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At least 217 records · Page 12Linked to original sources
PubMed2006

Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose-volume outcome relationships.

Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

Computer Simulation↗
PubMed2004

Three-dimensional visualization of neurovascular relationships in the posterior fossa: technique and clinical application.

OBJECT: The goal of this study was to describe the authors' technique for three-dimensional (3D) visualization of neurovascular relationships in the posterior fossa at the surface of the brainstem. This technique is based on the processing of high-resolution magnetic resonance (MR) imaging data. The principles and technical details involved in the accurate simultaneous visualization of vessels and cranial nerves as tiny structures are presented using explicit and implicit segmentation as well as volume rendering. METHODS: In this approach 3D MR constructive interference in steady state imaging data served as the source for image processing, which was performed using the Linux-based software tools SegMed for segmentation and Qvis for volume rendering. A sequence of filtering operations (including noise reduction and closing) and other software tools such as volume growing are used for a semiautomatic coarse segmentation. The subsequent 3D visualization in which implicit segmentation is used for the differentiation of cranial nerves, vessels, and brainstem is achieved by allocating opacity and color values and adjusting the related transfer functions. This method was applied to the presurgical evaluation in a consecutive series of 55 patients with neurovascular compression syndromes and the results were correlated to surgical findings. The potential for its use, further developments, and remaining problems are discussed. CONCLUSIONS: This method provides an excellent intraoperative real-time virtual view of difficult anatomical relationships.

Brain Stem↗
PubMed2006

The Gaggle: an open-source software system for integrating bioinformatics software and data sources.

BACKGROUND: Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing. RESULTS: In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment. We demonstrate that four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools. CONCLUSION: We have integrated diverse databases (for example, KEGG, BioCyc, String) and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer). Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and Pubmed abstracts (STRING web resource), creating an exploratory environment useful to 'web browser and spreadsheet biologists', to statistically savvy computational biologists, and those in between. The Gaggle uses Java RMI and Java Web Start technologies and can be found at http://gaggle.systemsbiology.net.

Computational Biology↗
PubMed2003

Construction of patient-specific surface models from MR images: application to bioelectromagnetism.

Patient-specific geometric models are needed in many engineering problems. This work reports a novel software tool developed to construct individualized triangulated surface models from MR images. The program consists of three main parts: segmentation, triangulation and registration. The software tool was developed under the UNIX operating system. The application area demonstrated in this work is bioelectromagnetism but the program can be used as well in other engineering problems. The tool has been successfully applied in numerous cases, both for the thorax and the head.

Algorithms↗
PubMed1993

Development of intelligent design associates: a case study.

A number of human factors data sets provides guidelines and recommendations for the system design process. Much of this information is available to the human factors engineer in design handbooks, textbooks, and periodicals. While human factors design information is both available and abundant, it is not necessarily readily accessible or in a format that is easily assimilated into a particular design scenario. This paper discusses the feasibility of incorporating human factors design data into intelligent, knowledge-based systems referred to as design associates. Successful implementation of any design associate is dependent upon two key issues: conversion of human factors data into a valid knowledge base, and overcoming the knowledge representation constraints imposed by an intelligent software tool. Detailed results of a recent effort to address these issues, and subsequently implement a design associate on a commercially available intelligent software tool, are presented. This particular associate, implemented in a rule-based tool environment, aids in the selection of visual display technologies.

Journal Article↗
PubMed2003

TPL-KATS-card sort: a tool for assessing structural knowledge.

The study of how individuals organize knowledge has been a popular endeavor for several decades. As a result, techniques have been developed to assess how individuals represent and organize knowledge internally. Although several conceptual knowledge elicitation methods have been developed and used to assess the organization of knowledge, their use is often labor intensive and time consuming. Presented here is a software tool that was developed to reduce the problems associated with manually administering the conceptual knowledge elicitation technique, or card sorting. The TPL-KATS-card sort software not only simplifies the administration of the task, but also adds features to the card-sorting task such as media insertion, time stamping, and instructorless administration. In the present article, an introduction to the card-sorting technique is provided, the new software tool is described, and the advantages of the software are detailed.

Concept Formation↗
PubMed2005

Toward supportive data collection tools for plant metabolomics.

Over recent years, a number of initiatives have proposed standard reporting guidelines for functional genomics experiments. Associated with these are data models that may be used as the basis of the design of software tools that store and transmit experiment data in standard formats. Central to the success of such data handling tools is their usability. Successful data handling tools are expected to yield benefits in time saving and in quality assurance. Here, we describe the collection of datasets that conform to the recently proposed data model for plant metabolomics known as ArMet (architecture for metabolomics) and illustrate a number of approaches to robust data collection that have been developed in collaboration between software engineers and biologists. These examples also serve to validate ArMet from the data collection perspective by demonstrating that a range of software tools, supporting data recording and data upload to central databases, can be built using the data model as the basis of their design.

Arabidopsis↗
PubMed2000

MuStaR and other software for locus-specific mutation databases.

As the human genome sequencing project nears completion, there has been a vast increase in the rate at which disease and nondisease associated variant sequences are being sought and detected. This has heightened the need for software with which to accumulate allelic variant (mutation) data, and with which to make the data accessible to the scientific community. Many ad hoc solutions have been developed by those interested in specific genes and diseases, and the creation of central databases which hold data for all genes has provided an alternative repository for some of the locus data. Despite this, few specialised software tools exist for researchers to create their own locus-specific allelic variant databases. This article describes methods available to potential curators, including software systems developed with the sole purpose of generating locus-specific mutation databases. In particular, the authors' own software, MuStaRtrade mark, is described. MuStaRtrade mark allows curators to maintain a database on a laptop computer if desired, while being able to export the data to an automatically generated Website which will run on any cgi compliant Web server. Searching the database and the submission of new mutations are made possible through fill-in Web forms. A number of other software tools which may be of use to curators are also described.

Chromosome Mapping↗
PubMed2003

The development of a theoretical framework and design tool for process usability assessment.

The purpose of usability engineering is to facilitate the deployment of new products by decreasing development costs and improving the quality of systems. This paper will discuss the development and delivery of a unique, theoretically based software tool that provides engineers and designers with easy access to the most recent advances in human-machine interface design. This research combines several theoretical views of the interaction process into a hybrid model. Based on this model, a software tool was produced that allows engineers to model the human interaction process within their design. The system then provides feedback on the interaction process through items such as: the amount of mental effort required by a user, the degree to which the system conforms to human capabilities, the expected time to complete the interaction, where potential human error may occur, as well as potential misunderstandings or points of confusion to the users. The designer may then use this information to improve the design of the system. Validation of this technique indicates that the hybrid model produces accurate predictions of usability attributes and that the technique transfers from the laboratory to the real world.

Adult↗
PubMed2004

HeiDATAProVIT-Heidelberg data archiving, tag assembling, processing and visualization tool.

The demands that have to be met by software tools for biomedical data evaluation strongly differ depending on the background of their application. In clinical routine emphasis is placed on ease of handling and application of standardized procedures, whereas in biomedical research the main focus lies on flexibility and extensibility. These contradictory requirements are reflected by the design principles of existing software solutions: programs for routine application are barely extensible or modifiable by the user and the complexity of highly flexible data processing tools for research purposes hampers the application of new methods to larger data volumes. This gap poses technical difficulties to the transfer of methods from research into clinical routine. The software we present in this paper bridges this discrepancy by incorporating two different levels of application. The lower level offers options to integrate custom written MATLAB((R)) processing routines and to add new evaluation schemes to a pool of existing procedures. The higher level allows for performing standard evaluations by accessing and applying these previously defined procedures. Four basic concepts were introduced to ensure that the program is both maximally flexible on a lower level and readily applicable on a higher level: the tag concept, the concept of modularized visualization, the dummy file concept, and the batchjob concept. These concepts are the key to flexibly assemble and apply the three universal stages of data evaluation: (1) archiving of acquired data, (2) processing the data using signal processing algorithms and (3) visualizing the results in appropriate graphical formats. The present paper illustrates the four concepts within the two levels of the software architecture. The basic functionality and usefulness of the program are demonstrated using an evaluation of gait analysis data as sample application. In summary, this software tool closely integrates a database for biomedical datasets and an extensible pool of evaluation and visualization procedures realized using MATLAB((R)). It is well suited both for data processing in clinical routine and for evaluation of measurement data in any medical research project.

Information Storage and Retrieval↗
PubMed1998

The integration of a novice user interface into a professional modeling tool.

This paper describes a software tool, the Oncology Thinking Cap (OncoTCAP) and reports on our efforts to develop a novice user interface to simplify the task of describing biological models of cancer and its treatment. Oncology Thinking Cap includes a modeling tool for making relationships explicit and provide dynamic feedback about the interaction between cancer cell kinetics, treatments, and patient outcomes. OncoTCAP supports student learning by making normally invisible processes visible and providing a representational tool that can be used to conduct thought experiments. We also describe our novice interface and report the results of initial usability testing.

Cell Cycle↗
PubMed2006

Simulation studies of field shaping in rotational radiation therapy.

This article presents simulation studies of field shaping in rotational radiation therapy by means of two categories of beam modifying devices: protectors and shapers. The protectors used are diminished copies of the organs at risk (OARs) and stay parallel to them during gantry rotation. Thus, each protector always keeps the corresponding OAR in its shadow, significantly reducing the irradiation. The shapers are used in order to obtain a more uniform dose distribution in the planning target volume (PTV) while preserving their initial orientation during gantry rotation. Thus, the use of beam modifying devices allows modulation of the beam intensity, to better fit irradiation requirements, at every gantry position. A software tool for calculations of geometrical position and dimensions of the beam modifying devices, using information about the shape, size, and position of the protected organ or area at risk as input, was developed. This tool was integrated into the in-house-developed Monte Carlo radiation therapy simulator (MCRTS), used to simulate the particle transport through the designed system. The verification of the software tool showed good agreement between experimental and simulation data, with discrepancies of less than 3%. Dose distributions in solid-geometry and voxel-based neck models were evaluated. Furthermore, the effectiveness of the shapers to modify the dose distribution outside the protected area was studied. Results demonstrated that the use of the shapers effectively improves dose uniformity. Studies using shapers of different materials were also carried out and resulted in similar dose distributions. The results of the simulation studies with a voxel-based model showed that rotational therapy with beam modifying devices offers adequate protection of the OAR and a uniform dose distribution outside the protected region.

Algorithms↗
PubMed2001

Molecular Biocomputing Suite: a word processor add-in for the analysis and manipulation of nucleic acid and protein sequence data.

In all fields of molecular biology, researchers are increasingly challenged by experiments planned and evaluated on the basis of nucleic acid and protein sequence data generally retrieved from public databases. Despite the wide spectrum of available Web-based software tools for sequence analysis, the routine use of these tools has disadvantages, particularly because of the elaborate and heterogeneous ways of data input, output, and storage. Here we present a Visual Basic-encoded Microsoft Word Add-In, the Molecular BioComputing Suite (MBCS), available at the BioTechniques Software Library (www.BioTechniques.com). The MBCS software aims to manage and expedite a wide range of sequence analyses and manipulations using an integrated text editor environment including menu-guided commands. Its independence of sequence formats enables MBCS to be used as a pivotal application between other software tools for sequence analysis, manipulation, annotation, and editing.

Amino Acid Sequence↗
PubMed2004

GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes.

BACKGROUND: An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes. It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb. RESULTS: GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database. It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes. Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools. This can be displayed at the protein level using GeneOrder3.0. Whole genome alignments of genes are presented in both a table and a dot plot. This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences. CONCLUSIONS: GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly." AVAILABILITY: http://binf.gmu.edu/genometools.html and http://pasteur.atcc.org:8050/GeneOrder3.0.

Chromosome Mapping↗
PubMed2003

3D CT modeling of hepatic vessel architecture and volume calculation in living donated liver transplantation.

The aim of this study was to evaluate a software tool for non-invasive preoperative volumetric assessment of potential donors in living donated liver transplantation (LDLT). Biphasic helical CT was performed in 56 potential donors. Data sets were post-processed using a non-commercial software tool for segmentation, volumetric analysis and visualisation of liver segments. Semi-automatic definition of liver margins allowed the segmentation of parenchyma. Hepatic vessels were delineated using a region-growing algorithm with automatically determined thresholds. Volumes and shapes of liver segments were calculated automatically based on individual portal-venous branches. Results were visualised three-dimensionally and statistically compared with conventional volumetry and the intraoperative findings in 27 transplanted cases. Image processing was easy to perform within 23 min. Of the 56 potential donors, 27 were excluded from LDLT because of inappropriate liver parenchyma or vascular architecture. Two recipients were not transplanted due to poor clinical conditions. In the 27 transplanted cases, preoperatively visualised vessels were confirmed, and only one undetected accessory hepatic vein was revealed. Calculated graft volumes were 1110 +/- 180 ml for right lobes, 820 ml for the left lobe and 270 +/- 30 ml for segments II+III. The calculated volumes and intraoperatively measured graft volumes correlated significantly. No significant differences between the presented automatic volumetry and the conventional volumetry were observed. A novel image processing technique was evaluated which allows a semi-automatic volume calculation and 3D visualisation of the different liver segments.

Adult↗
PubMed1999

The development cycle of a pharmaceutical discovery chemi-informatics system.

The rate at which we now produce, test, and warehouse new compound structures in the Discovery process strains our ability to evaluate and comprehend the information that results [Fayyad U. Database Programming and Design 1998;11(3):24]. With the advent of robotic systems and specialized software tools, the profusion of data yielded by the pharmaceutical discovery process is testing the manageability and usefulness of the information resource. Clearly, the challenge faced by Discovery today lies not in the generation of data, but in the generation of software tools that provide the means to store, extract, analyze, and display the data contained within the this expanding resource, and thereby meet the needs of the disciplines participating in the Discovery process. In this review a schematic of a chemi-informatics system, that aids our adaptation to the evolving Discovery process and the expanded flow of pharmaceutical data, is discussed.

Database Management Systems↗
PubMed2004

An architecture for biological information extraction and representation.

MOTIVATIONS: Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data. RESULTS: In this paper, we present a general architecture, called ALFA, for information extraction and representation from diverse biological data. The ALFA architecture consists of: (i) a networked, hierarchical, hyper-graph object model for representing information from heterogeneous data sources in a standardized, structured format; and (ii) a suite of integrated, interactive software tools for information extraction and representation from diverse biological data sources. As part of our research efforts to explore this space, we have currently prototyped the ALFA object model and a set of interactive software tools for searching, filtering, and extracting information from scientific text. In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation, and representation of information from scientific text. We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation. CONTACT: aditya_vailaya@agilent.com.

Abstracting and Indexing↗