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PubMed1995

Macintosh sequence analysis software. DNAStar's LaserGene.

The analysis of information in nucleotide and amino acid sequence data from an investigator's own laboratory, or from the ever-growing worldwide databases, is critically dependent on well planned and written software. Although the most powerful packages previously have been confined to workstations, there has been a dramatic increase over the last few years in the sophistication of the programs available for personal computers, as the speed and power of these have increased. A wide choice of software is available for the Macintosh, including the LaserGene suite of programs from DNAStar. This review assesses the strengths and weaknesses of LaserGene and concludes that it provides a useful and comprehensive range of sequence analysis tools.

Minicomputers↗

PubMed1995

Reengineering materiel management using computer technology.

The Materiel Management Department in today's hospital is in a uniquely advantageous position. It can better support the hospital's mission by applying current techniques in material management systems automation together with current computing technology as part of a broad-based reengineering process. Materiel management executives, suppliers, software developers, and hardware manufacturers now have all the necessary tools to create and implement a flexible, cost-effective, complete, paperless system. The model system offers tremendous advantages in terms of increased productivity and reduced total cost. This article discusses the process and the tools and techniques that should be considered.

Hospital Restructuring↗

PubMed2006

Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data.

The rapid accumulation of microarray data translates into an urgent need for tools to perform integrative microarray analysis. Integrative Array Analyzer is a comprehensive analysis and visualization software toolkit, which aims to facilitate the reuse of the large amount of cross-platform and cross-species microarray data. It is composed of the data preprocess module, the co-expression analysis module, the differential expression analysis module, the functional and transcriptional annotation module and the graph visualization module.

Algorithms↗

PubMed1998

Social marketing and MARTIN: tools for organizing, analyzing, and interpreting qualitative data.

The purpose of this article is to discuss how the computer software program MARTIN and social marketing concepts (understanding the consumer perspective, exchange, marketing mix, and segmentation) were used as organizational, analytical, and interpretive tools for qualitative data. The qualitative data are from a case study on citizen participation in a health reform policy in British Columbia. The concept of broad-based public participation is a fundamental element of health promotion and citizenship. There is a gap, however, between the promise and reality of citizen participation in health promotion. Emerging from the analysis was an understanding of the societal circumstances that inhibited or fostered participation. This article describes how the code-based, theory-building attributes of the MARTIN software facilitated a new conceptualization of participatory citizenship and generated new insights into understanding why some people participate and others do not.

British Columbia↗

PubMed2004

A new quality improvement study every day? Using QTools to build quality improvement projects around primary care electronic medical record systems.

Greater and more appropriate use of information technology has been proposed by the US Institute of Medicine as one way in which the quality of health care can be improved. Electronic medical record systems offer particular advantages because they can support clinicians at the point of care as well as allowing patient care to be monitored over time. Developing quality improvement tools that make use of the electronic medical record can, however, be difficult and often requires special software. This paper describes a system called QTools that provides a range of general-purpose tools to support quality improvement work in Norwegian primary care. The paper discusses how QTools has been used in two studies involving over 100,000 patient consultations and how it is supporting current work to improve the prescription of anti-hypertensive drugs. Features that have not yet been used in a quality improvement study are also discussed.

Data Collection↗

PubMed2004

Comparative analysis of gene sets in the Gene Ontology space under the multiple hypothesis testing framework.

The Gene Ontology (GO) resource can be used as a powerful tool to uncover the properties shared among, and specific to, a list of genes produced by high-throughput functional genomics studies, such as microarray studies. In the comparative analysis of several gene lists, researchers maybe interested in knowing which GO terms are enriched in one list of genes but relatively depleted in another. Statistical tests such as Fisher's exact test or Chi-square test can be performed to search for such GO terms. However, because multiple GO terms are tested simultaneously, individual p-values from individual tests do not serve as good indicators for picking GO terms. Furthermore, these multiple tests are highly correlated, usual multiple testing procedures that work under an independence assumption are not applicable. In this paper we introduce a procedure, based on False Discovery Rate (FDR), to treat this correlated multiple testing problem. This procedure calculates a moderately conserved estimator of q-value for every GO term. We identify the GO terms with q-values that satisfy a desired level as the significant GO terms. This procedure has been implemented into the GoSurfer software. GoSurfer is a windows based graphical data mining tool. It is freely available at http://www.gosurfer.org.

Algorithms↗

PubMed2005

GIS analysis for the marine environmental data off Karnataka coast.

Geographic Information System (GIS) is used to develop the Oceanographic Information System (OIS) for marine environmental data off Karnataka coast. Its goal is to provide a set of tools for oceanographic and bathymetry data assessment and products like graphs, query system for the users. The most significant interfaces are the GIS based Map-query and Contour visualization. The interfaces are user-friendly and oriented towards bridging the gap between user's knowledge and the technical knowledge required to operate the software system. The OIS also provides users with other analysis tools like query based reports and graphs. OIS can be used as a powerful tool to synthesize not only all the data off Karnataka coast but for comprehensive interpretation and forecasting of marine environmental ecosystems for any region. This system has been applied to the Karnataka Coastal Environment, India and it is very useful for the clients and policy makers.

Chlorophyll↗

PubMed2001

Visualization methods in analysis of detailed chemical kinetics modelling.

Sensitivity analysis, principal component analysis of the sensitivity matrix, and rate-of-production analysis are useful tools in interpreting detailed chemical kinetics calculations. This paper deals with the practical use and communication of the sensitivity analysis and the related methods are discussed. Some limitations of sensitivity analysis, originating from the mathematical concept (e.g. first-order or brute force methods) or from the software-specific implementation of the method, are discussed. As supplementary tools to the current methods, three novel visual tools for analysis of detailed chemical kinetics mechanisms are introduced: (a) scaled sensitivity analysis which is especially suited for studying initiation reactions where the span of reaction rates is high; (b) automated generation of reaction pathway plots which provides an immediate graphical illustration of the chemical processes occurring; (c) explorative (or chemometric) analysis of accumulated rate of progress matrices which assist in the identification of reaction subsets. The application of these tools are demonstrated by analysing NOx enhanced oxidation of methane at 700-1200 K.

Journal Article↗

PubMed2004

CisML: an XML-based format for sequence motif detection software.

SUMMARY: CisML is an XML-based format for sequence motif detection software. This proposed standard is applicable to many types of sequence motif detection programs. It is intended to facilitate the integration of data and the comparison of results from different software packages, and to simplify the development of downstream tools. XSL stylesheets are provided for easy generation of text, html and graphical reports from CisML-formatted data. AVAILABILITY: http://zlab.bu.edu/CisML/ SUPPLEMENTARY INFORMATION: Example CisML-formatted data and XSL stylesheets for report generation are available along with the sample output.

Amino Acid Motifs↗

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↗

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

[The development of a multivision glare tester].

This paper presents a new kind of multivision glare tester. Its composition, function, hardware, software and application are introduced. The tester provides a practical tool for evaluating visual function change under glare-producing conditions.

Contrast Sensitivity↗

PubMed1998

JADE: an approach for interconnecting bioinformatics databases.

To achieve the integration of biological data available on the World Wide Web and maintained in diverse sources such as GDB, Genbank or Acedb, we have developed a software called Jade. Jade allows programmers to create analytic tools and graphical user interfaces for one or more existing bioinformatics data sources. These tools can then be interchanged, compared and reused without making modifications in the data sources themselves. The system is implemented in the Java programming language and will run equally well on Macintosh, Windows or Unix workstations. Jade is free and can be used immediately by all interested parties.

Computational Biology↗

PubMed2004

PCOGR: phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms.

BACKGROUND: The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of orthologous groups (COGs). There are several bioinformatic studies that made use of this database to determine (hyper)thermophile-specific proteins by searching for COGs containing (almost) exclusively proteins from (hyper)thermophilic genomes. However, public software to perform individually definable group-specific searches is not available. RESULTS: The tool described here exactly fills this gap. The software is accessible at http://www.uni-wh.de/pcogr and is linked to the COG-database. The user can freely define two groups of organisms by selecting for each of the (current) 66 organisms to belong either to groupA, to the reference groupB or to be ignored by the algorithm. Then, for all COGs a specificity index is calculated with respect to the specificity to groupA, i. e. high scoring COGs contain proteins from the most of groupA organisms while proteins from the most organisms assigned to groupB are absent. In addition to ranking all COGs according to the user defined specificity criteria, a graphical visualization shows the distribution of all COGs by displaying their abundance as a function of their specificity indexes. CONCLUSIONS: This software allows detecting COGs specific to a predefined group of organisms. All COGs are ranked in the order of their specificity and a graphical visualization allows recognizing (i) the presence and abundance of such COGs and (ii) the phylogenetic relationship between groupA- and groupB-organisms. The software also allows detecting putative protein-protein interactions, novel enzymes involved in only partially known biochemical pathways, and alternate enzymes originated by convergent evolution.

Escherichia coli↗

PubMed2003

Dynamic quiz bank: a portable tool set for authoring and managing distributed, Web-based educational programs in radiology.

RATIONALE AND OBJECTIVES: The authors performed this study to evaluate a portable, platform-independent software program that enables users from remote sites to transform raw materials (eg, text, images, video) into Web-ready, interactive tutorials and examinations. MATERIALS AND METHODS: The software program evaluated consists of three modules: a network-based interface developed in the Java programming language, an Oracle 8i relational database with liaison software, and shell scripts developed in the Perl programming language to automate the authoring, maintenance, and updating of content in a dynamic quiz bank (DBQ). Four faculty members, one radiology resident, and two undergraduates majoring in computer science volunteered to create questions for the DQB and to evaluate ease of authoring. RESULTS: Faculty members with various levels of computer proficiency were able to establish a comprehensive DQB of more than 1,000 interactive questions. These radiologists reported the scripts reliable and easy to use. The DQB, offered in a pathology course for 2nd-year medical students, was used by 151 students and may have played a role in improving standardized test scores. Eighty-seven percent (n = 131) of the students believed that the DQB was extremely useful as an educational tool. CONCLUSION: The DQB software program facilitated access to, and authoring and maintenance of, Web-based educational materials developed in the departments of radiology and pathology.

Computer-Assisted Instruction↗

PubMed2005

Donors' blood group declaration before donation can be used as a tool for electronic crossmatching.

Electronic crossmatching (E-XM) is used to detect ABO incompatibility. In developing countries, as many of the donations are from first-time donors, it is difficult to guarantee the accuracy of the ABO/Rh label on these units to use them for E-XM. This problem was overcome with a new software 'hemosoft', using donors' blood group declaration before donation as a tool for E-XM. During registration, donors either declare their blood group or give no comment. For, ABO/Rh grouping, either two results from different donations or only one in concordant with the declaration before donation is needed. If there is a conflict, second typing is performed from the unit segment. If donors give no declaration, two different technicians perform typing, one from the sample tube and the other from the unit segment. Of 18,618 donations performed, 640 (3%) were repeated and the rest were first-time donations. In 16,327, typing was performed once, as the blood group declaration and the typing results were identical. In 2407, grouping was performed twice, as donors gave no declaration or conflicts between declaration and typing results were found. No labelling or wrong unit-release errors were detected in units donated, typed and labelled in our centre. In 26,402 donations, 16,314 (61.8%) E-XMs were performed. No major haemolytic transfusion reaction was recorded. Donors' ABO/Rh declaration before donation can be used as a tool for E-XM, instead of the requirement for serological confirmation or a second donation to guarantee grouping.

ABO Blood-Group System↗

PubMed2006

Sedimentation velocity analytical ultracentrifugation and SEDFIT/c(s): limits of quantitation for a monoclonal antibody system.

Sedimentation velocity analytical ultracentrifugation (SV-AUC) has emerged in the biopharmaceutical industry as a technique to detect small quantities of protein aggregates. However, the limits of detection and quantitation of these aggregates are not yet well understood. Although diverse factors (molecule, instrument, technique, and software dependent) preclude an all-encompassing measurement of these limits for the complete system, it is possible to use simulated data to determine the quantitation limits of the data analysis software aspect. The current study examines the performance of the SEDFIT/c(s) data analysis tool with simulated antibody monomer/dimer and monomer/aggregate systems. Under completely ideal conditions (zero noise, known meniscus, and shape factor homogeneity), the software limit of quantitation was 0.01% for the monomer/aggregate system and 0.03% for the less well-resolved monomer/dimer system. Under more realistic conditions (0.005 OD root mean square [RMS] noise, shape factor variability, and long solution column), the software limits of quantitation were 0.2 and 0.6% (0.002 and 0.006 OD) for the monomer/aggregate and monomer/dimer systems, respectively. Interestingly, diminished quantitation accuracy at very low levels of oligomer was not accompanied by deterioration of fit quality (as measured by root mean square deviation [RMSD] and residuals bitmap images).

Animals↗

PubMed2002

Computer-assisted instruction of carpal bone radiograph interpretation.

This paper describes the development of a computer-assisted self-directed learning module to teach carpal bone radiograph interpretation to clinical clerks, and the evaluation of its efficacy as a teaching tool. The module was developed using commercially available authoring software and in collaboration with radiologists. Following an eight-month period where the module was a mandatory component of the clerkship rotation in emergency medicine, a convenience sample of 36 volunteers from various levels of medical training were recruited, and their ability to interpret carpal radiographs was tested in an objective structured clinical examination (OSCE). The scores of the clinical clerks who had completed the module were shown to be similar to the scores of emergency medicine residents with specific experience and training in this skill (mean: 5 vs. 6), and different from the scores of trainees who had not completed the module and had no specific training in this skill (mean: 5 vs. 2). This study suggests that our module may be an effective tool in teaching this skill to clinical clerks.

Canada↗