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At least 1,783 records · Page 99Linked to original sources
PubMed1995

SAMSON: a software package for the biopolymer primary structure analysis.

The SAMSON package is a tool for advanced analysis of primary DNA, RNA and protein structures. The package consists of 16 programs performing statistical analysis and comparison of biopolymer sequences, search for homologies, translation of DNA and RNA sequences into amino acid sequences, splicing of RNA sequences and restriction map construction, recognition of functionally related sites in biopolymer molecules, textual analysis of DNA and RNA regulatory sites and prediction of intermolecular hybridization sites in DNA and RNA molecules.

Algorithms↗
PubMed2004

Developing complex signaling models using GENESIS/Kinetikit.

The development of biologically realistic models of signaling pathways is a demanding process, involving computational challenges as well as those arising from the complexity of detailed pathway models. We have developed the General Neural Simulation System (GENESIS) and Kinetikit (GENESIS/Kinetikit), a graphical simulation environment for modeling biochemical signaling pathways using deterministic and stochastic methods. A library of models of several common signaling pathways complements the software. This combination of numerical computation engines, graphical modeling tools, and library of models is designed to build on the cumulative development of models and techniques from many sources. The complete simulation environment and demonstration models are available from (http://stke.sciencemag.org/cgi/content/full/sigtrans;2004/219/pl4/DC1; also at http://www.ncbs.res.in/~bhalla/kkit/download.html). The associated library of signaling pathways is based on published experimental and simulation studies and is curated to ensure that the simulation outcomes match published results. Models in the library are maintained in a database (http://doqcs.ncbs.res.in). Individual pathway models can be combined to build complex signaling network simulations. The overall goal of this process is to attain sufficient biological realism in models to directly compare their outcomes with experiments and to improve our understanding of complex signaling.

Computational Biology↗
PubMed2000

[Electronic documentation in medicine; flexible concepts versus isolated solutions].

Computer-based medical documentation so far proved advantageous especially through standardization of data entry and increased access speed. Additional benefits can be achieved through the implementation of integrated, cross-project documentation tools and their integration into the clinical work-flow, which allow data to be used for a wide variety of applications (e.g. quality management, clinical research, clinic management). The presence of incompatible documentation software often complicates the realization of these goals. Implementation of new documentation tools therefore should consider flexibility and multiple-use of data as primary design goals. In the presented paper requirements for flexible documentation tools are introduced. The Entity-Attribute-Value-Model is described as a possible means of implementation. Practical experiences made with a prototype application are reported.

Germany↗
PubMed2006

Development and validation of MIX: comprehensive free software for meta-analysis of causal research data.

BACKGROUND: Meta-analysis has become a well-known method for synthesis of quantitative data from previously conducted research in applied health sciences. So far, meta-analysis has been particularly useful in evaluating and comparing therapies and in assessing causes of disease. Consequently, the number of software packages that can perform meta-analysis has increased over the years. Unfortunately, it can take a substantial amount of time to get acquainted with some of these programs and most contain little or no interactive educational material. We set out to create and validate an easy-to-use and comprehensive meta-analysis package that would be simple enough programming-wise to remain available as a free download. We specifically aimed at students and researchers who are new to meta-analysis, with important parts of the development oriented towards creating internal interactive tutoring tools and designing features that would facilitate usage of the software as a companion to existing books on meta-analysis. RESULTS: We took an unconventional approach and created a program that uses Excel as a calculation and programming platform. The main programming language was Visual Basic, as implemented in Visual Basic 6 and Visual Basic for Applications in Excel 2000 and higher. The development took approximately two years and resulted in the 'MIX' program, which can be downloaded from the program's website free of charge. Next, we set out to validate the MIX output with two major software packages as reference standards, namely STATA (metan, metabias, and metatrim) and Comprehensive Meta-Analysis Version 2. Eight meta-analyses that had been published in major journals were used as data sources. All numerical and graphical results from analyses with MIX were identical to their counterparts in STATA and CMA. The MIX program distinguishes itself from most other programs by the extensive graphical output, the click-and-go (Excel) interface, and the educational features. CONCLUSION: The MIX program is a valid tool for performing meta-analysis and may be particularly useful in educational environments. It can be downloaded free of charge via http://www.mix-for-meta-analysis.info or http://sourceforge.net/projects/meta-analysis.

Causality↗
PubMed2002

Using the AIDA--www.2aida.org--diabetes simulator. Part 1: recommended guidelines for health-carers planning to teach with the software.

AIDA is a novel diabetes-computing program freely available from www.2aida.org on the Web. The software is intended to serve as an educational support tool and can be used by anyone-patient with diabetes, relative of patient, health-care professional, or student-who has a minimal knowledge of the pathophysiology of diabetes. However, to obtain maximum benefit from the program, a teacher or demonstrator may be helpful. How much (or little) experience should the potential teacher have prior to giving formal lessons with the program? There is no hard or fast "rigid" answer to this. However, one of the aims of this article is to try and encourage people to consider these issues. In this respect it is important to make clear that health-carers cannot just download the program and start teaching with it the next day (or week) if they want their patients to get the most out of lessons with the program. As with many teaching interventions, the rewards of education-"what one gets out of it"-are in part dependent on the effort that one is willing to put in. Therefore teachers have to invest some time and effort into finding out how they can best work with the program to teach their patients in their particular local hospital/clinic setting. A further purpose of this article, and the one that follows in a future issue, is to generate some guidelines and provide some minimum recommendations for small group teaching sessions using AIDA. Previous experience of the authors has revealed a number of ways to improve the outcome of lessons that make use of the software. Among the most important points seem to be the preparation of the teacher, consideration of how to impart preliminary information to help patients understand the pathophysiology of diabetes, the optimum selection of topics to be covered, the arrangement of the lessons, how to involve each of the participants, and how to deal with questions. Other important topics include how to spot and deal with some of the difficulties that may be encountered by participants who apparently seem disinterested, obtaining feedback from the lessons, and practical ideas on how to lead a class.

Communication↗
PubMed1990

The evaluation of radioactive microsphere data: remarks on the use of the BMDP and SAS statistical software packages.

We investigated the suitability of BMDP and SAS as an integrated tool for the evaluation of regional blood flow data obtained from the radioactive microsphere technique. Both packages were applied to a recent study on muscle blood flow with a 3-factorial design. The organization of data and files, the strategy of data reduction, and the evaluation by means of statistical and graphical techniques are shown. The method may be applied to any microsphere study design. A considerable amount of time can be saved and data integrity may be improved. The statistical quality of the results may benefit from the broad spectrum of statistical tests available.

Algorithms↗
PubMedDate not supplied

SGS--Spatial Genetic Software: a computer program for analysis of spatial genetic and phenotypic structures of individuals and populations.

We have developed a program called Spatial Genetic Software (SGS), which provides a user-friendly Windows tool to analyze both local and broad scale genetic and phenotypic structure. It can deal with nearly any type of genetic data, codominant (allozyme, PCR-RFLP, microsatellite) or dominant (RAPD, AFLP) markers, or biparentally (nuclear) or uniparentally (cpDNA and mtDNA) inherited markers. Data based on any of these markers can be analyzed, either as individual genotypes within a single population (local scale) or as allele or haplotype frequencies from different populations (broad scale). We also include a simple approach to analysis of spatial structure for continuous quantitative traits. The program implements various parameters to analyze spatial genetic and phenotypic structure: Moran's index, Geary's index, number of alleles in common, and approaches using genetic distances and F(ST) values. The statistical significance of all measures is verified by the use of a permutation test. The results are assessed by graphics that can be integrated, via the clipboard, to other Windows programs. The details of the computations are given in a table and can be stored as ASCII files.

Demography↗
PubMedDate not supplied

Computer database for melanoma: a clinical management and research tool to ensure continuous quality assessment.

The need for an efficient method to handle data and for chart documentation is more apparent today than at any time in the past. High volume clinics for screening, diagnosis, and treatment are the rule rather than the exception in modern practice. A papermill medical record department or tumor registry fails on a day-to-day basis because of inefficiency of data collection, filing, storage, and abstraction. Requirements of the Joint Commission for the Accreditation of Health Care Organizations (JCAHO) include the setting of standards and the ability to query data to ensure the standards are met. A PC-based software program has been developed with the following features: (1) ongoing timed queries of the data are possible on any variable collected in the database to monitor trends in the standards established for care in the clinic; (2) a daily update of the database is performed so that it may be used as a clinical management tool, acting as an electronic medical record or as a clinical research tool; (3) the software will summarize the chart by abstracting a predetermined list of key data elements to improve clinical efficiency; (4) chart documentation is improved for Medicare coding requirements to maximize physician reimbursement; and (5) clinic notes and referral letters are generated the same day as the clinic visit to allow patients to have a copy of their clinic notes or for same day FAXing to the referring doctors. To date, > 1,200 patients with melanoma have been registered and entered into the system.(ABSTRACT TRUNCATED AT 250 WORDS)

Databases, Factual↗
PubMed2026

PathMED: an R toolkit for single-sample molecular scoring and machine learning with omics data.

MOTIVATION: Molecular scoring is a popular approach for studying pathway-level functional alterations with omics data. Using molecular scores for tasks such as single-sample molecular characterisation, phenotype prediction or disease stratification has several advantages compared to using omics data directly. Molecular scores provide biological interpretability and are more generalisable across datasets, facilitating data integration and machine learning applications. However, numerous scoring methods are available through different software packages, and currently there is a lack of tools to easily use these scores for model training and prediction. RESULTS: We developed pathMED, an R/Bioconductor package that unifies various scoring methods in a simple framework. Furthermore, pathMED also contains a machine learning module to train and test models that use the calculated molecular scores to predict clinical outcomes. We demonstrate some of its potential applications in three use cases using public omics data. We showed the generalisability of machine learning models trained on transcriptomic scores in predicting clinical outcomes when deploying on proteomic scores. We also demonstrated the application of transcriptomics scores in predicting breast cancer treatment response and identifying pathways strongly associated to tumour biology and treatment response. Finally, we demonstrated the benefit of integrating a novel gene set dissection step into the analysis pipeline to resolve disease heterogeneity at the pathway level. AVAILABILITY: PathMED is freely available in the Bioconductor repository (https://bioconductor.org/packages/release/bioc/html/pathMED.html). Code to reproduce the analyses is publicly available at https://github.com/GENyO-BioInformatics/pathMED_article.

Software↗
PubMed2000

RADARx: Recognizing, Assessing, and Documenting Adverse Rx events.

BACKGROUND: Adverse events are a leading cause of morbidity and mortality. Adverse Drug Events (ADEs) are frequent, under-reported, costly, and largely preventable. Computerized tools expose effectively ADEs and can reduce their impact. METHODS: RADARx is a Veterans Administration (VA) VistA-compatible M software program that integrates computerized ADE screening, probability assessment, documentation, and reporting capabilities. Data dictionary mapping tools have enabled RADARx implementation at 3 sites. All RADARx alerts generated at VA Medical Center (VAMC) Nashville from 7/1/99 to 9/30/99 were evaluated. RESULTS: Total ADEs documented using RADARx numbered 57. RADARx discovered 34 ADEs and 48 'potential' ADEs; 23 ADEs were found using traditional means. Overall, 11% of RADARx alerts were true positives. Pharmacist review of the 8-20 alerts generated daily costs between 10 and 30 minutes.

Adverse Drug Reaction Reporting Systems↗
PubMed1994

Innovations in intra-aortic balloon pump management: computer modem technology.

The computer modem technology being developed by Datascope Corporation for the purpose of off-site intra-aortic balloon pump (IABP) monitoring was clinically evaluated in 30 patients requiring IABP support. The Datascope System 95 model IABP with built-in modem was used on all patients. Remote communications via a personal computer with modem were conducted under both routine and emergency settings. The Datascope PC IABP software was evaluated for its user compatibility, efficiency, diagnostic capability and overall usefulness as a clinical tool. During the eight month evaluation period, 87 remote communications were conducted for both routine and emergency IABP evaluation checks. Adjustments were recommended on 22 occasions relevant to balloon timing, trigger mode selection and augmentation volume settings. Eight communications were initiated in emergency settings due to a variety of patient conditions. Emergency intervention was successful in diagnosing and resolving critical situations including atrial arrhythmias, pacemaker timing, low cardiac output syndrome, loss of trigger source, catheter malpositioning and poor augmentation. The diagnostic capabilities and efficient means of data collection by the computer software provide the clinician with a valuable tool for routine IABP clinical monitoring, as well as emergency problem resolution.

Adult↗
PubMed2003

An automated method for neuroanatomic and cytoarchitectonic atlas-based interrogation of fMRI data sets.

Analysis and interpretation of functional MRI (fMRI) data have traditionally been based on identifying areas of significance on a thresholded statistical map of the entire imaged brain volume. This form of analysis can be likened to a "fishing expedition." As we become more knowledgeable about the structure-function relationships of different brain regions, tools for a priori hypothesis testing are needed. These tools must be able to generate region of interest masks for a priori hypothesis testing consistently and with minimal effort. Current tools that generate region of interest masks required for a priori hypothesis testing can be time-consuming and are often laboratory specific. In this paper we demonstrate a method of hypothesis-driven data analysis using an automated atlas-based masking technique. We provide a powerful method of probing fMRI data using automatically generated masks based on lobar anatomy, cortical and subcortical anatomy, and Brodmann areas. Hemisphere, lobar, anatomic label, tissue type, and Brodmann area atlases were generated in MNI space based on the Talairach Daemon. Additionally, we interfaced these multivolume atlases to a widely used fMRI software package, SPM99, and demonstrate the use of the atlas tool with representative fMRI data. This tool represents a necessary evolution in fMRI data analysis for testing of more spatially complex hypotheses.

Brain↗
PubMed2005

SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci.

In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses of linkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large number of samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data, we developed a robust and user-friendly software platform with a series of tools for analysis in association study with high efficiency. The platform has been well evaluated by several sets of real data.

Genetic Predisposition to Disease↗
PubMed1999

Genomics via optical mapping. III: Contiging genomic DNA.

In this paper, we describe our algorithmic approach to constructing an alignment of (contiging) a set of restriction maps created from the images of individual genomic (uncloned) DNA molecules digested by restriction enzymes. Generally, these DNA segments are sized in the range of 1-4 Mb. The goal is to devise contiging algorithms capable of producing high-quality composite maps rapidly and in a scaleable manner. The resulting software is a key component of our physical mapping automation tools and has been used to create complete maps of various microorganisms (E. coli, P. falciparum and D. radiodurans). Experimental results match known sequence data.

Algorithms↗
PubMed2004

Lessons from the implementation of a near patient anticoagulant monitoring service in primary care.

OBJECTIVE: To evaluate the implementation of a primary care, nurse-led, near patient anticoagulant monitoring service. DESIGN: Action research workshops, supported by questionnaires and clinical audit, to define the strengths and weaknesses of the service and the effectiveness of the computerised decision support system used to set the dosage of anticoagulant and time interval to the next appointment. SETTING: 13 general practices that implemented anticoagulant monitoring in a primary care organisation in south east England. PARTICIPANTS: 18 practice nurses, 72% of whom had over 20 years' clinical experience; the university-based investigators and managers from the primary care organisation. MAIN OUTCOME MEASURE: The nurses felt that the patients preferred the practice-based service, finding it more personal and accessible. However, circumstances arose where the nurse's intuition had to override the software's advice. The nurses found it stressful when they were unclear whether their decision making represented acceptable variation or dangerous practice. An audit tool was developed to measure the extent to which there was variation from the software's recommendation, and patterns of variation emerged. Most evident was that nurses responded to uncertainty by practising cautiously, shortening the interval until the next visit and slightly reducing the recommended dose of warfarin. CONCLUSIONS: The group, by sharing their experiences through a structured series of workshops, developed an understanding of when it might be appropriate to vary from the decision support software's recommendations and how this could be audited. The technological solution modelled on hospital practice proved hard to implement in primary care.

Anticoagulants↗
PubMed1989

Computerized materiel management. MMs become increasingly sophisticated.

The materiel management automation environment is undoubtedly exploding. Hospitals which already rely upon computer systems continue to expand the tasks they perform and department they serve. Even hospitals which have not become reliant upon computers now bring considerable knowledge to the table when negotiating to obtain their first systems. In general, materiel managers continue to grow more sophisticated in hardware and software matters. Most view automation as one the most effective tools they and their hospitals have in controlling expenses. The coming years will surely produce much more system integration as materiel managers begin merging the extensive capabilities of computers with the specific needs and goals of their facilities.

Catalogs, Commercial as Topic↗
PubMed2003

IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes.

IMGT/PhyloGene is an on-line software package for comparative analysis of immunoglobulin (IG) and T cell receptor (TR) variable genes of all vertebrate species, newly implemented in IMGT, the international ImMunoGeneTics information system ((R)). IMGT/PhyloGene is strongly associated with the IMGT gene and allele nomenclature and with the IMGT unique numbering for V-REGION, which directly creates standardized alignments from IMGT reference sequences. IMGT/PhyloGene is the first tool to use the IMGT expertized and standardized data for automated comparative analyses, and the first on-line software package for phylogenetic reconstruction to be integrated to a sequence database. Starting from a standardized alignment of selected sequences, IMGT/PhyloGene computes a matrix of evolutionary distances, builds a tree using the Neighbor-Joining (NJ) algorithm, and outputs various graphical tree representations. The resulting IMGT/PhyloGene tree is then used as a support for studying the evolution of particular subregions, such as the CDR-IMGT (Complementarity Determining Regions) or the V-RS (Variable gene Recombination Signals). IMGT/PhyloGene is freely available at http://imgt.cines.fr.

Databases, Nucleic Acid↗
PubMed2002

Software for signaling networks, electronic and cellular.

Cellular signaling networks have many similarities with electronic circuits. Therefore, the tools used to test and analyze electronic circuits can be adapted to analyze cellular signaling processes. Lok describes some of these signaling network analysis tools, their underlying principles, and their limitations.

Feedback, Physiological↗