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PubMedDate not supplied

A CD-ROM prototype of a multimedia-based interactive tool and guide, to perform quality control tests for the computed tomography scanners.

Quality control tests for CT scanners are very important for correct machine performance, and for the radiation protection of patients and medical personnel. As proliferation of CT scanners continues, the need for distributable software tools to perform quality control tests becomes evident. A multimedia tool and guide will help medical physicists and technologists to perform these tests easily and correctly. The guide can be easily accessible in CD-ROM, or networked on the Internet. The user, medical physicist or technologist, can find in the present guide the pertinent theoretical information and the procedures necessary to perform the quality control tests, with the help of texts, CT images and photographs, narration and video. The results of the tests are automatically compared with machine specifications and acceptable values set by international bodies, and are stored in a table.

CD-ROM↗
PubMed2005

MILVA: an interactive tool for the exploration of multidimensional microarray data.

MOTIVATION: Clustering techniques such as k-means and hierarchical clustering are commonly used to analyze DNA microarray derived gene expression data. However, the interactions between processes underlying the cell activity suggest that the complexity of the microarray data structure may not be fully represented with discrete clustering methods. RESULTS: A newly developed software tool called MILVA (microarray latent visualization and analysis) is presented here to investigate microarray data without separating gene expression profiles into discrete classes. The underpinning of the MILVA software is the two-dimensional topographic representation of multidimensional microarray data. On this basis, the interactive MILVA functions allow a continuous exploration of microarray data driven by the direct supervision of the biologist in detecting activity patterns of co-regulated genes. AVAILABILITY: The MILVA software is freely available. The software and the related documentation can be downloaded from http://www.ncrg.aston.ac.uk/Projects/milva. User 'surrey' as username and '3245' as password to login. The software is currently available for Windows platform only.

Cluster Analysis↗
PubMedDate not supplied

Data visualization during the early stages of drug discovery.

Multidimensional compound optimization is a new paradigm in the drug discovery process, yielding efficiencies during early stages and reducing attrition in the later stages of drug development. The success of this strategy relies heavily on understanding this multidimensional data and extracting useful information from it. This paper demonstrates how principled visualization algorithms can be used to understand and explore a large data set created in the early stages of drug discovery. The experiments presented are performed on a real-world data set comprising biological activity data and some whole-molecular physicochemical properties. Data visualization is a popular way of presenting complex data in a simpler form. We have applied powerful principled visualization methods, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), to help the domain experts (screening scientists, chemists, biologists, etc.) understand and draw meaningful decisions. We also benchmark these principled methods against relatively better known visualization approaches, principal component analysis (PCA), Sammon's mapping, and self-organizing maps (SOMs), to demonstrate their enhanced power to help the user visualize the large multidimensional data sets one has to deal with during the early stages of the drug discovery process. The results reported clearly show that the GTM and HGTM algorithms allow the user to cluster active compounds for different targets and understand them better than the benchmarks. An interactive software tool supporting these visualization algorithms was provided to the domain experts. The tool facilitates the domain experts by exploration of the projection obtained from the visualization algorithms providing facilities such as parallel coordinate plots, magnification factors, directional curvatures, and integration with industry standard software.

Drug Design↗
PubMed1998

The bio-objects project. Part I: the object data model core elements.

MOTIVATION: Scientific data reside in a number of different data sources, both public and commercial, and are accessible through various software applications. Data and software interoperability is becoming a critical issue in the research community. In our opinion, the need to develop a unified object model for biotechnology must be recognized. Herein, we present a prototype and core elements for the Object Data Model, a central part of our future commercial product development. RESULTS: We have designed a first layer of the Object Data Model that will be used for further commercial application development. The CBioBase object was designed as a citable, stable and core data element for the Object Data Model. General relationships between objects and application components were established. AVAILABILITY: Software tools will be provided with a future DNASIS product to access various elements of the Object Model. We are planning to assemble C++ libraries and Java binary files into BioObjects SDK (software development kit) for those interested in software implementation using the described object model. CONTACT: smaltch@msn.com or smaltch@hitachi-soft.com

Biotechnology↗
PubMed2006

inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons.

BACKGROUND: Systematic genome comparisons are an important tool to reveal gene functions, pathogenic features, metabolic pathways and genome evolution in the era of post-genomics. Furthermore, such comparisons provide important clues for vaccines and drug development. Existing genome comparison software often lacks accurate information on orthologs, the function of similar genes identified and genome-wide reports and lists on specific functions. All these features and further analyses are provided here in the context of a modular software tool "inGeno" written in Java with Biojava subroutines. RESULTS: InGeno provides a user-friendly interactive visualization platform for sequence comparisons (comprehensive reciprocal protein--protein comparisons) between complete genome sequences and all associated annotations and features. The comparison data can be acquired from several different sequence analysis programs in flexible formats. Automatic dot-plot analysis includes output reduction, filtering, ortholog testing and linear regression, followed by smart clustering (local collinear blocks; LCBs) to reveal similar genome regions. Further, the system provides genome alignment and visualization editor, collinear relationships and strain-specific islands. Specific annotations and functions are parsed, recognized, clustered, logically concatenated and visualized and summarized in reports. CONCLUSION: As shown in this study, inGeno can be applied to study and compare in particular prokaryotic genomes against each other (gram positive and negative as well as close and more distantly related species) and has been proven to be sensitive and accurate. This modular software is user-friendly and easily accommodates new routines to meet specific user-defined requirements.

Base Sequence↗
PubMed2002

Pathfinder and other tools for analyzing signal transduction networks.

Many electronic design tools are, at their core, tools for analyzing interacting networks of components in which there is a definite causal sense of direction in each interaction: outputs affect inputs, but not vice versa. Simplifying or restricting a network of protein interactions so that this kind of directedness holds makes the same category of software tools applicable. In signal transduction cascades the direction is usually given by "kinase phosphorylates substrate." This paper examines a few kinds of directed network analysis tools in the context of signal transduction.

Algorithms↗
PubMed2004

Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations.

The stability of standard gene expression is an elementary prerequisite for internal standardisation of target gene expression data and many so called housekeeping genes with assumed stable expression can exhibit either up- or down-regulation under some experimental conditions. The developed, and herein presented, software called BestKeeper determines the best suited standards, out of ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment. All data processing is based on crossing points. The BestKeeper software tool was validated on four housekeeping genes and 10 members of the somatotropic axis differentially expressed in bovine corpora lutea total RNA. The BestKeeper application and necessary information about data processing and handling can be downloaded on http://www.wzw.tum.de/gene-quantification/bestkeeper.html.

Animals↗
PubMed1992

Mouse liver protein database: a catalog of proteins detected by two-dimensional gel electrophoresis.

Alterations in the abundance or structure of mouse liver proteins are being studied using two-dimensional gel electrophoresis (2-DE) to build a database of protein changes correlating with exposure to ionizing radiation or toxic chemicals. Thus far, studies have included the analysis of proteins from the offspring of exposed parents or from the exposed individuals themselves. In order to characterize and identify proteins found altered by such exposures, sex- and strain-related differences in protein patterns have been analyzed, and the subcellular locations of a large portion of the mapped proteins have been determined. As part of these studies, data are collected and stored using a variety of computer hardware and software tools that allow the accumulation of information on the origin of samples, gel identification, experiment description, and protein similarities and differences. This accumulation of information constitutes the mouse liver protein database. Relational database software is used to tie the different facets of the database together so that the results of a variety of experiments can be compared and interrelated. The database optimizes the information obtained from 2-DE gel sets by allowing use of the data for many purposes, including monitoring of gel resolution to ensure the collection of high quality data and correlation of protein effects induced by different agents. This first edition of the Argonne National Laboratory mouse liver protein database lays the foundation for future work and communication that should elucidate the significance of observed protein effects as possible markers of exposure to toxic agents.

Animals↗
PubMed2004

Health and environment information systems for exposure and disease mapping, and risk assessment.

A large number of chemicals are used on a regular basis in modern society. Thousands of new chemicals are added each year, many of which may have toxic properties constituting potential health hazards. Rapid assessment of the risk associated with the use of these chemicals is therefore essential to protect people from exposure to potentially harmful substances. Exposures to chemicals (and physical agents) are typically unevenly distributed geographically as well as temporally. Disease occurrence also shows geographically varying patterns. Geographic information systems (GIS) may be used to produce maps of exposure and/or disease to reveal spatial patterns. Exposure mapping using advanced GIS modeling may enhance exposure assessment in environmental epidemiology studies. Disease maps can be valuable tools in risk assessment to explore changes in disease patterns potentially associated with changes in environmental exposures. Spatial variations in risk and trends related to distance from pollution sources may be studied using software tools such as the Rapid Inquiry Facility, developed by the U.K. Small Area Health Statistics Unit and enhanced in the European Health and Environment Information System project, for an initial quick evaluation of any potential health hazards associated with an environmental pollutant.

Cross-Sectional Studies↗
PubMed1998

New tools and resources for analysing protein structures and their interactions.

The determination of protein structures has furthered our understanding of how various proteins perform their functions. With the large number of structures currently available in the PDB, it is necessary to be able to easily study these proteins in detail. Here new software tools are presented which aim to facilitate this analysis; these include the PDBsum WWW site which provides a summary description of all PDB entries, the programs TOPS and NUCPLOT to plot schematic diagrams representing protein topology and DNA-binding interactions, SAS a WWW-based sequence-analysis tool incorporating structural data, and WWW servers for the analysis of protein-protein interfaces and analyses of over 300 haem-binding proteins.

Amino Acid Sequence↗
PubMed2006

XRate: a fast prototyping, training and annotation tool for phylo-grammars.

BACKGROUND: Recent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists. RESULTS: We have developed an open source software tool, xrate, for working with reversible, irreversible or parametric substitution models combined with stochastic context-free grammars. xrate efficiently estimates maximum-likelihood parameters and phylogenetic trees using a novel "phylo-EM" algorithm that we describe. The grammar is specified in an external configuration file, allowing users to design new grammars, estimate rate parameters from training data and annotate multiple sequence alignments without the need to recompile code from source. We have used xrate to measure codon substitution rates and predict protein and RNA secondary structures. CONCLUSION: Our results demonstrate that xrate estimates biologically meaningful rates and makes predictions whose accuracy is comparable to that of more specialized tools.

Algorithms↗
PubMed2006

Integration of two-dimensional LC-MS with multivariate statistics for comparative analysis of proteomic samples.

LC-MS-based proteomics requires methods with high peak capacity and a high degree of automation, integrated with data-handling tools able to cope with the massive data produced and able to quantitatively compare them. This paper describes an off-line two-dimensional (2D) LC-MS method and its integration with software tools for data preprocessing and multivariate statistical analysis. The 2D LC-MS method was optimized in order to minimize peptide loss prior to sample injection and during the collection step after the first LC dimension, thus minimizing errors from off-column sample handling. The second dimension was run in fully automated mode, injecting onto a nanoscale LC-MS system a series of more than 100 samples, representing fractions collected in the first dimension (8 fractions/sample). As a model study, the method was applied to finding biomarkers for the antiinflammatory properties of zilpaterol, which are coupled to the beta2-adrenergic receptor. Secreted proteomes from U937 macrophages exposed to lipopolysaccharide in the presence or absence of propanolol or zilpaterol were analysed. Multivariate statistical analysis of 2D LC-MS data, based on principal component analysis, and subsequent targeted LC-MS/MS identification of peptides of interest demonstrated the applicability of the approach.

Adrenergic beta-Antagonists↗
PubMed2003

Brain perfusion imaging of a craniopharyngioma by transcranial duplex sonography.

BACKGROUND AND PURPOSE: The aim of this study was to test a new ultrasound software tool to assess pathological perfusion in a brain tumor patient. METHODS: Tissue harmonic imaging (THI) enables an improved depiction of brain morphology, employing nonlinear parenchyma and ultrasound contrast agent (UCA) backscatter information. With specialized software, morphological information can be separated from perfusion information. Both can be superimposed at a preferred mixing ratio in a single image. RESULTS: Using THI and a perfluoropropane-based UCA, a pathologic perfusion pattern described by abnormal perfused areas in the tumor region could be demonstrated. After superimposing morphologic and perfusion information, subtle structural tumor inhomogeneities were depicted. Craniopharyngioma structure and perfusion defect were confirmed by T2-weighted and perfusion-weighted magnetic resonance imaging. CONCLUSION: Transcranial duplex sonography in combination with contrast specific imaging methods might be helpful to visualize perfusion defects without loss of morphological information.

Adult↗
PubMed2004

Implementation of an ADME enabling selection and visualization tool for drug discovery.

The pharmaceutical industry has large investments in compound library enrichment, high throughput biological screening, and biopharmaceutical (ADME) screening. As the number of compounds submitted for in vitro ADME screens increases, data analysis, interpretation, and reporting will become rate limiting in providing ADME-structure-activity relationship information to guide the synthetic strategy for chemical series. To meet these challenges, a software tool was developed and implemented that enables scientists to explore in vitro and in silico ADME and chemistry data in a multidimensional framework. The present work integrates physicochemical and ADME data, encompassing results for Caco-2 permeability, human liver microsomal half-life, rat liver microsomal half-life, kinetic solubility, measured log P, rule of 5 descriptors (molecular weight, hydrogen bond acceptors, hydrogen bond donors, calculated log P), polar surface area, chemical stability, and CYP450 3A4 inhibition. To facilitate interpretation of this data, a semicustomized software solution using Spotfire was designed that allows for multidimensional data analysis and visualization. The solution also enables simultaneous viewing and export of chemical structures with the corresponding ADME properties, enabling a more facile analysis of ADME-structure-activity relationship. In vitro and in silico ADME data were generated for 358 compounds from a series of human immunodeficiency virus protease inhibitors, resulting in a data set of 5370 experimental values which were subsequently analyzed and visualized using the customized Spotfire application. Implementation of this analysis and visualization tool has accelerated the selection of molecules for further development based on optimum ADME characteristics, and provided medicinal chemistry with specific, data driven structural recommendations for improvements in the ADME profile.

Absorption↗
PubMed2003

Poxvirus orthologous clusters: toward defining the minimum essential poxvirus genome.

Increasingly complex bioinformatic analysis is necessitated by the plethora of sequence information currently available. A total of 21 poxvirus genomes have now been completely sequenced and annotated, and many more genomes will be available in the next few years. First, we describe the creation of a database of continuously corrected and updated genome sequences and an easy-to-use and extremely powerful suite of software tools for the analysis of genomes, genes, and proteins. These tools are available free to all researchers and, in most cases, alleviate the need for using multiple Internet sites for analysis. Further, we describe the use of these programs to identify conserved families of genes (poxvirus orthologous clusters) and have named the software suite POCs, which is available at www.poxvirus.org. Using POCs, we have identified a set of 49 absolutely conserved gene families-those which are conserved between the highly diverged families of insect-infecting entomopoxviruses and vertebrate-infecting chordopoxviruses. An additional set of 41 gene families conserved in chordopoxviruses was also identified. Thus, 90 genes are completely conserved in chordopoxviruses and comprise the minimum essential genome, and these will make excellent drug, antibody, vaccine, and detection targets. Finally, we describe the use of these tools to identify necessary annotation and sequencing updates in poxvirus genomes. For example, using POCs, we identified 19 genes that were widely conserved in poxviruses but missing from the vaccinia virus strain Tian Tan 1998 GenBank file. We have reannotated and resequenced fragments of this genome and verified that these genes are conserved in Tian Tan. The results for poxvirus genes and genomes are discussed in light of evolutionary processes.

Amino Acid Sequence↗
PubMedDate not supplied

[Bioinformatics and GenEnv database in biological risk management].

Identification and molecular typing of environmental isolates by molecular techniques requires knowledge of the genetic characteristics of the microbe species being examined. The introduction of automated sequences has greatly speeded up the entire sequencing process as well as improved the accuracy of the collected information. Bioinformatics tools have become indispensable not only for setting up research studies, but also for storing, organizing and managing enormous quantities of sequencing data. Despite its great advantages, the use of bioinformatics is hindered by difficulties in learning how to use its software tools. The GenEnv database was developed to provide operators involved in biological risk management with a user-friendly tool for sequence analysis. Presently, there are over 20.000 sequence records, and over 9000 bacterial species represented in the database. The initial gene set comprises rDNA16S, rpoB, gyrB. The system allows sequence-driven microbe identification as well as the development of study protocols for research on specific microbe species. Nucleotide sequences are represented graphically. The GenEnv database was designed as a tool for public health operators but also offers wide prospects for scientific research.

Computational Biology↗
PubMed2005

The Web as an educational tool for/in learning/teaching bioinformatics statistics.

Statistics provides essential tool in Bioinformatics to interpret the results of a database search or for the management of enormous amounts of information provided from genomics, proteomics and metabolomics. The goal of this project was the development of a software tool that would be as simple as possible to demonstrate the use of the Bioinformatics statistics. Computer Simulation Methods (CSMs) developed using Microsoft Excel were chosen for their broad range of applications, immediate and easy formula calculation, immediate testing and easy graphics representation, and of general use and acceptance by the scientific community. The result of these endeavours is a set of utilities which can be accessed from the following URL: http://gmein.uib.es/bioinformatica/statistics. When tested on students with previous coursework with traditional statistical teaching methods, the general opinion/overall consensus was that Web-based instruction had numerous advantages, but traditional methods with manual calculations were also needed for their theory and practice. Once having mastered the basic statistical formulas, Excel spreadsheets and graphics were shown to be very useful for trying many parameters in a rapid fashion without having to perform tedious calculations. CSMs will be of great importance for the formation of the students and professionals in the field of bioinformatics, and for upcoming applications of self-learning and continuous formation.

Computational Biology↗