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PubMed2005

HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data.

BACKGROUND: Many efforts in microarray data analysis are focused on providing tools and methods for the qualitative analysis of microarray data. HDBStat! (High-Dimensional Biology-Statistics) is a software package designed for analysis of high dimensional biology data such as microarray data. It was initially developed for the analysis of microarray gene expression data, but it can also be used for some applications in proteomics and other aspects of genomics. HDBStat! provides statisticians and biologists a flexible and easy-to-use interface to analyze complex microarray data using a variety of methods for data preprocessing, quality control analysis and hypothesis testing. RESULTS: Results generated from data preprocessing methods, quality control analysis and hypothesis testing methods are output in the form of Excel CSV tables, graphs and an Html report summarizing data analysis. CONCLUSION: HDBStat! is a platform-independent software that is freely available to academic institutions and non-profit organizations. It can be downloaded from our website http://www.soph.uab.edu/ssg_content.asp?id=1164.

Algorithms↗

PubMed1997

[Computerization experience in a day hospital of integrated radiochemotherapy].

INTRODUCTION: We report on a cost-effective easy-access software developed for the functional integration of the clinical records and history of oncologic patients with the management of the Day Hospital of the Radiotherapy Department of the University Hospital A. Gemelli, in Rome. MATERIAL AND METHODS: The software was designed to archive the clinical records and history of oncologic patients and the relative chemotherapy, to manage the examination scheduling, to draw up nursing files with the planned therapy and to make statistical analyses of the department activity. Five forms are available: the patient form, recording patient data; the admission form, recording the type of therapy (e.g., chemotherapy, tests, medical examinations, etc.), the relative cost and chemotherapy protocol, detailing for instance the type of drug; the nursing file, detailing chemotherapy schedule and the dilution of each drug; the menu, to select and retrieve any record. The minimum configuration requires a 386 Intel CPU, 4 Mb RAM and 4 Mb free on the hard disk. The software is the File Maker Pro 2.1 for Windows which can interact with Apple Macintosh computers. RESULTS: Since October, 1995, we have saved the clinical records of 272 oncologic outpatients (2415 entries in all), with a mean of 201/month. This computer system permitted us to save and retrieve data for both clinical and didactic purposes and to plan our activity. CONCLUSIONS: One year after it was implemented and used in clinical practice, the system is a cost-effective and user-friendly tool for the management of the Radiochemotherapy Day Hospital of our Radiotherapy Department.

Combined Modality Therapy↗

PubMed2003

Human-mouse alignments with BLASTZ.

The Mouse Genome Analysis Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment programs that suited the various needs. For investigating issues regarding genome evolution, a particularly sensitive method was needed to permit alignment of a large proportion of the neutrally evolving regions. We selected a program called BLASTZ, an independent implementation of the Gapped BLAST algorithm specifically designed for aligning two long genomic sequences. BLASTZ was subsequently modified, both to attain efficiency adequate for aligning entire mammalian genomes and to increase its sensitivity. This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results.

Animals↗

PubMed1998

Multiagency outcome evaluation of children's services: a case study.

Outcome monitoring has become a focus of accountability for public and nonprofit human service agencies. Besides providing answers to funders' questions about the services' impact, outcome monitoring helps administrators improve program effectiveness. After a three-year development period and a one-year implementation experience, SumOne for Kids represents a technically advanced outcome-monitoring system for children's mental health and/or child welfare services. Initiated, designed, and tested by 31 children's service agencies throughout Pennsylvania, and with state bureaucrats' and policy makers' encouragement, SumOne for Kids represents an effort to create a bottom-up/top-down process for implementing a statewide outcome-monitoring system. This article describes the genesis of this outcome-monitoring system, primary design principles, use of social validation for outcome selection, resolution of methodological difficulties, and reasons for selecting functional over clinical outcomes. The article reviews lessons learned through the development experience instructive to children's service managers, program evaluators, and industry leaders interested in establishing outcome-monitoring systems.

Child↗

PubMed1999

Estimating medical resources required following a nuclear event.

Large quantities of medical resources are necessary for the treatment of patients suffering from acute radiation syndrome in combination with blast and thermal injuries (combined injuries). So far, however, there is no tool available for evaluating the resources required for the treatment of combined injuries. The purpose of this manuscript is to describe the scientific basis for a newly developed software tool designed to estimate the medical resources needed for treating the combined injuries of individuals/high numbers of casualties who may be involved in civil defense, emergency medical care and various military activities (namely out of area) in the case of a nuclear event.

Blast Injuries↗

PubMed2001

Evaluation of clinical information systems. What can be evaluated and what cannot?

The evaluation of clinical information systems is essential as they are increasingly used in clinical routine and may even influence patient outcome on the basis of reminder functions and decision support. Therefore we try to answer three questions in this paper: what to evaluate; how to evaluate; how to interpret the results. Those key questions lead to the discussion of goals, methods and results of evaluation studies in a common context. We will compare the objectivist and the subjectivist evaluation approach and illustrate the evaluation process itself in some detail, discussing different phases of software development and potential evaluation techniques in each phase. We use four different practical examples of evaluation studies that were conducted in various settings to demonstrate how defined evaluation goals may be achieved with a limited amount of resources. This also illustrates advantages, limitations and costs of the different evaluation methods and techniques that may be used when evaluating clinical information systems.

Decision Support Systems, Clinical↗

PubMed1991

Downloading from MEDLINE: a comparison of personal database software.

The compatibility of downloaded MEDLINE references with software packages designed for maintenance of personal bibliographic databases is considered. The nine packages reviewed enable one to import batches of records downloaded from one or more presentations of the MEDLINE database, online or CD-ROM; and enable the user to re-format records into the various styles required by journal editors. Some basic features of the packages are tabulated, and details of record-importing facilities are described. Details of suppliers and prices are given.

Catalogs, Commercial as Topic↗

PubMed1991

Design and implementation of an electronic investigational drug accountability system.

A software system designed to maintain protocol-specific investigational drug accountability records is described. The University of Texas M. D. Anderson Cancer Center and Cygnus Systems Development, Inc., worked together to create an electronic investigational drug accountability system (IDRx), which meets the requirements of the National Cancer Institute. This system performs record keeping, stores information on drugs and protocols, and generates standard and customized reports. On-screen assistance makes it easy to use. Security is achieved by granting access only to authorized users, and an audit trail is automatically generated. Systematic implementation at M. D. Anderson, initially in the investigational drug control area and subsequently in the satellite pharmacies, has resulted in increased accuracy and efficiency, and few problems have been encountered. The IDRx software package is useful for keeping records, generating reports, and tracking and evaluating data associated with an investigational drug accountability system.

Cancer Care Facilities↗

PubMed1994

MAMCAT: an expert system for distinguishing between mammillary and catenary compartmental models.

MAMCAT is a user-friendly, interactive, graphics-based PC program for addressing a common compartmental model discrimination problem in the framework of model indistinguishability theory: can mammillary and catenary models of the same order be distinguished from each other? The software is designed to teach the theory and solve specific problems. The user is guided step-by-step through definitions, examples, theory and problem solution. Topological properties are used first to screen out some distinguishable models and thereby reduce the number of candidates for indistinguishability. Transfer function analysis is then used to explore the remaining candidates. Analytical results for up to 5-compartment models are given and a more general algorithm is induced from these results.

Algorithms↗

PubMed1994

A Monte Carlo program for the calculation of contrast, noise and absorbed dose in diagnostic radiology.

A Monte Carlo computer program has been developed for the simulation of X-ray photon transport in diagnostic X-ray examinations. The simulation takes account of the incident photon energy spectrum and includes a phantom (representing the patient), an anti-scatter grid and an image receptor. The primary objective for developing the program was to study and optimise the design of anti-scatter grids. The program estimates image quality in terms of contrast and signal-to-noise ratio, and radiation risk in terms of mean absorbed dose in the patient. It therefore serves as a tool for the optimisation of the radiographic procedure. A description is given of the program and the variance-reduction techniques used. The computational method was validated by comparison with measurements and other Monte Carlo simulations.

Computer Simulation↗

PubMed1995

The Scenario-Based Engineering Process (SEP): a user-centered approach for the development of health care systems.

The Scenario-based Engineering Process (SEP) is a user-focused methodology for large and complex system design. This process supports new application development from requirements analysis with domain models to component selection, design and modification, implementation, integration, and archival placement. It is built upon object-oriented methodologies, domain modeling strategies, and scenario-based techniques to provide an analysis process for mapping application requirements to available components. We are using SEP in the health care applications that we are developing. The process has already achieved success in the manufacturing and military domains and is being adopted by many organizations. SEP should prove viable in any domain containing scenarios that can be decomposed into tasks.

Artificial Intelligence↗

PubMed1994

Automated metrics for user interface design and evaluation.

Automated metrics will allow user interfaces to be partially evaluated early in the development process. They allow potential problems to be identified and corrected prior to user testing, saving both time and money. As a result, improved interfaces can be developed without additional costs. Both task-independent and task-sensitive automated metrics appear promising. Task-independent metrics should prove most useful for predicting user preferences and somewhat useful for predicting user performance. Task-sensitive metrics should prove useful for predicting both user preferences and performance. Several metrics are introduced and research directions are discussed.

Computer Systems↗

PubMed1994

Medical data and knowledge management by integrated medical workstations: summary and recommendations.

The health care professional workstation will function as an interface between the user and the patient data as well as an interface pertinent medical knowledge. Appropriate knowledge focus will require the workstation to recognize the concepts and structure of patient data, and understand the scope and access methods of knowledge sources. Issues are organized around five major themes: (i) structure, (ii) reliability and validation, (iii) views, (iv) location, and (v) ethical and legal. Conventional database representations can effectively address data structure and format variations that will inevitably persist in local data stores. The reliability of data and the validation of knowledge are critical issues that may determine the ultimate utility of clinical workstations. Alternative views of patient information and knowledge sources represent the true power of an intelligent data portal, represented by a well-designed clinical workstation. Both data and knowledge are optimally represented in decentralized information networks, although the confidentiality and ownership of this information must be respected. Evolutionary progress toward consistent representations of knowledge and patient data will be facilitated by the establishment of self-documentation standards for the developers of data encoding systems and knowledge sources, perhaps extended from the preliminary model afforded by the Unified Medical Language System (UMLS).

Computer Security↗

PubMed1994

Major issues in user interface design for health professional workstations: summary and recommendations.

Lack of good user interfaces has been a major impediment to the acceptance and routine use of health-care professional workstations. Health-care providers, and the environment in which they practice, place strenuous demands on the interface. User interfaces must be designed with greater consideration of the requirements, cognitive capabilities, and limitations of the end-user. The challenge of gaining better acceptance and achieving widespread use of clinical information systems will be accentuated as the variety and complexity of multi-media presentation increases. Better understanding of issues related to cognitive processes involved in human-computer interactions is needed in order to design interfaces that are more intuitive and more acceptable to health-care professionals. Critical areas which deserve immediate attention include: improvement of pen-based technology, development of knowledge-based techniques that support contextual presentation, and development of new strategies and metrics to evaluate user interfaces. Only with deliberate attention to the user interface, can we improve the ways in which information technology contributes to the efficiency and effectiveness of health-care providers.

Cognition↗

PubMed1997

Cognitive evaluation: how to assess the usability of information technology in healthcare.

As the adoption of information technology has increased, so too has the demands that these systems become more adapted to the physicians and nurses environments, to make access and management of information easier. The developers of information systems in Healthcare must use quality management techniques to ensure that their product will satisfy given requirements. This underlines the importance of the preliminary phase where Users Requirements are elicited. Some methodologies, such as KAVAS (E.M.S. Van Gennip, F. Grémy, Med. Inform. 18, 1993, 179) chose to use a continuous assessment protocol as a key strategy for quality management. At each stage of the conception and development of a prototype, the assessment checks that it conforms to the expectation of the users' requirements. The methodology of evaluation is then seen as a dynamic process which is able to improve the design and development of a dedicated system. The purpose of this paper is to demonstrate the necessity to include a cognitive evaluation phase in the process of evaluation by: (1) evaluating the integration (usability) of the I.T. in the activity of the users; and (2) understanding the motives underlying their management of information. This will help the necessary integration of information management in the workload of the healthcare professionals and the compatibility of the prototypes with the daily activity of the users.

Cognition↗

PubMed1990

[Construction of a computerized database for gastric cancer patients].

Gastric cancer is one of the most frequent malignant diseases in Taiwan. However, the result of treatment was poor. Since two years ago, we adopted the 'extended radical operation' for gastric cancer, in order to improve the post operative survival of patients with gastric cancer. For evaluating the results and prognosis, we used microcomputer and commercial software to design a computerized database for gastric cancer. The whole system includes three main operations. (1) Basic File Maintenance. (2) Data Analysis and Statistics. (3) Follow-up Data Managements. The operation is under Chinese system with pull-down menu and on-screen help. Rapid and accurate data analysis are the main advantages, and automatic plotting of data to bar/line chart is one of the characteristics by using this computerized database. Other characteristics include error-trapped function, item coding and data transformation.

Adult↗

PubMedDate not supplied

Image analysis methods for solitary pulmonary nodule characterization by computed tomography.

Computer software was designed for classifying solitary pulmonary nodules (SPNs) into benign and malignant from their CT images, using image analysis methods. The system made use of three features, computed from the CT density matrix of the SPN, and a class-discriminating algorithm. System evaluation was performed on 51 histologically confirmed SPNs of indeterminate CT diagnosis. Overall classification accuracy in distinguishing benign and malignant SPNs was 90.2%, while 83.3% of the benign and 93.9% of the malignant SPNs were correctly classified. The proposed system may be of value to the radiologist in assessing the probability of malignancy in patients with a solitary pulmonary nodule.

Adult↗

PubMedDate not supplied

Evaluating and validating very large knowledge-based systems.

Most knowledge-based systems for use in medicine have been developed in response to specific problems such as the diagnosis of abdominal or chest pain in an accident and emergency department, or the diagnosis and treatment of meningitis. There is a role for a general decision support system capable of answering queries about any aspect of medicine, particularly in primary care. However, evaluating such a knowledge base requires more elaborate methodology than a simple iterative test and refine cycle. At the design stage an adequate knowledge base structure is required to allow focused modification of the knowledge base when errors are discovered. During the prolonged evaluation cycle the partially formed knowledge base must be tested with such techniques as validation checks for consistency and completeness and examination of characteristics of problem-solving procedures. Finally a variety of criteria that represent the performance, robustness, flexibility, predictability, validity, coverage, relevance and congruity of the knowledge base are needed for a full description of the system's worth. Two case studies from the Oxford System of Medicine project are provided as examples of this philosophy: validating specific medical facts and comparing two methods for aggregating reasoning for and against a decision option.

Artificial Intelligence↗