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At least 595 records · Page 33Linked to original sources
PubMed1997

Simulated surgery on computed tomography and magnetic resonance images: an aid for intraoperative radiotherapy.

Intraoperative radiotherapy (IORT) is a relatively new technique in which irradiation with electrons is performed during an open surgery procedure. This approach poses significant problems in obtaining accurate dosimetry, since neither the pre- nor the postoperative patient images actually matches the irradiation field. Our objective was to implement a software tool able to provide an estimate of the dose distribution, overcoming the problem of the geometrical mismatch between the images and the surgical field during the irradiation. The program was developed in the C programming language, on a noncommercial version of a Philips EasyVision workstation. The application allows to create a new data set by manipulating the preoperative computed tomography and magnetic resonance images in order to simulate the final geometry of the surgical area during the IORT procedure. The exact dose distribution can then be calculated by transferring these new images to a standard radiotherapy planning system. Also an approximate dose distribution can be quickly displayed by superimposing isodose curves obtained from a water phantom. The proposed approach introduces a helpful tool for dosimetry and planning in IORT protocols, improving their accuracy and safety and allowing for more objective quality control and patient follow-up.

Brain Neoplasms↗
PubMed2002

Prediction of intestinal absorption: comparative assessment of GASTROPLUS and IDEA.

We have assessed two commercial software tools employing physiologically based models for prediction of intestinal absorption in human. IDEA 2.0 and GASTROPLUS 3.1.0 were compared both in their ability to predict fraction absorbed for a set of 28 drugs and in terms of the functionality offered. The emphasis was placed on the practical usefulness to pharmaceutical drug discovery. Predictions were assessed for three levels of input data (i) pure in silico input, (ii) thermodynamic solubility and in silico permeability, (iii) thermodynamic solubility and human colon carcinoma cell line (CACO-2) permeability. We found the pure in silico prediction ability of the tools to be comparable with 70% correct classification rate. With measured input data the IDEA prediction rate improved to 79% while GASTROPLUS stayed at 70%. In terms of functionality GASTROPLUS is a powerful system for the trained user. Open access to model parameters, diagnostic tools and the ability to integrate data make it particularly suitable for the later stages of discovery and development. IDEA is web based and presents a simple interface suitable for widespread use with minimal training. However the limited functionality and inconvenient handling of multiple compound batches currently restrict the usefulness of version 2.0 for drug discovery.

Intestinal Absorption↗
PubMed2001

Graphical treatment simulation and automated collision detection for conformal and stereotactic radiotherapy treatment planning.

The purpose of this work is to develop a "room's eye view" graphical simulation program with an automated collision detection option, to assist a treatment planning user to visualize the treatment setup checking at the same time the feasibility of his plan. The program simulates the treatment process using accurate three-dimensional graphical models of the gantry, table, and that of an average patient. This allows the use of any mechanical movement concerning the radiotherapy unit. The simulation of the mechanical movements and their limitations are according to IEC standards and thus compatible with any radiotherapy machine. Graphical methods for collision detection between the models guarantee speed and accuracy. The module simulates the treatment setup with accuracy better than 2 degrees for any tested case. When a collision takes place a warning message is displayed. In this paper a software tool is developed that can be used as a stand-alone program or embedded in any treatment planning system. The visualization of the treatment fields prior to treatment permits the geometric feasibility of the plan, thus adding one more step toward the automation of the treatment process.

Computer Simulation↗
PubMed2004

SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.

We developed a software tool (SlidingBayes) for recombination analysis based on Bayesian phylogenetic inference. Sliding-Bayes provides a powerful approach for detecting potential recombination, especially between highly divergent sequences and complex HIV-1 recombinants for which simpler methods like neighbor joining (NJ) may be less powerful. SlidingBayes guides Markov Chain Monte Carlo (MCMC) sampling performed by MrBayes in a sliding window across the alignment (Bayesian scanning). The tool can be used for nucleotide and amino acid sequences and combines all the modeling possibilities of MrBayes with the ability to plot the posterior probability support for clustering of various combinations of taxa.

Algorithms↗
PubMedDate not supplied

Context trees: representing co-operative healthcare activities in IREP.

The IREP Project is based on the concept of 'rehabilitation programme' (LLP--Life Long Programme). It consists in a global vision of the patient's therapeutic-rehabilitative path, that is realised by the description, selection, adaptation and evaluation of generalised protocols. This paper discusses the issues arising in the definition of multidisciplinary rehabilitation programmes involving the co-operation of independent teams. A methodology to formalise and collect descriptions of programmes is presented. A programme is considered as a set of interconnected activities, represented as a graph of Activity Modules, organised in Context Trees; the resulting structured representation is the framework to implement timely and effective communication services in a global information system on rehabilitation. Based on this experience, a set of possible requirements for software tools to formalise and manage programmes have been suggested; it was the basis for the realisation of a first prototype under field test in a rehabilitation environment by other partners of the IREP Project.

Decision Support Techniques↗
PubMed2004

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.

STRIDE is a software tool for secondary structure assignment from atomic resolution protein structures. It implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations. The STRIDE web server provides access to this tool and allows visualization of the secondary structure, as well as contact and Ramachandran maps for any file uploaded by the user with atomic coordinates in the Protein Data Bank (PDB) format. A searchable database of STRIDE assignments for the latest PDB release is also provided. The STRIDE server is accessible from http://webclu.bio.wzw.tum.de/stride/.

Databases, Protein↗
PubMed2001

Supporting medical decisions with vector decision trees.

The article presents the extension of a common decision tree concept to a multidimensional - vector - decision tree constructed with the help of evolutionary techniques. In contrary to the common decision tree the vector decision tree can make more than just one suggestion per input sample. It has the functionality of many separate decision trees acting on a same set of training data and answering different questions. Vector decision tree is therefore simple in its form, is easy to use and analyse and can express some relationships between decisions not visible before. To explore and test the possibilities of this concept we developed a software tool--DecRain--for building vector decision trees using the ideas of evolutionary computing. Generated vector decision trees showed good results in comparison to classical decision trees. The concept of vector decision trees can be safely and effectively used in any decision making process.

Algorithms↗
PubMed1995

Exploration and virtual experimentation in a local neuroscience database.

Work is currently being done by a number of groups to investigate the possibility of creating one or more neuroscience databases. These databases could provide: (1) a means for conveying complete descriptions of experiments; (2) a platform for virtual experiments; (3) and an interface where modeling and experimental results could be exchanged. This paper describes work towards creating a local database with these capabilities by creating a set of experimental neurophysiology software tools that are tied to a database of experiment descriptions via external scripting mechanisms. These tools provide a means of exploring results and data that can lead to insights into the data that suggest new avenues of research. Because the scriptability of the tools allows for automation of re-analysis of the data, virtual experiments for testing new hypotheses over large datasets becomes possible. Such virtual experiments are particularly relevant to computational neuroscience, as they allow hypotheses generated by models to be immediately tested without further collection of experimental data.

Animals↗
PubMed2006

A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria.

We devised software tools to systematically investigate the contents and contexts of bacterial tRNA and tmRNA genes, which are known insertion hotspots for genomic islands (GIs). The strategy, based on MAUVE-facilitated multigenome comparisons, was used to examine 87 Escherichia coli MG1655 tRNA and tmRNA genes and their orthologues in E.coli EDL933, E.coli CFT073 and Shigella flexneri Sf301. Our approach identified 49 GIs occupying approximately 1.7 Mb that mapped to 18 tRNA genes, missing 2 but identifying a further 30 GIs as compared with Islander [Y. Mantri and K. P. Williams (2004), Nucleic Acids Res., 32, D55-D58]. All these GIs had many strain-specific CDS, anomalous GC contents and/or significant dinucleotide biases, consistent with foreign origins. Our analysis demonstrated marked conservation of sequences flanking both empty tRNA sites and tRNA-associated GIs across all four genomes. Remarkably, there were only 2 upstream and 5 downstream deletions adjacent to the 328 loci investigated. In silico PCR analysis based on conserved flanking regions was also used to interrogate hotspots in another eight completely or partially sequenced E.coli and Shigella genomes. The tools developed are ideal for the analysis of other bacterial species and will lead to in silico and experimental discovery of new genomic islands.

Computational Biology↗
PubMed2005

Dizzy: stochastic simulation of large-scale genetic regulatory networks.

We describe Dizzy, a software tool for stochastically and deterministically modeling the spatially homogeneous kinetics of integrated large-scale genetic, metabolic, and signaling networks. Notable features include a modular simulation framework, reusable modeling elements, complex kinetic rate laws, multi-step reaction processes, steady-state noise estimation, and spatial compartmentalization.

Algorithms↗
PubMed2006

Automated quantification tool for high-throughput proteomics using stable isotope labeling and LC-MSn.

LC-MSn has become a popular option for high-throughput quantitative proteomics, thanks to the availability of stable-isotope labeling reagents. However, the vast quantity of data generated from LC-MSn continues to make the postacquisition quantification analyses challenging, especially in experiments involving multiple samples per experimental condition. To facilitate data analysis, we developed a computer program, QUIL, for automated protein quantification. QUIL accounts for the dynamic nature of spectral background and subtracts this background accordingly during ion chromatogram reconstruction. For elution profile identification, QUIL minimizes the inclusion of coeluted neighbor peaks, yet tolerates imperfect peak shapes. Outlier-resistant methods have been implemented for better protein ratio estimation. The utility of QUIL was validated by quantitative analyses of a standard protein as well as complex protein mixtures, which were labeled with cICAT or 18O and analyzed using LCQ, LTQ, or FT-ICR instruments. For samples that no prior knowledge of relative protein quantities was available, Western blotting was performed for confirmation. For the standard protein, the coefficient of variation (CV) of peptide ratio estimation was 6%. For complex mixtures, the median CV for protein ratio calculations was less than 10%. Computed protein abundance ratios exhibited a relatively high degree of correlation with those obtained from Western blot analyses. Compared with a widely used commercial software tool, QUIL showed improvement in ion chromatogram construction and peak integration and significantly reduced relative errors in abundance ratio assessment.

Animals↗
PubMed2002

"Soap-Bubble" visualization and quantitative analysis of 3D coronary magnetic resonance angiograms.

In order to compare coronary magnetic resonance angiography (MRA) data obtained with different scanning methodologies, adequate visualization and presentation of the coronary MRA data need to be ensured. Furthermore, an objective quantitative comparison between images acquired with different scanning methods is desirable. To address this need, a software tool ("Soap-Bubble") that facilitates visualization and quantitative comparison of 3D volume targeted coronary MRA data was developed. In the present implementation, the user interactively specifies a curved subvolume (enclosed in the 3D coronary MRA data set) that closely encompasses the coronary arterial segments. With a 3D Delaunay triangulation and a parallel projection, this enables the simultaneous display of multiple coronary segments in one 2D representation. For objective quantitative analysis, frequently explored quantitative parameters such as signal-to-noise ratio (SNR); contrast-to-noise ratio (CNR); and vessel length, sharpness, and diameter can be assessed. The present tool supports visualization and objective, quantitative comparisons of coronary MRA data obtained with different scanning methods. The first results obtained in healthy adults and in patients with coronary artery disease are presented.

Adult↗
PubMed2006

Systems biology as a foundation for genome-scale synthetic biology.

As the ambitions of synthetic biology approach genome-scale engineering, comprehensive characterization of cellular systems is required, as well as a means to accurately model cell-scale molecular interactions. These requirements are coincident with the goals of systems biology and, thus, systems biology will become the foundation for genome-scale synthetic biology. Systems biology will form this foundation through its efforts to reconstruct and integrate cellular systems, develop the mathematics, theory and software tools for the accurate modeling of these integrated systems, and through evolutionary mechanisms. As genome-scale synthetic biology is so enabled, it will prove to be a positive feedback driver of systems biology by exposing and forcing researchers to confront those aspects of systems biology which are inadequately understood.

Biology↗
PubMed2004

Genomic data visualization on the Web.

UNLABELLED: Many types of genomic data can be represented in matrix format, with rows corresponding to genes and columns corresponding to gene features. The heat map is a popular technique for visualizing such data, plotting the data on a two-dimensional grid and using a color scale to represent the magnitude of each matrix entry. Prism is a Web-based software tool for generating annotated heat map visualizations of genome-wide data quickly. The tool provides a selection of genome-specific annotation catalogs as well as a catalog upload capability. The heat maps generated are clickable, allowing the user to drill down to examine specific matrix entries, and gene annotations are linked to relevant genomic databases. AVAILABILITY: http://noble.gs.washington.edu/prism

Computer Graphics↗
PubMed1997

3D reconstruction of prostate from ultrasound images.

The aim of our study was to obtain a 3D model of the prostate from the ultrasound images and to represent it and calculate its volume. The establishing of prostate volume represents a necessary stage in choosing the method of solving prostate adenoma. The evaluation of the prostate volume can be done by transabdominal or endorectal echography. If the second method is not available it is necessary to use the echographic estimation of the volume of the prostate adenoma by suprapubian examination. This method lacks precision. In order to have a more accurate calculation of the prostate's volume than the ellipsoid approximation given by the echographic equipment, we designed a software tool for handling and management of digital images. The primary information is composed of two 2D digital images obtained by digitising the frames acquired from an 3.5 MHz ultrasound equipment for two incidences: sagittal and transversal. The bitmaps were filtered to reduce the noise and a contour detection algorithm was used. Further, the new 2D detected contours were processed with the help of an interactive image editor toward a 3D reconstruction of the prostate. The examiner can perform rotations and translations on the 2D projections and can adjust the angle between them. The resulting object (the 3D model of the prostate) was adjusted accordingly and its volume was displayed. The software was implemented on a PC system and was used in the Urology Clinic for several cases. It has been shown that, compared with the value provided by the approximation of the echographic equipment, a more accurate value of the volume of the prostate was obtained.

Algorithms↗
PubMed2003

Detecting spatial patterns in biological array experiments.

Chemical genetic screening and DNA and protein microarrays are among a number of increasingly important and widely used biological research tools that involve large numbers of parallel experiments arranged in a spatial array. It is often difficult to ensure that uniform experimental conditions are present throughout the entire array, and as a result, one often observes systematic spatially correlated errors, especially when array experiments are performed using robots. Here, the authors apply techniques based on the discrete Fourier transform to identify and quantify spatially correlated errors superimposed on a spatially random background. They demonstrate that these techniques are effective in identifying common spatially systematic errors in high-throughput 384-well microplate assay data. In addition, the authors employ a statistical test to allow for automatic detection of such errors. Software tools for using this approach are provided.

Analysis of Variance↗
PubMedDate not supplied

The use of computer based structure-activity relationships in the risk assessment of industrial chemicals.

The concept of a two-step approach toward the assessment of toxicity endpoints for a chemical is proposed. The first step involves the selection of chemical analogues for which toxicity data is available in a noncongeneric database. The next step is the derivation of a Quantitative Structure-Activity Relationship (QSAR) for the chemical domain, predetermined by the selection rules. The software tools needed for the computer implementation of such an approach are summarized. By making use of them, we have derived aquatic toxicity QSARs, of which two are given as example. The latter pertain to chemicals that have been automatically extracted from noncongeneric databases, after defining the substructure recognition rules implied by the putative mechanism of toxicity.

Animals↗
PubMed2006

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis.

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein-structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at www.migenas.org (click 'Start Toolkit').

Animals↗