesses is limited. To realistically evaluate the software, a vaccine manufacturing process under development at Merck & Company is simulated. Case studies from the vaccine process are presented as examples of how ABP and ISP can be used to shed light on real-world processing issues.

Biotechnology↗

PubMed1991

A new microcomputer software system evaluation paradigm: the medical perspective.

The new fourth-generation software has enormously eased the burden of computing for users, but they have also created a confusing, difficult problem in software evaluation and selection. Therefore it is argued that a sound and complete evaluation paradigm is a key element in an efficient and effective software system design and use process. While much has been written about software evaluation in general, in the medical field, the guidances and recommendations previously provided are too general to be of practical use. Considering also the other weaknesses of conventional evaluation paradigms we have decided to develop a more adequate one which will have a solid theoretical framework, specific guidances, strict and well-defined taxonomic space, and a fair ranking approach. In the present paper we will therefore introduce our new evaluation paradigm and show its applicability in evaluation and selection of medical software systems according to their usability.

Classification↗

PubMed2006

Three-dimensional analysis of pulmonary nodules by MSCT with Advanced Lung Analysis (ALA1) software.

PURPOSE: The purpose of this study was to test the reproducibility of the three-dimensional (3D) Advanced Lung Analysis software (3D-ALA, GE Healthcare) in the estimation of pulmonary nodule volume. MATERIALS AND METHODS: We retrospectively reviewed the unenhanced multislice CT scans (Lightspeed Pro 16 GE) of 77 patients with a solitary pulmonary nodule (n=71) or metastatic pulmonary disease (n=6). A total of 103 pulmonary nodules (19 well-circumscribed, 45 juxtavascular and 39 juxtapleural) were analysed grouped into five classes based on diameter: <5 mm, 10 nodules (9.7%); >or=5 to <10 mm, 25 nodules (24.2%); >or=10 mm to <15 mm, 41 nodules (39.8%); >or=5 to <18 mm, 14 nodules (13.6% ); >or=8 to <30 mm, 13 nodules (12.62%). The following acquisition parameters were used: slice thickness 0.625 mm, reconstruction interval 0.4 mm, pitch 0.562:1, 140 kV, 300 mAs, field of view 13 cm, bone kernel. For each of the 103 nodules three, 3D volume measurements were obtained by the 3D-ALA software. The reproducibility of nodule segmentation was evaluated according to a visual score (1=optimal, >or=95%; 2=fair, 90-95%; 3=poor, 0.05). CONCLUSIONS: Three-dimensional volume measurement with ALARiassunto 1 software is reproducible for all nodules as regards dimension and site. ALA-1 software provided a good and reproducible volume measurement in well-circumscribed and most juxtavascular nodules. Volumetric evaluation and reproducibility of volume estimation in juxtapleural pulmonary nodules, particularly those adjacent to diaphragmatic pleura, is inadequate, and software improvement is needed.

Aged↗

PubMedDate not supplied

Structure and software tools of AIDA.

AIDA consists of a set of software tools to allow for fast development and easy-to-maintain Medical Information Systems. AIDA supports all aspects of such a system both during development and operation. It contains tools to build and maintain forms for interactive data entry and on-line input validation, a database management system including a data dictionary and a set of run-time routines for database access, and routines for querying the database and output formatting. Unlike an application generator, the user of AIDA may select parts of the tools to fulfill his needs and program other subsystems not developed with AIDA. The AIDA software uses as host language the ANSI-standard programming language MUMPS, an interpreted language embedded in an integrated database and programming environment. This greatly facilitates the portability of AIDA applications. The database facilities supported by AIDA are based on a relational data model. This data model is built on top of the MUMPS database, the so-called global structure. This relational model overcomes the restrictions of the global structure regarding string length. The global structure is especially powerful for sorting purposes. Using MUMPS as a host language allows the user an easy interface between user-defined data validation checks or other user-defined code and the AIDA tools. AIDA has been designed primarily for prototyping and for the construction of Medical Information Systems in a research environment which requires a flexible approach. The prototyping facility of AIDA operates terminal independent and is even to a great extent multi-lingual. Most of these features are table-driven; this allows on-line changes in the use of terminal type and language, but also causes overhead. AIDA has a set of optimizing tools by which it is possible to build a faster, but (of course) less flexible code from these table definitions. By separating the AIDA software in a source and a run-time version, one is able to write implementation-specific code which can be selected and loaded by a special source loader, being part of the AIDA software. This feature is also accessible for maintaining software on different sites and on different installations.

Database Management Systems↗

PubMed1994

Safety-critical software and current standards initiatives.

This paper sets out to examine the role of standards in the development of safety-critical software. It starts with a brief discussion on the nature and role of standards and then moves on to identify some of the standards making bodies. Safety-critical software is next discussed and the problems of software safety are contrasted with those of traditional electromechanical devices. There then follows a review of some of the current initiatives to produce standards addressing the development of safety-critical systems containing software. Two standards are then examined in detail to provide an insight into what requirements are placed on the developers of safety-critical software. Lastly, mention is made of some weaknesses that are inherent in today's standards, and some of the efforts that are being made to address these problems are discussed.

Accidents, Occupational↗

PubMed1994

An overview of software assessment.

Many engineering systems, especially those required to be particularly dependable, traditionally undergo inspections and assessments of safeness and fitness for purpose. Often some form of 'certificate' is provided by the assessment authority. To an increasing degree these systems are beginning to contain software components. The question naturally arises: how can the software component be assessed? This paper explores the feasibility and limitations of software assessment and the link between the process of developing the software and the quality of the resulting software product.

Europe↗

PubMed2005

Introducing DoT-U2--an XML-based knowledge supported checklist software for documentation of a newborn clinical screening examination.

In a project concerning the German newborn screening examination "U2" we developed a software system called DoT-U2 for concurrent documentation at the point of care. Physicians can enter findings in(to) a tree structured protocol with management of logical dependencies. Additionally, all findings except free text annotations can be entered by speech recognition. The software system program is written in Java and uses separate XML-based modules both for knowledge and language representation. It can, therefore, easily be adapted to other languages and further documentation scenarios. We showed the high flexibility of the software system by integrating it in a completely new setting in Salt Lake City without major problems. We found that modular software development with platform independent Java and XML leads to highly flexible software which can be adapted to very different scenarios without knowing their requirements ahead of time.

Decision Making, Computer-Assisted↗

PubMed2006

Development of quantification software using model-based segmentation of left ventricular myocardium in gated myocardial SPECT.

Gated myocardial single photon emission computed tomography (SPECT) is being used for the diagnosis of coronary artery diseases. In this study, we developed new software for the quantification of volumes and ejection fraction (EF) on the gated myocardial SPECT data using a cylindrical model. Volumes and EF by developed software were validated by comparing with those quantified by quantitative gated SPECT (QGS) software. Cylinder model for left ventricular myocardium was used to eliminate background activity and count profiles across the myocardium were fitted to the Gaussian curve to determine the endocardial and epicardial boundary. End-diastolic volume (EDV), end-systolic volume (ESV) and EF were calculated using this boundary information. Gated myocardial SPECT was performed in 83 patients. EDV, ESV and EF values estimated using present method were compared to those obtained using the commercialized software QGS, and reproducibility in the parameter estimation was assessed. EF, EDV and ESV obtained using two methods were correlated well (correlation coefficients = 0.96, 0.96 and 0.98). The correlation between the parameters repetitively estimated from the same data set by an operator was very high (correlation coefficients = 0.96, 0.99 and 0.99 for EF, EDV and ESV). On the repeated acquisition, reproducibility was also high with correlation coefficients of 0.89, 0.97 and 0.98. The present software will be useful for the development of new parameters for describing the perfusion and function of the LV.

Aged↗

PubMed2005

A component-based software environment for visualizing large macromolecular assemblies.

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.

Capsid↗

PubMed2004

Adaptive software for head-operated computer controls.

Head-operated computer controls provide an alternative means of computer access for people with disabilities who are unable to use a standard mouse. However, a person's disability may limit his or her neck movements as well as upper extremity movements. Software was developed which automatically adjusts the interface sensitivity to the needs of a particular user. This adaptive software was evaluated in two stages. First, 16 novice head-control users with spinal-cord injury or multiple sclerosis used head controls with and without the adaptive software. The adaptive software was associated with increased speed in standardized icon selection exercises (p < 0.05). A small increase in accuracy was also observed. In addition, five current head-control users evaluated the software in a real-world setting. One of these five subjects perceived an improvement in comparison to his current head-control system.

Activities of Daily Living↗

PubMed2003

The "X-Ray RheumaCoach" software: a novel tool for enhancing the efficacy and accelerating radiological quantification in rheumatoid arthritis.

BACKGROUND: Precise diagnosis and follow up treatment of rheumatoid arthritis (RA) requires objective quantification, which is still lacking. For this purpose, radiological analyses are considered to be the most appropriate method. OBJECTIVE: To develop computer assisted quantification software that is particularly applicable to joint scoring in rheumatic disorders. METHODS: 3914 radiographs from hands and feet of 190 patients with RA were collected, expertly examined, analysed, and statistically evaluated. Radiographs were quantified using the conventional Larsen score and the "X-Ray RheumaCoach" (XRRC) software. The XRRC is a Java stand alone application which can support and accelerate, but not fully automate, the scoring procedure in RA. The scorer can apply both the Larsen and the Ratingen-Rau scores. RESULTS: Compared with conventional scoring procedures, the XRRC software accelerated quantification time by approximately 25%. The program, which is now available on the internet free of charge, ran stably and proved to be a consistently valuable tool. CONCLUSIONS: Compared with conventional scoring methods, the XRRC software offers several advantages: (a) structured data analysis and input that minimises variance by standardisation; (b) faster and more precise calculation of sum scores and indices; (c) permanent data storing and fast access to the software's database; (d) the possibility of cross calculation to other scores; (e) "user friendly" technology and a dedicated help program; (f) fast access and data transfer through the internet if desired; and (g) reliable documentation of results in a specially designed printout.

Arthritis, Rheumatoid↗

PubMedDate not supplied

Quality assurance of medical software.

Quality assurance is a topical issue within the software industry, and various methodological solutions aimed at improving software quality have been proposed. Medical software is generally deemed safety-critical and, as such, should be subject to control procedures exceeding those applicable to general-purpose software. The user/purchaser of medical equipment has an important part to play in the drive for higher-quality medical software, and ways in which the user can influence commercial suppliers are outlined. The implications of existing and planned legislation are also discussed.

Consumer Behavior↗

PubMed1997

Summary recommendations for responsible monitoring and regulation of clinical software systems. American Medical Informatics Association, The Computer-based Patient Record Institute, The Medical Library Association, The Association of Academic Health Science Libraries, The American Health Information Management Association, and The American Nurses Association.

Clinical software systems are becoming ubiquitous. A growing literature documents how these systems can improve health care delivery, but concerns about patient safety must now be formally addressed. In 1996, the U.S. Food and Drug Administration (FDA) called for discussions on regulation of software programs as medical devices. In response, a consortium of organizations dedicated to improving health care through information technology developed recommendations for the responsible regulation and monitoring of clinical software systems by users, vendors, and regulatory agencies. These recommendations were revised and approved by the American Medical informatics Association Public Policy Committee and Board. Other organizations reviewed, modified, and approved the recommendations, and the Boards of Directors of most of the organizations in the consortium endorsed the guidelines. The consortium proposes four categories of clinical system risk and four classes of monitoring and regulatory action that can be applied on the basis of the risk level. The consortium recommends that most clinical software systems be supervised locally and that developers of health care information systems adopt a code of good business practices. Budgetary and other constraints limit the type and number of systems that the FDA can regulate effectively; therefore, the FDA should exempt most clinical software systems and focus on systems that pose high clinical risk and provide limited opportunity for competent human intervention.

Clinical Medicine↗

PubMed2003

Developing high-quality educational software.

The development of effective educational software requires a systematic process executed by a skilled development team. This article describes the core skills required of the development team members for the six phases of successful educational software development. During analysis, the foundation of product development is laid including defining the audience and program goals, determining hardware and software constraints, identifying content resources, and developing management tools. The design phase creates the specifications that describe the user interface, the sequence of events, and the details of the content to be displayed. During development, the pieces of the educational program are assembled. Graphics and other media are created, video and audio scripts written and recorded, the program code created, and support documentation produced. Extensive testing by the development team (alpha testing) and with students (beta testing) is conducted. Carefully planned implementation is most likely to result in a flawless delivery of the educational software and maintenance ensures up-to-date content and software. Due to the importance of the sixth phase, evaluation, we have written a companion article on it that follows this one. The development of a CD-ROM product is described including the development team, a detailed description of the development phases, and the lessons learned from the project.

Computer Simulation↗

PubMed1997

Three-dimensional reconstruction of histological sections using modern product-design software.

BACKGROUND: Computer-based, three-dimensional reconstruction of histological sections is necessary for solving a diversity of questions in morphology and anatomy. Programming software for this purpose is difficult and time-consuming. Therefore, we tested if commercially available product-design software is useful for reconstructing anatomical virtual models. METHODS: We used Alias Wavefront Studio software on a Silicon Graphics workstation. Sections were projected with a newly developed microslide projector on a digitizing board and digitized interactively. Alternatively, pictures of sections were digitized on screen. The resulting set of contours was used as scaffold around which a surface was created manually. RESULTS: Repeated creation of the same object and subsequent measurements gave results that will be sufficiently reliable for many purposes. The visual presentation of objects satisfy highest demands. Little time is needed to reconstruct simple objects, and the time used for complex virtual models is acceptable. Manipulation of objects on screen is nearly in real time and rendering speed is high. CONCLUSIONS: Product-design software packages are a readily available and useful option for anatomists who want to do virtual reconstructions quickly without programming software themselves.

Animals↗

PubMed2002

Flow cytometric S-phase fraction measurement in breast carcinoma: Influence of software and histogram resolution.

BACKGROUND: S-phase fraction (SPF) measurement by flow cytometry is a clinically useful prognostic factor in patients with breast carcinoma. Standardized SPF determination is essential. As part of a multicenter study, we evaluated the influence of the choice of software and histogram resolution (256, 512, or 1,024 channels) on SPF quantification. METHODS: One hundred thirty-three DNA histograms were analyzed in three laboratories with Modfit 5.2, Modfit LT, and Multicycle AV software. Strict rules for histogram interpretation and software management were applied. The following five options were compared: MF 5.2 1024, MF 5.2 256, MF LT 256, MC AV 256, and MC AV 512. RESULTS: In the DNA diploid and aneuploid groups, SPF distributions were not statistically different among the five options. Excellent quantitative correlations were obtained between pairs of options. When using tertiles as cutpoints for SPF classification, concordance rates ranged from 79.7% to 93.2% for DNA diploid samples and from 87.8% to 95.9% for DNA aneuploid samples, the best results being obtained with software working with a similar histogram resolution. CONCLUSIONS: Standardized use of commercially available software, including the choice of histogram resolution, provides comparable SPF results.

Breast Neoplasms↗

PubMed2005

Rapid recognition of aberrant dHPLC elution profiles using the Transgenomic Navigator software.

Despite the availability of numerous technologies for detecting mutations, only a few have been formatted for automated mutation calling. Here, we evaluate the utility of the Transgenomic Navigator software to facilitate automated detection of aberrant denaturing high performance liquid chromatography (dHPLC) elution profiles. We used dHPLC to identify germline variants in MSH6, NEIL2, NEIL3, and OGG1 in 172 patients with multiple colorectal adenomas. 3,747 dHPLC profiles were analysed with the Navigator software using three levels of analysis, each differing in the degree of operator input. 43.5% (60/138) and 98.3% (59/60) of products with profiles distinct from wild type ('outliers') harboured novel variants under Level 1 and Levels 2/3 analysis conditions, respectively. We also assessed the utility of the software to rapidly detect samples carrying common polymorphisms by analysing regions of the genes that harbour polymorphisms with minor allele frequencies between 8 and 40%, therein analysing 2,784 profiles. We showed that 1573/1612 (97.6%) and 1137/1172 (97.0%) of PCR products were correctly classified as wild-type and variant, respectively (Level 3 analysis conditions). Finally, we assessed the utility of the software to detect novel variants in fragments that also harboured common polymorphisms and showed that 59/61 (96.7%) of products with profiles outlying both the wild type and polymorphism groups harboured novel variants. We conclude that the Navigator software provides an excellent tool for rapid discrimination of aberrant dHPLC elution profiles that harbour sequence variants.

Chromatography, High Pressure Liquid↗

PubMed2003

Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels.

Efficient analysis of protein expression by using two-dimensional electrophoresis (2-DE) data relies on the use of automated image processing techniques. The overall success of this research depends critically on the accuracy and the reliability of the analysis software. In addition, the software has a profound effect on the interpretation of the results obtained, and the amount of user intervention demanded during the analysis. The choice of analysis software that best meets specific needs is therefore of interest to the research laboratory. In this paper we compare two advanced analysis software packages, PDQuest and Progenesis. Their evaluation is based on quantitative tests at three different levels of standard 2-DE analysis: spot detection, gel matching and spot quantitation. As test materials we use three gel sets previously used in a similar comparison of Z3 and Melanie, and three sets of gels from our own research. It was observed that the quality of the test gels critically influences the spot detection and gel matching results. Both packages were sensitive to the parameter or filter settings with respect to the tendency of finding true positive and false positive spots. Quantitation results were very accurate for both analysis software packages.

Animals↗