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PubMed1996

Determination of sleep and wakefulness with the actigraph data analysis software (ADAS).

Current evidence has shown that, overall, actigraphy is an excellent tool for unobtrusive documentation of sleep/wake activity in normal individuals. However, a number of methodological issues remain to be resolved to warrant its use in clinical research. In this paper, we report the results of a study aimed at the development of a new scoring software that can accurately identify sleep and wakefulness. Using total sleep time as an index of comparison, the software was optimized on a calibration sample and prospectively tested on a validation sample. A strong correlation coefficient (r = 0.93, p < 0.008), with an average discrepancy value of 10 minutes, was observed for the calibration sample. The application of the optimal software to the validation sample revealed an even higher correlation coefficient (r = 0.97, p < 0.0001), with an average discrepancy value of 12 minutes.

Adult↗
PubMed2005

Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST).

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from http://liru.ars.usda.gov/mainbioinformatics.html. With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum.

Algorithms↗
PubMed2004

Barriers to proliferation of electronic medical records.

BACKGROUND: Error reduction, quality improvement and lowering of cost can all be achieved through electronic integration of healthcare providers. Proliferation of standard electronic health records/ electronic medical records (EHR/EMR) software is an essential precursor of this integration. Proliferation of EHR/EMR software has not occurred in the United States. OBJECTIVE: To characterise users and non-users of EHR/EMR software, identify potential barriers to proliferation, examine the extent of standardisation across reported EHR/EMR and suggest possible solutions to identified barriers. METHODS: We performed a secondary analysis of member survey data collected by the American Academy of Family Physicians (AAFP) in January 2003. The purpose of the survey was to measure interest in an AAFP-sponsored EHR/EMR service. We examined demographic and purchasing data from the survey by gender, population density, region and age. We also counted the number of different software vendors reported by users of an EHR/EMR to assess the number of users with unique software. RESULTS: Of the 35,554 members contacted, 5517 (15.5%) responded. Of those responding, 1297 (23.5%) reported use of an EHR/EMR. Of the members responding, 81% reported interest in EHR/EMR software and 61% reported cost as a major reason for not purchasing it. At least 264 different EHR/ EMR software programs are currently in use. On average, the percentage of respondents with the same EHR/EMR software is 0.4%. DISCUSSION: The number of AAFP members with unique EHR/EMR software is very large. Fragmentation, caused by the use of hundreds of unique systems, is a major barrier to proliferation of these systems. Many of the barriers to proliferation could be mitigated through the tools and techniques available through Free and Open Source Software (FOSS).

Adult↗
PubMed2002

[Quality assurance for the assessment of postoperative pain: proposal of procedures and questionnaires].

OBJECTIVES: This study presents a tool including survey questionnaires and a specific data-processing software for the data processing, allowing health care providers to assess the quality of postoperative pain management in surgical wards. STUDY DESIGN: Descriptive study. METHODS: A committee including anesthesiologists, nurses and epidemiologists had elaborated and tested three survey questionnaires to assess patients, nurses and medical staff satisfaction respectively. Specific data processing software was issued out of the final questionnaires. It allowed a quick analysis of items possibly, explaining inadequate postoperative pain management. After this adjustment, this tool was used in three different surgical wards, named A, B, C. RESULTS: The rate of answer (of investigated persons) being over 50%, data resulting from the survey performed in the surgical wards A and B were considered valid. The items which could explain insufficient pain relief were classified into 4 levels: patients assertion (ex: more than 50% of patients experienced persistent postoperative pain); practices evaluation (ex: 42 to 72% health care providers declared being aware of analgesic procedures); behavior's evaluation (ex: 19 to 34% of health care providers considered persistent postoperative pain to be useful for monitoring); and surgical wards potential (ex: 21 to 61% of health care providers took a specific course on pain management). Pros and cons of this tool were carefully examined and subsequent strategies defined. CONCLUSIONS: This survey's device should allow health care providers to assess the quality of postoperative pain management in surgical wards. Its validation is currently developed to improve its use, and keep the most performing indicators, showing an adequate postoperative pain management.

Adult↗
PubMed1999

Automated analysis of interatomic contacts in proteins.

MOTIVATION: New software has been designed to assist the molecular biologist in understanding the structural consequences of modifying a ligand and/or protein. RESULTS: Tools are described for the analysis of ligand-protein contacts (LPC software) and contacts of structural units (CSU software) such as helices, sheets, strands and residues. Our approach is based on a detailed analysis of interatomic contacts and interface complementarity. For any ligand or structural unit, these software automatically: (i) calculate the solvent-accessible surface of every atom; (ii) determine the contacting residues and type of interaction they undergo (hydrophobic-hydrophobic, aromatic-aromatic, etc.); (iii) indicate all putative hydrogen bonds. LPC software further predicts changes in binding strength following chemical modification of the ligand. AVAILABILITY: Both LPC and CSU can be accessed through the PDB and are integrated in the 3DB Atlas page of all PDB files. For any given file, the tools can also be accessed at http://www.pdb.bnl. gov/pdb-bin/lpc?PDB_ID= and http://www.pdb.bnl. gov/pdb-bin/csu?PDB_ID= with the four-letter PDB code added at the end in each case. Finally, LPC and CSU can be accessed at: http://sgedg.weizmann.ac.il/lpc and http://sgedg.weizmann.ac.il/csu.

Automation↗
PubMed2006

G-InforBIO: integrated system for microbial genomics.

BACKGROUND: Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs. RESULTS: The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses. CONCLUSION: The G-InforBIO system simplifies genome analyses by integrating several available software programs to allow efficient handling and manipulation of genome data. G-InforBIO is freely available from the download site.

Algorithms↗
PubMedDate not supplied

A handheld computer smoking intervention tool and its effects on physician smoking cessation counseling.

OBJECTIVE: The objective of this study was to evaluate a handheld computer smoking cessation intervention tool designed to assist physicians in their smoking cessation counseling with patients. METHODS: This study used a pre/post survey design, with a 4-month trial period for the software. Study participants included 22 faculty and resident physicians from the University of Virginia. Paired samples t tests were used to assess mean differences in the 4 main subscales (physician behavior, attitudes, comfort related to counseling patients about smoking cessation, and knowledge). RESULTS: No statistically significant mean differences were found for physician behavior (mean increase = 0.44, P = .55) or physician attitude (mean increase = 0.44, P = .16). A statistically significant mean increase of 2.29 was observed for the physician comfort subscale (t = 3.87, df = 16, P = .001). Physicians indicated improved comfort in counseling patients about smoking cessation (P = .007) and improved comfort in using the Public Health Service Clinical Practice Guidelines (P = .012). CONCLUSION: Physician comfort level in counseling patients about smoking cessation can be improved through handheld computer software. When used in conjunction with other practice modifications, this tool has the potential to improve physician smoking cessation intervention practices.

Adult↗
PubMed1992

Computer assisted data collection for stereology: rationale and description of point counting stereology (PCS) software.

The paper describes microcomputer software for point counting stereology. Stereology includes a collection of statistical methods that quantify the images of light and transmission electron microscopy. The methods use test grids placed over images to collect raw data, which includes counts of points, intersections, transections, and profiles. In turn, the counts are included in stereological equations that give estimates of compartmental volumes, surfaces, lengths, or numbers. These parameters describe the composition of a structure in three-dimensional space. The PCS (point counting stereology) System Software III serves as a data collection, storage, and management tool. Users set up point counting protocols without programming, enter data by pressing predefined function (MS-DOS) or alphabetic keys (UNIX), store data in files, select files for analysis, and calculate results as stereological densities. The latest version of the PCS software includes a new user interface and is designed as a research "front end" that can feed data either into the calculation tools of a stereology tutorial (Bolender, 1992, this issue) or into the analysis routines of quantitative morphology databases (Bolender and Bluhm, 1992).

Animals↗
PubMed2004

TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA.

UNLABELLED: TargetFinder is a PC/Windows program for interactive effective antisense oligonucleotide (AO) selection based on mRNA accessible site tagging (MAST) and secondary structures of target mRNA. To make MAST result intuitive, both the alignment result and tag frequency profile is illustrated. As theoretical reference, secondary structure and single strand probability profile of target mRNA is also represented. All of these sequences and profiles are displayed in aligned mode, which facilitates identification of the accessible sites in target mRNA. Graphical, user-friendly interface makes TargetFinder a useful tool in AO target site selection. AVAILABILITY: The software is freely available at http://www.bioit.org.cn/ao/targetfinder.htm CONTACT: sqwang@nic.bmi.ac.cn.

Algorithms↗
PubMed2005

Coding observational data: a software solution.

The analysis of observational data, particularly from social interactions, is often made difficult by the process of transcribing the verbal and behavioral interactions, having observers code on the transcriptions, and then transferring those codes to a statistical analysis program. The advent of computer-aided coding schemes has, to some extent, eliminated this laborious and time-consuming process. However, existing programs may not fulfill the needs of all of the researchers interested in this methodology, and furthermore, the expense of current systems may put these tools out of reach for some. The Observational Data Coding System (ODCS) software package presented here is a flexible coding tool designed to make efficient the process of coding observational data. A control panel allows the researcher to customize the program and coding system to suit his or her research questions. A variety of media (including video, audio, image, and text) can be read directly into the Windows-based program; trained observers can then code a variety of factors via buttons on the screen while the file is playing. An example of using the program to analyze conversation is provided. ODCS is a flexible, free tool for the coding of observational data.

Adult↗
PubMedDate not supplied

[Basic principles of system software maintenance for multi-functional non-invasive spectrophotometric diagnostic devices and complexes].

Due to the promotion of methods and devices of non-invasive spectrophotometric diagnostics in the sphere of medicine, software support for such diagnostic systems has been growing to be a topical issue. The general ideology of designing the system software support for multi-function spectrophotometric diagnostic tools is under discussion in the paper. The need in a multi-stratum structure of presenting, analyzing and processing the diagnostic findings, i.e. beginning from physical result interpretation to its common medical interpretation, is substantiated.

Diagnosis, Computer-Assisted↗
PubMed1988

Biological applications of the SAS system: an overview.

The SAS system provides biologists with a flexible, easy to use software package for data analysis. Through a combination of data management tools, a wide variety of pre-programmed procedures for sorting, graphing, and statistical analysis and a sophisticated programming language, SAS software can perform all analytical needs for most problems. The recent availability of SAS software on mainframes other than IBM, and more recently on the microcomputer, means that most scientists can have access to the software. In this review we discuss the structure of the SAS language and demonstrate its power in the analysis of biological problems. Although to a lesser extent now than originally, the SAS system is statistically oriented and a working knowledge of statistics is recommended before using its statistical capabilities. However, all biologists will find its data management and summarization capabilities very useful.

Biology↗
PubMedDate not supplied

MASTOS: Mammography Simulation Tool for design Optimization Studies.

Mammography is a high quality imaging technique for the detection of breast lesions, which requires dedicated equipment and optimum operation. The design parameters of a mammography unit have to be decided and evaluated before the construction of such a high cost of apparatus. The optimum operational parameters also must be defined well before the real breast examination. MASTOS is a software package, based on Monte Carlo methods, that is designed to be used as a simulation tool in mammography. The input consists of the parameters that have to be specified when using a mammography unit, and also the parameters specifying the shape and composition of the breast phantom. In addition, the input may specify parameters needed in the design of a new mammographic apparatus. The main output of the simulation is a mammographic image and calculations of various factors that describe the image quality. The Monte Carlo simulation code is PC-based and is driven by an outer shell of a graphical user interface. The entire software package is a simulation tool for mammography and can be applied in basic research and/or in training in the fields of medical physics and biomedical engineering as well as in the performance evaluation of new designs of mammography units and in the determination of optimum standards for the operational parameters of a mammography unit.

Algorithms↗
PubMed2025

MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.

Evolutionary sparse learning uses supervised machine learning to build evolutionary models where genomic sites loci are parameters. It uses the Least Absolute Shrinkage and Selection Operator with bi-level sparsity to connect a specific phylogenetic hypothesis with sequence variation across genomic loci. The MyESL software addresses the need for open-source tools to perform evolutionary sparse learning analyses, offering features to preprocess input phylogenomic alignments, post-process output models to generate molecular evolutionary metrics, and make Least Absolute Shrinkage and Selection Operator regression adaptable and efficient for phylogenetic trees and alignments. The core of MyESL, which constructs models with logistic regressions using bi-level sparsity, is written in C++. Its input data preprocessing and result post-processing tools are developed in Python. Compared to other tools, MyESL is more computationally efficient and provides evolution-friendly inputs and outputs. These features have already enabled the use of MyESL in two phylogenomic applications, one to identify outlier sequences and fragile clades in inferred phylogenies and another to build genetic models of convergent traits. In addition to the use in a Python environment, MyESL is available as a standalone executable compatible across multiple platforms, which can be directly integrated into scripts and third-party software. The source code, executable, and documentation for MyESL are openly accessible at https://github.com/kumarlabgit/MyESL.

Phylogeny↗
PubMedDate not supplied

[Estimate of potential health benefits of the reduction of air pollution with PM10 in Trieste, Italy].

OBJECTIVES: Estimate of the possible benefits, in Trieste, of a reduction of PM10 to values not over 60, 50, 40, 30, 20, 10 microg/mc, utilizing data of PM10 of the year 2002 as cause specific deaths and admissions. DESIGN: Cause specific deaths and admissions attributable to short term effects of PM10 calculated by software AirQ, utilizing Relative Risk from MISA 1 study (as published in 2002). SETTING: Trieste (Italy). MAIN OUTCOMES MEASURES: Cause specific deaths and admissions. RESULTS: Using air pollution data for 2002, 1.8% (CI 95% 0.6%; 2.9%) of natural deaths, 2.2% (CI 95% 0.6%; 3.7%) of cardiovascular deaths and 2.5% (CI 95% 0; 7.3%) of respiratory deaths, 1.5% (CI 95% 0.6; 2.4%) of cardiovascular admissions and 1.6% (CI 95% 0; 3.3%) of respiratory admissions were attributable to PM10 concentrations over 20 microg/mc. CONCLUSIONS: AirQ software proved to be a valid and reliable tool to estimate the potential short term effects of air pollution. Special attention is required to choose the relative risks to be utilized.

Air Pollutants↗
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↗
PubMed2006

GeneTools--application for functional annotation and statistical hypothesis testing.

BACKGROUND: Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for tools facilitating interpretation of biological data in "batch" mode. However, such tools often leave the investigator with large volumes of apparently unorganized information. To meet this interpretation challenge, gene-set, or cluster testing has become a popular analytical tool. Many gene-set testing methods and software packages are now available, most of which use a variety of statistical tests to assess the genes in a set for biological information. However, the field is still evolving, and there is a great need for "integrated" solutions. RESULTS: GeneTools is a web-service providing access to a database that brings together information from a broad range of resources. The annotation data are updated weekly, guaranteeing that users get data most recently available. Data submitted by the user are stored in the database, where it can easily be updated, shared between users and exported in various formats. GeneTools provides three different tools: i) NMC Annotation Tool, which offers annotations from several databases like UniGene, Entrez Gene, SwissProt and GeneOntology, in both single- and batch search mode. ii) GO Annotator Tool, where users can add new gene ontology (GO) annotations to genes of interest. These user defined GO annotations can be used in further analysis or exported for public distribution. iii) eGOn, a tool for visualization and statistical hypothesis testing of GO category representation. As the first GO tool, eGOn supports hypothesis testing for three different situations (master-target situation, mutually exclusive target-target situation and intersecting target-target situation). An important additional function is an evidence-code filter that allows users, to select the GO annotations for the analysis. CONCLUSION: GeneTools is the first "all in one" annotation tool, providing users with a rapid extraction of highly relevant gene annotation data for e.g. thousands of genes or clones at once. It allows a user to define and archive new GO annotations and it supports hypothesis testing related to GO category representations. GeneTools is freely available through www.genetools.no

Algorithms↗