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At least 469 records · Page 26Linked to original sources
PubMed2003

Online tool for the discrimination of equi-distributions.

BACKGROUND: For many applications one wishes to decide whether a certain set of numbers originates from an equiprobability distribution or whether they are unequally distributed. Distributions of relative frequencies may deviate significantly from the corresponding probability distributions due to finite sample effects. Hence, it is not trivial to discriminate between an equiprobability distribution and non-equally distributed probabilities when knowing only frequencies. RESULTS: Based on analytical results we provide a software tool which allows to decide whether data correspond to an equiprobability distribution. The tool is available at http://bioinf.charite.de/equifreq/. CONCLUSIONS: Its application is demonstrated for the distribution of point mutations in coding genes.

Amino Acid Sequence↗
PubMed2005

Software and expert system for the management of chronic hepatitis B.

Whereas the doubling time of overall biomedical knowledge bases has been estimated at about 19 years, the body of indexed information related to HBV has doubled in the last 8 years; the one related to HBV and antivirals has doubled in the last 5 years and the one related to Interferon and contraindications has doubled in less than 48 months. In Hepatology, as well as in other fast changing areas of medicine, the demand that clinical decision should always be based on the best verified knowledge available, is becoming more and more difficult to comply with. The Italian network of competence for hepatic diseases (Liver Unit Networks Association or LUNA) was established in 2003 with the patronage of the Italian Ministry of Health, with the primary goal of promoting advanced clinical research and real-time information exchange among the participating centres, facilitating knowledge sharing and identification of best practices. The ICT infrastructure designed for this purpose includes four sets of online accessible software tools:

Chronic Disease↗
PubMed2006

MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences.

BACKGROUND: Proteomics is the study of the proteome, and is critical to the understanding of cellular processes. Two central and related tasks of proteomics are protein identification and protein characterization. Many small laboratories are interested in the characterization of a small number of proteins, e.g., how posttranslational modifications change under different conditions. RESULTS: We have developed a software tool called MassSorter for administrating and analyzing data from peptide mass fingerprinting experiments on proteins with known amino acid sequences. It is meant for small scale mass spectrometry laboratories that are interested in posttranslational modifications of known proteins. Several experiments can be compared simultaneously, and the matched and unmatched peak values are clearly indicated. The hits can be sorted according to m/z values (default) or according to the sequence of the protein. Filters defined by the user can mark autolytic protease peaks and other contaminating peaks (keratins, proteins co-migrating with the protein of interest, etc.). Unmatched peaks can be further analyzed for unexpected modifications by searches against a local version of the UniMod database. They can also be analyzed for unexpected cleavages, a highly useful feature for proteins that undergo maturation by proteolytic cleavage, creating new N- or C-terminals. Additional tools exist for visualization of the results, like sequence coverage, accuracy plots, different types of statistics, 3D models, etc. The program and a tutorial are freely available for academic users at http://www.bioinfo.no/software/massSorter. CONCLUSION: MassSorter has a number of useful features that can promote the analysis and administration of MS-data.

Algorithms↗
PubMed2005

Airway wall thickness in cigarette smokers: quantitative thin-section CT assessment.

PURPOSE: To design and validate a dedicated software tool to measure airway dimensions on thin-section computed tomographic (CT) images and to use the tool to prospectively compare airway wall thickness in nonsmokers with normal lung function with that in smokers with and without chronic obstructive pulmonary disease (COPD). MATERIALS AND METHODS: All subjects gave written informed consent. The study was approved by local ethics committee. With Laplacian of Gaussian algorithm, software was tested in phantom and excised sheep lung fixed in inflation and validated with Bland-Altman analysis. Study prospectively included nine nonsmokers (six women, three men; mean age, 53 years +/- 5.6 [standard error of the mean]) with normal lung function (group 1), seven smokers (three women, four men; mean age, 56 years +/- 5.6) with normal lung function (group 2), and eight smokers (zero women, eight men; mean age, 65 years +/- 4.0) with COPD. Calculations were determined with spirometrically gated CT: For each selected bronchus, the wall area (WA), internal area (IA), airway caliber (sum of IA and WA), and WA/IA ratio were calculated. For each patient, summation of WA to summation of IA (SigmaWA/SigmaIA) ratio, which reflected normalized airway wall thickness, was calculated. Groups were compared by using analysis of variance with generalized linear model and unpaired t test. Pearson correlation coefficient was used to assess correlation between software measurements and pulmonary function test results. RESULTS: Comparison of measurements in phantom and excised sheep lung with algorithm measurements revealed that the latter were reliable and repeatable. In clinical study, SigmaWA/SigmaIA ratio was significantly different among three groups (P < .001). Normalized airway wall thickness and IA were significantly related to lung function test data, including forced expiratory volume in 1 second (r = -0.54, P = .006), specific airway conductance (r = -0.45, P = .03), and forced expiratory flow between 25% and 75% of vital capacity (r = -0.65, P < .001). CONCLUSION: This software provides accurate and reproducible measurements of IA and WA of bronchi on thin-section CT images and demonstrates that in vivo normalized airway wall thickness was larger in smokers with COPD than it was in smokers or nonsmokers without COPD.

Animals↗
PubMed2003

Biopathways representation and simulation on hybrid functional Petri net.

The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we firstly define a novel notion of Petri net called Hybrid Functional Petri Net (HFPN). Then, we introduce a software tool, Genomic Object Net, for representing and simulating biopathways, which we have developed by employing the architecture of HFPN. In order to show the usefulness of Genomic Object Net for representing and simulating biopathways, we show two HFPN representations of gene regulation mechanisms of Drosophila melanogaster (fruit fly) circadian rhythm and apoptosis induced by Fas ligand. The simulation results of these biopathways are also correlated with biological observations. The software is available to academic users from http://www.GenomicObject.Net/.

Animals↗
PubMedDate not supplied

Development of a new Clinical Engineering Management Tool & Information System (CLE-MANTIS).

The evolution of the field of biomedical technology has led to the diffusion of an impressive number of medical devices into healthcare institutions. In this environment, Clinical Engineering Departments (CEDs) are expanding their role in healthcare technology management, by changing their structure and introducing quality systems in order to improve their services and monitor the outcomes. In the framework of the national project BIOTECHNET II, a software tool for the management of biomedical technology, named CLE-MANTIS, has been developed, with the aim to assist CEDs in their tasks. CLE-MANTIS functions include the upkeep of an inventory, the support and monitoring of scheduled maintenance, corrective maintenance, vigilance, equipment acquisition and replacement, service contract management and user training. The system offers clinical engineers the possibility to monitor and evaluate the quality and cost-effectiveness of their departments through the monitoring of quality and cost indicators. This paper presents the main features and functions of the system.

Biomedical Engineering↗
PubMedDate not supplied

Multiple receptor populations: binding isotherms and their numerical analysis.

This paper reviews present models and methods of parameter estimation in relationships describing receptor-ligand interactions in equilibrium, as used in the author's laboratory. The state-of-the-art and the present experience can be summarized as follows: 1) Binding isotherms (relationships of bound and free/total ligand concentrations) are superpositions of several elementary terms describing the ligand binding to individual binding sites (receptors) present in the biological material investigated. The "nonspecific binding" is usually represented by a linear term. 2) The elementary terms are most frequently described by a rectangular hyperbola, Hill (power) function, or a rational function (binding of several ligand molecules to one molecule of receptor). Heterologous displacement requires specific functions which, however, can be transformed into one of the elementary terms. 3) Parameters (binding capacities, dissociation constants, Hill coefficients, etc.) can most reliably be estimated by nonlinear regression methods. However, these methods frequently fail to yield physically relevant values if initial estimates are far from "real" values, or if the data are strongly scattered. Some of the available routines (e.g., LIGAND) offer manifold tools to solve these difficulties. 4) The "affinity spectrum", a relationship between binding capacities and equilibrium constants, shows the presence of individual binding sites in the binding system in question. The spectrum can be constructed either by Fourier analysis, or by a stepwise procedure (computation of binding capacity for several dissociation constants). The former way of analysis is demanding; software tools are rare. 5) The "STEP" routine based on Hill/Scatchard linearization routines yields profiles similar to affinity spectra, but offers, in addition, values of Hill coefficients of individual binding populations. Values obtained can be used as initial estimates for nonlinear regression. 6) Selection of a suitable model, its testing, numerical procedures, statistical estimates, etc. frequently entail severe difficulties which are approached in the available software packages in different ways, none of them is usually optimal.

Animals↗
PubMed2005

TERMTrial--terminology-based documentation systems for cooperative clinical trials.

Within cooperative groups of multi-center clinical trials a standardized documentation is a prerequisite for communication and sharing of data. Standardizing documentation systems means standardizing the underlying terminology. The management and consistent application of terminology systems is a difficult and fault-prone task, which should be supported by appropriate software tools. Today, documentation systems for clinical trials are often implemented as so-called Remote-Data-Entry-Systems (RDE-systems). Although there are many commercial systems, which support the development of RDE-systems there is none offering a comprehensive terminological support. Therefore, we developed the software system TERMTrial which consists of a component for the definition and management of terminology systems for cooperative groups of clinical trials and two components for the terminology-based automatic generation of trial databases and terminology-based interactive design of electronic case report forms (eCRFs). TERMTrial combines the advantages of remote data entry with a comprehensive terminological control.

Clinical Trials as Topic↗
PubMed2004

[Software-assisted CT-postprocessing of the carotid arteries].

PURPOSE: A software assistant for automatic evaluation of CT-angiograms (CTA) was developed. It should enable the visualization of the vessel lumen and the quantitative evaluation of a stenosis. CTA examinations of patients with suspected carotid artery stenoses were used for the evaluation of the software assistant. MATERIALS AND METHODS: Twelve Patients with suspected high-grade stenosis of the carotid arteries underwent a CTA examination using a multislice CT scanner. The data were analyzed and evaluated using the new software assistant. The results were compared with the data of digital subtraction angiography (DSA) of these patients. RESULTS: The time of digital postprocessing with the new software-assistant took about six minutes on average. Contour extraction of the vessel, MIP and curved MPR (c-MPR) and orthogonal cross-sectional images of the vessels were calculated, followed by an automatic quantification of stenosis by the use of the c-MPR. A good correlation was found between CTA and DSA data regarding the stenosis grade (r = 0.82). Furthermore, some information could be provided about the plaque morphology. CONCLUSION: The software-assisted detection and analysis of carotid artery stenosis with the new developed program is possible within a justifiable time. DSA- and CTA-data did not show a significant difference in stenosis grading. Further development of software tools could lead to a better characterization of plaque morphology.

Carotid Arteries↗
PubMed1998

[Evidence-based medicine. How to use biomedical literature to solve clinical problems. Italian Group on Evidence-Based Medicine-GIMBE].

Clinical practice is constantly changing, the rate of changing is accelerating and consequently it may even take years before the results of clinical research will be incorporated in day-to-day practice. So, there is a large gap between what the biomedical literature contains and the care that most of patients receive. The gap is widened by the extensive processing that results of clinical research require before they can be used. Evidence-based medicine is a new approach to health care promoting the collection, interpretation, and integration of valid, important and applicable research-derived evidence. The best available evidence, moderated by patient circumstances and preferences, is applied to improve the quality of clinical judgements. There are many information tools that facilitate the practice of evidence-based medicine. These include users' guides to the medical literature, strategies to improve the yield of MEDLINE searches, standardized formats for abstracts of journal articles and guidelines, new journals, systematic reviews and meta-analyses, resources on-line and software tools bringing high quality information to the point of clinical decision making. However, these tools are poorly spread and physicians lack of necessary skills for their effective utilization. In this article the authors describe guidelines for efficient and effective utilization of biomedical information tools to solve clinical problems and improve the quality and the cost/effectiveness of health care.

Evidence-Based Medicine↗
PubMed2006

HiRes--a tool for comprehensive assessment and interpretation of metabolomic data.

UNLABELLED: The increasing role of metabolomics in system biology is driving the development of tools for comprehensive analysis of high-resolution NMR spectral datasets. This task is quite challenging since unlike the datasets resulting from other 'omics', a substantial preprocessing of the data is needed to allow successful identification of spectral patterns associated with relevant biological variability. HiRes is a unique stand-alone software tool that combines standard NMR spectral processing functionalities with techniques for multi-spectral dataset analysis, such as principal component analysis and non-negative matrix factorization. In addition, HiRes contains extensive abilities for data cleansing, such as baseline correction, solvent peak suppression, removal of frequency shifts owing to experimental conditions as well as auxiliary information management. Integration of these components together with multivariate analytical procedures makes HiRes very capable of addressing the challenges for assessment and interpretation of large metabolomic datasets, greatly simplifying this otherwise lengthy and difficult process and assuring optimal information retrieval. AVAILABILITY: HiRes is freely available for research purposes at http://hatch.cpmc.columbia.edu/highresmrs.html

Algorithms↗
PubMed1996

Protein fold recognition by sequence threading: tools and assessment techniques.

Protein fold recognition has been approached by threading an amino acid sequence onto a library of folds, calculating a sequence-structure compatibility score, and ranking these scores. Due to imperfections in the empirically derived pairwise potential functions and the necessarily heuristic approach to the sequence-structure alignment problem, the method benefits from the assessment of threaded models to evaluate the most probable structures among the list of possible folds. THREADER and ANALYST, software tools available through the Internet, facilitate the alignment and assessment steps of a threading prediction. No process has been found to be universally reliable for the detection of folds related to the structure of a known input sequence, but several useful steps and approaches are discussed.

Algorithms↗
PubMed2002

Stochastic trees and the StoTree modeling environment: models and software for medical decision analysis.

In this paper we present a review of stochastic trees, a convenient modeling approach for medical treatment decision analyses. Stochastic trees are a generalization of decision trees that incorporate useful features from continuous-time Markov chains. We also discuss StoTree, a freely available software tool for the formulation and solution of stochastic trees, implemented in the Excel spreadsheet environment.

Decision Support Systems, Clinical↗
PubMed1986

Data structures for DNA sequence manipulation.

Two data structures designated Fragment and Construct are described. The Fragment data structure defines a continuous nucleic acid sequence from a unique genetic origin. The Construct defines a continuous sequence composed of sequences from multiple genetic origins. These data structures are manipulated by a set of software tools to simulate the construction of mosaic recombinant DNA molecules. They are also used as an interface between sequence data banks and analytical programs.

Base Sequence↗
PubMed2003

The Protein Data Bank and structural genomics.

The Protein Data Bank (PDB; http://www.pdb.org/) continues to be actively involved in various aspects of the informatics of structural genomics projects--developing and maintaining the Target Registration Database (TargetDB), organizing data dictionaries that will define the specification for the exchange and deposition of data with the structural genomics centers and creating software tools to capture data from standard structure determination applications.

Animals↗
PubMed2003

Decision support system for managing oil spill events.

The Mediterranean environment is exposed to various hazards, including oil spills, forest fires, and floods, making the development of a decision support system (DSS) for emergency management an objective of utmost importance. The present work presents a complete DSS for managing marine pollution events caused by oil spills. The system provides all the necessary tools for early detection of oil-spills from satellite images, monitoring of their evolution, estimation of the accident consequences and provision of support to responsible Public Authorities during clean-up operations. The heart of the system is an image processing-geographic information system and other assistant individual software tools that perform oil spill evolution simulation and all other necessary numerical calculations as well as cartographic and reporting tasks related to a specific management of the oil spill event. The cartographic information is derived from the extant general maps representing detailed information concerning several regional environmental and land-cover characteristics as well as financial activities of the application area. Early notification of the authorities with up-to-date accurate information on the position and evolution of the oil spill, combined with the detailed coastal maps, is of paramount importance for emergency assessment and effective clean-up operations that would prevent environmental hazard. An application was developed for the Region of Crete, an area particularly vulnerable to oil spills due to its location, ecological characteristics, and local economic activities.

Accidents↗
PubMed2004

An application of visible human database in radiotherapy: tutorial for image guided external radiotherapy (TIGER).

BACKGROUND AND PURPOSE: Three-dimensional conformal radiotherapy and intensity modulated radiotherapy allow accurate dose delivery on target volumes. Due to the different background among specialists involved in target volume definition, the contouring emerges as one of the most questionable steps in treatment planning procedures. A software tool devoted to contouring training, named tutorial for image guided external radiotherapy ('TIGER'), based on the Visible Human Project images data-set, is described. MATERIALS AND METHODS: TIGER is addressed to facilitate the learning of axial anatomical images, to promote the training and reproducibility in contouring process, to allow the availability of a tool to enhance the 'drill and practice' approach in training programs. TIGER includes three different environments: Anatomic tutorial devoted to facilitate a self-learning approach to axial body sections; Contouring tutorial addressed to practice contouring process of anatomical structures and to undergo a test program prepared by tutors; Teacher's tools to offer to tutors the opportunity to insert new outlines in TIGER-database, according to local needs or conventions, and to use them in tutorial programs. TIGER-database is grouped in six main anatomical sections: head and neck, male thorax, female thorax, abdomen, male pelvis, and female pelvis. Overall 432 corresponding CT-VH images and 1189 contours of 134 different anatomical structures and lymphatic drainage areas are available. The access to the TIGER software is allowed by ESTRO web site (http://www.estro.be). CONCLUSIONS: TIGER provides an interactive human anatomy cross-sectional oriented source to facilitate the interpretation of CT scan images usually contoured in daily practice. It offers a drill tool to facilitate the learning of a reproducible contouring procedure.

Databases as Topic↗
PubMed1996

A simple computer based system to analyze Morris water maze trials on-line.

The development of a system for the acquisition, analysis and storage of data from open-field water-maze procedures in which rats learn to escape from water onto a hidden platform is described. The use of an object-oriented programming language simplifies the programming of the application and provides scientists without formal training in computer programming the ability to create their own software application. The core hardware is an IBM-compatible AT 486 computer and a video capture board. The Microsoft Windows compatible software is written in G (LabVIEW) and presents the user a graphically based 'virtual instrument' thus simulating functions of real instruments which can be interactively accessed. The graphical approach allows the programmer to make fast and simple adaptations of the software to suit the specific experimental problem. Image analysis software tools (Concept V.i) were integrated into this system which has been used successfully for over 2 years in our lab.

Animals↗