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PubMed2004

Capturing biological information with class-responsibility-collaboration cards.

UNLABELLED: Class-responsibility-collaboration (CRC) cards have been used extensively in the software industry for defining complex object-oriented software requirements. We have adapted this tool to capture information about biological components, collaborators and responsibilities within these collaborations, which is not captured by current annotation tools. CRC cards should provide a common ground that will facilitate communication between biologist and computer scientists. AVAILABILITY: A CRC card template, XML representation and XML schema are freely available at http://people.musc.edu/~zhengw/CRCCard/CRC_Card_Index.html SUPPLEMENTARY INFORMATION: Supplemental Figures 1-4.

Computational Biology↗
PubMed1994

Contemporary issues in HIM. Software engineering--what does it mean to you?

There have been significant advances in the way we develop software in the last two decades. Many companies are using the new process oriented approach to software development. Companies that use the new techniques and tools have reported improvements in both productivity and quality, but there are still companies developing software the way we did 30 years ago. If you saw the movie Jurassic Park, you saw the perfect way not to develop software. The programmer in the movie was the only person who knew the details of the system. No processes were followed, and there was no documentation. This was an absolutely perfect prescription for failure. Some of you are probably familiar with the term hacker which describes a person who spends hours sitting at a terminal hacking out code. Hackers have created some outstanding software products, but with today's complex systems, most companies are trying to get away from their dependence on hackers. They are instead turning to the process-oriented approach. When selecting software vendors, don't just look at the functionality of a product. Try to determine how the vendor develops software, and determine if you are dealing with hackers or a process-driven company. In the long run, you should get better, more reliable products from the latter.

Engineering↗
PubMed2026

PYRAMA: an open-source tool for advanced meta-analysis of genome wide association studies.

MOTIVATION: Genome-wide association study (GWAS) meta-analysis tools are essential for integrating summary statistics across multiple cohorts, thereby increasing statistical power and validating genetic associations. Widely cited tools, such as METAL, PLINK, and GWAMA, have facilitated numerous significant discoveries in the field of GWAS. Nevertheless, these tools offer a limited set of meta-analysis methods and typically require users to have prior experience with command-line tools to be executed. RESULTS: We present here PYRAMA, an open-source tool which is designed for meta-analysis of genome wide association studies. This work introduces an easy-to-use software package that includes several meta-analysis methods that are absent in similar software packages. PYRAMA is faster compared to other tools, supports robust methods for analysis and meta-analysis, fixed-effects, random-effects and Bayesian meta-analysis and it is currently the only tool that supports meta-analysis with imputation of summary statistics. It is available both as a standalone tool and as a freely available web server. AVAILABILITY AND IMPLEMENTATION: https://github.com/pbagos/PYRAMA, https://doi.org/10.5281/zenodo.17830449.

Genome-Wide Association Study↗
PubMed1998

Modular workcells: modern methods for laboratory automation.

Laboratory automation is beginning to become an indispensable survival tool for laboratories facing difficult market competition. However, estimates suggest that only 8% of laboratories will be able to afford total laboratory automation systems. Therefore, automation vendors have developed alternative hardware configurations called 'modular automation', to fit the smaller laboratory. Modular automation consists of consolidated analyzers, integrated analyzers, modular workcells, and pre- and post-analytical automation. These terms will be defined in this paper. Using a modular automation model, the automated core laboratory will become a site where laboratory data is evaluated by trained professionals to provide diagnostic information to practising physicians. Modem software information management and process control tools will complement modular hardware. Proper standardization that will allow vendor-independent modular configurations will assure success of this revolutionary new technology.

Automation↗
PubMed1996

Drug identification in biological matrices using capillary electrophoresis and chemometric software.

Drugs and their metabolites in biological specimens are analyzed by a variety of techniques. Capillary electrophoresis could provide another useful approach because of its unique selectivity and high resolving power. For routine use, however, rugged methods must be developed and combined with detection that confirms peak purity and identity in difficult sample matrices, such as, urine. In this study, capillary electrophoresis is used with diode array detection, and chemometric software is employed for spectral analysis. The software includes a series of chemometric tools. Principle Component Analysis and Iterative Target Transform Factor Analysis are used to inspect each electropherogram for spectral homogeneity of the peaks and to deconvolute comigrations. These algorithms are used to confirm the assay results. This approach is tested and demonstrated for the analysis of amphetamine and common interferences in human urine.

Electrophoresis, Capillary↗
PubMed2005

A block-free hidden Markov model for genotypes and its application to disease association.

We present a new stochastic model for genotype generation. The model offers a compromise between rigid block structure and no structure altogether: It reflects a general blocky structure of haplotypes, but also allows for "exchange" of haplotypes at nonboundary SNP sites; it also accommodates rare haplotypes and mutations. We use a hidden Markov model and infer its parameters by an expectation-maximization algorithm. The algorithm was implemented in a software package called HINT (haplotype inference tool) and tested on 58 datasets of genotypes. To evaluate the utility of the model in association studies, we used biological human data to create a simple disease association search scenario. When comparing HINT to three other models, HINT predicted association most accurately.

Algorithms↗
PubMed1993

Tutorial: using Microsoft Excel for health care CQI.

The transition from QA to CQI in health care calls for decentralized data collection and analysis in conjunction with the use of personal computers to support CQI team activities. In this article, we discuss recent advances in PC software and hardware technology that make possible revolutionary changes in health care quality data management. We also present detailed examples of how to use Microsoft Excel 4.0 as a single software platform to support commonly used CQI tools and analyses.

Computer Graphics↗
PubMed2002

CGO: utilizing and integrating gene expression microarray data in clinical research and data management.

Clinical GeneOrganizer (CGO) is a novel windows-based archiving, organization and data mining software for the integration of gene expression profiling in clinical medicine. The program implements various user-friendly tools and extracts data for further statistical analysis. This software was written for Affymetrix GeneChip *.txt files, but can also be used for any other microarray-derived data. The MS-SQL server version acts as a data mart and links microarray data with clinical parameters of any other existing database and therefore represents a valuable tool for combining gene expression analysis and clinical disease characteristics.

Computational Biology↗
PubMed2005

Accessibility compliance rates of consumer-oriented Canadian health care Web sites.

Vast amounts of consumer-based health care information are widely available on the World Wide Web. However, for some this material is inaccessible due to reliance on specialized computer equipment or software known as assistive technology. These tools, designed for people with sensory, physical, or learning disabilities, act as a median to interpret Web pages in accessible ways. Unfortunately, many websites, including those with health-related content are not designed to accommodate this equipment. No research has yet been published examining the extent of this problem in Canadian consumer-oriented health care sites. The purpose of this study was to investigate the percentage of accessible consumer-based health care websites of Canadian origin. A listing of such sites was randomly sampled for study inclusion. Each was assessed for accessibility based on the World Wide Web Consortium (W3C) Web Accessibility Initiative (WAI) Web Content Accessibility Guidelines (WCAG) 1.0 using the validation software Bobby. The results indicated that only about 40% of pages investigated were free of errors in accordance with WCAG 1.0 Priority 1 level. Websites should be constructed in compliance with these standards to better accommodate those using assistive devices.

Access to Information↗
PubMedDate not supplied

COLUMBUS Orbital Facility and Automated Transfer Vehicle: a challenge for agency & industry.

Long term continuous operation of the COLUMBUS Orbital Facility (COF) flight- and ground segment requires continuous mission control and operations support capability to ensure proper operation and configuration of the COF systems in support of ongoing science and technology payloads. The ISS logistics scenario will be supported by the Automated Transfer Vehicle (ATV). These operational needs require the built-up of a new ground infrastructure in Europe and USA, enabling an efficient operations for preparation, planning and mission execution. The challenge for the European space community consists in the development and operation of a user friendly operational environment but keeping costs within budgetary constraints. Results of detailed definition studies performed by both agency and industry for the ground infrastructure indicate solutions to those technical and programmatic requirements by using of existing centers and facilities, re-use of C/D phase products (Hardware, Software) and COTS equipment to avoid costly new developments, using engineering expertise of the industrial personnel from flight element phase C/D. The concept for operations execution defines the task sharing between Operations Control Facilities (OCF), Operations Support Facilities and User Operations Sites. Operations support consists of on-line engineering support, off-line engineering support, payload integration, logistics support and crew training support performed by industry. DASA RI has made internal investments in organizational concepts for mission operations as well as in mission technologies and tools based on the standard COLUMBUS Ground Software (CGS) toolset and on knowledge based systems to enable an efficient industrial operations support. These tools are available as prototypes being evaluated in a simulated operational environment.

Astronauts↗
PubMed1988

Software selection: can a demonstration computer package help?

Using a demonstration package (demo) is one method of reviewing software which a foodservice manager is considering for purchase. There are a large number of software programs available, and the number is always increasing. Once the foodservice manager has established the criteria for selecting software, the programs which appear to meet those criteria must be evaluated. This article discusses the use of a demo as part of the evaluation process. A demo is a promotional tool used by vendors to demonstrate their software. Part or all of the program, with limitations on the amount of data that may be entered into the software, is normally provided. Advantages and disadvantages of demos are discussed, and the authors' experience using a demo is reported. A program demonstration checklist is provided. The advantages and disadvantages of reviewing the entire program and observing a vendor's demonstration are also discussed.

Food Services↗
PubMed1995

Education review: a computer-assisted instructional tool to assist students in developing an epidemiological research proposal.

The development of an epidemiological research proposal can be a difficult assignment for junior health information management students. The article demonstrates how a computer-assisted instructional (CAI) tool was developed to assist students in the development of an epidemiological research proposal. Surveys were conducted to determine where students were having the most problems, information about writing a research proposal was gathered and organized into an appropriate format, appropriate software (Hypercard) was chosen, the final CAI tool (the Research and Grant Writer) was developed, and positive feedback was obtained from junior health information management students using the CAI tool.

Attitude↗
PubMed2003

Automatic concept extraction from spoken medical reports.

OBJECTIVE: The objective of this project is to investigate methods whereby a combination of speech recognition and automated indexing methods substitute for current transcription and indexing practices. METHODS: We based our study on existing speech recognition software programs and on NOMINDEX, a tool that extracts MeSH concepts from medical text in natural language and that is mainly based on a French medical lexicon and on the UMLS. For each document, the process consists of three steps: (1) dictation and digital audio recording, (2) speech recognition, (3) automatic indexing. The evaluation consisted of a comparison between the set of concepts extracted by NOMINDEX after the speech recognition phase and the set of keywords manually extracted from the initial document. The method was evaluated on a set of 28 patient discharge summaries extracted from the MENELAS corpus in French, corresponding to in-patients admitted for coronarography. RESULTS: The overall precision was 73% and the overall recall was 90%. Indexing errors were mainly due to word sense ambiguity and abbreviations. A specific issue was the fact that the standard French translation of MeSH terms lacks diacritics. A preliminary evaluation of speech recognition tools showed that the rate of accurate recognition was higher than 98%. Only 3% of the indexing errors were generated by inadequate speech recognition. DISCUSSION: We discuss several areas to focus on to improve this prototype. However, the very low rate of indexing errors due to speech recognition errors highlights the potential benefits of combining speech recognition techniques and automatic indexing.

Abstracting and Indexing↗
PubMed2001

An effective and economical solution for digitizing and analyzing video recordings of the microcirculation.

OBJECTIVE: To assemble an economical system for analysis of microcirculation movies. METHODS: Images of cremaster microvessels were recorded onto sVHS video cassettes. These recordings were digitized onto a Macintosh computer using a MiroMotion DC30 plus video compression card and Adobe Premiere software, which permits video rate (25-30 fps) capture of full-sized (768 x 576 PAL, 640 x 480 NTSC) frames. Once captured, images were analyzed using NIH Image software. RESULTS: Combination of the Macintosh computer, the MiroMotion card, and Adobe Premiere allowed capture of high-resolution images at video rate, with the only limitation to sequence length being available hard-drive space. Captured movies could be directly accessed using the freely available NIH Image software. Use of built-in analysis tools and custom-written macros greatly facilitated rapid, accurate, and reproducible analysis of parameters such as blood flow velocity, leukocyte rolling velocity, and firm adhesion. CONCLUSIONS: Low-priced hardware and software aimed at the home-video enthusiast can be combined with free image-analysis software to provide a powerful image-analysis solution for study of the microcirculation.

Animals↗
PubMed2006

Sixteen-channel multidetector row computed tomography versus coronary angiography in a surgical view.

BACKGROUND: Invasive coronary angiography (ICA) is the gold standard for the diagnosis of coronary artery disease and also for imaging procedures for preoperative planning of coronary artery bypass grafting (CABG). Sixteen-multidetector row computed tomography (MDCT) represents an alternative depiction of coronary vessels. METHODS: Preoperative exams included ICA and MDCT in 50 patients. Two blinded surgical readers independently investigated both diagnostic modalities regarding location, severity, and morphology of the stenoses. The right coronary artery, left anterior descending branch, and circumflex branch--each divided in 3 sections--and the left main artery with a diameter (3) 1.5 mm were rated in both procedures, and the percentage of complete evaluations by MDCT was assessed. RESULTS: Heart rate was 72 +/- 8 bpm. Forty-six percent of patients received a complete MDCT evaluation, and 54% received an incomplete MDCT evaluation. In 62% of these incompletely examined patients, 1 branch was not completely analyzable, in 31% 2 branches; and in 7% all 3 branches. In total, 9% of all segments were incompletely assessed. Investigators detected coronary stenoses in complete evaluations with a sensitivity of 94% and a specificity of 95%. Positive predictive value was 87% and negative predictive value was 98%. Plaque classification in soft and hard plaques was possible. CONCLUSION: Sixteen-MDCT is not a viable alternative diagnostic tool at present. However, although the percentage of incomplete evaluated patients is more then 50%, only 9% of all segments were incompletely assessable. If this technology can be further improved, especially its software, it will become a valid diagnostic tool for coronary artery disease.

Coronary Angiography↗
PubMed2006

User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability.

Active contour segmentation and its robust implementation using level set methods are well-established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intrarater and interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing. Analogous results for lateral ventricle segmentation are provided.

Brain↗
PubMed2005

Parameter-space screening: a powerful tool for high-throughput crystal structure determination.

The determination of protein structures on a genomic scale requires both computing capacity and efficiency increases at many stages along the complex process. By combining bioinformatics workflow-management techniques, cluster-based computing and popular crystallographic structure-determination software packages, an efficient and powerful new tool for structural biology/genomics has been developed. Using the workflow manager and a simple web interface, the researcher can, in a few easy steps, set up hundreds of structure-determination jobs, each using a slightly different set of program input parameters, thus efficiently screening parameter space for the optimal input-parameter combination, i.e. a set of parameters that leads to a successful structure determination. Upon completion, results from the programs are harvested, analyzed, sorted based on success and presented to the user via the web interface. This approach has been applied with success in more than 30 cases. Examples of successful structure determinations based on single-wavelength scattering (SAS) are described and include cases where the 'rational' crystallographer-based selection of input parameters values had failed.

Computational Biology↗
PubMed2006

The CatchMod toolbox: easy and guided access to ICT tools for Water Framework Directive implementation.

Web-based toolboxes are handy tools to inform experienced users of existing software in their disciplines. However, for the implementation of the Water Framework Directive, a much more diverse public (water managers, consultancy firms, scientists, etc.) will ask for a very wide diversity of Information and Communication Technology (ICT) tools. It is obvious that the users of a web-based ICT-toolbox providing all this will not be experts in all of the disciplines and that a toolbox for ICT tools for Water Framework Directive implementation should thus go beyond just making interesting web-links. To deal with this issue, expert knowledge is brought to the users through the incorporation of visitor-geared guidance (materials) in the Harmoni-CA toolbox. Small workshops of expert teams were organized to deliver documents explaining why the tools are important, when they are required and what activity they support/perform, as well as a categorization of the multitude of available tools. An integration of this information in the web-based toolbox helps the users to browse through a toolbox containing tools, reports, guidance documents and interesting links. The Harmoni-CA toolbox thus provides not only a virtual toolbox, but incorporates a virtual expert as well.

Conservation of Natural Resources↗