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PubMed2006

The Mouse Genome Database (MGD): updates and enhancements.

The Mouse Genome Database (MGD) integrates genetic and genomic data for the mouse in order to facilitate the use of the mouse as a model system for understanding human biology and disease processes. A core component of the MGD effort is the acquisition and integration of genomic, genetic, functional and phenotypic information about mouse genes and gene products. MGD works within the broader bioinformatics community to define referential and semantic standards to facilitate data exchange between resources including the incorporation of information from the biomedical literature. MGD is also a platform for computational assessment of integrated biological data with the goal of identifying candidate genes associated with complex phenotypes. MGD is web accessible at http://www.informatics.jax.org. Recent improvements in MGD described here include the incorporation of an interactive genome browser, the enhancement of phenotype resources and the further development of functional annotation resources.

Animals↗

PubMed2005

The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses.

The Botany Array Resource provides the means for obtaining and archiving microarray data for Arabidopsis thaliana as well as biologist-friendly tools for viewing and mining both our own and other's data, for example, from the AtGenExpress Consortium. All the data produced are publicly available through the web interface of the database at http://bbc.botany.utoronto.ca. The database has been designed in accordance with the Minimum Information About a Microarray Experiment convention -- all expression data are associated with the corresponding experimental details. The database is searchable and it also provides a set of useful and easy-to-use web-based data-mining tools for researchers with sophisticated yet understandable output graphics. These include Expression Browser for performing 'electronic Northerns', Expression Angler for identifying genes that are co-regulated with a gene of interest, and Promomer for identifying potential cis-elements in the promoters of individual or co-regulated genes.

Arabidopsis↗

PubMed2002

Information extraction for enhanced access to disease outbreak reports.

Document search is generally based on individual terms in the document. However, for collections within limited domains it is possible to provide more powerful access tools. This paper describes a system designed for collections of reports of infectious disease outbreaks. The system, Proteus-BIO, automatically creates a table of outbreaks, with each table entry linked to the document describing that outbreak; this makes it possible to use database operations such as selection and sorting to find relevant documents. Proteus-BIO consists of a Web crawler which gathers relevant documents; an information extraction engine which converts the individual outbreak events to a tabular database; and a database browser which provides access to the events and, through them, to the documents. The information extraction engine uses sets of patterns and word classes to extract the information about each event. Preparing these patterns and word classes has been a time-consuming manual operation in the past, but automated discovery tools now make this task significantly easier. A small study comparing the effectiveness of the tabular index with conventional Web search tools demonstrated that users can find substantially more documents in a given time period with Proteus-BIO.

Abstracting and Indexing↗

PubMed2005

Exploring relationships and mining data with the UCSC Gene Sorter.

In parallel with the human genome sequencing and assembly effort, many tools have been developed to examine the structure and function of the human gene set. The University of California Santa Cruz (UCSC) Gene Sorter has been created as a gene-based counterpart to the chromosome-oriented UCSC Genome Browser to facilitate the study of gene function and evolution. This simple, but powerful tool provides a graphical display of related genes that can be sorted and filtered based on a variety of criteria. Genes may be ordered based on such characteristics as expression profiles, proximity in genome, shared Gene Ontology (GO) terms, and protein similarity. The display can be restricted to a gene set meeting a specific set of constraints by filtering on expression levels, gene name or ID, chromosomal position, and so on. The default set of information for each gene entry-gene name, selected expression data, a BLASTP E-value, genomic position, and a description-can be configured to include many other types of data, including expanded expression data, related accession numbers and IDs, orthologs in other species, GO terms, and much more. The Gene Sorter, a CGI-based Web application written in C with a MySQL database, is tightly integrated with the other applications in the UCSC Genome Browser suite. Available on a selected subset of the genome assemblies found in the Genome Browser, it further enhances the usefulness of the UCSC tool set in interactive genomic exploration and analysis.

Computational Biology↗

PubMed2004

BIRD: Bio-Image Referral Database. Design and implementation of a new web based and patient multimedia data focused system for effective medical diagnosis and therapy.

This paper presents a low cost software platform prototype supporting health care personnel in retrieving patient referral multimedia data. These information are centralized in a server machine and structured by using a flexible eXtensible Markup Language (XML) Bio-Image Referral Database (BIRD). Data are distributed on demand to requesting client in an Intranet network and transformed via eXtensible Stylesheet Language (XSL) to be visualized in an uniform way on market browsers. The core server operation software has been developed in PHP Hypertext Preprocessor scripting language, which is very versatile and useful for crafting a dynamic Web environment.

Database Management Systems↗

PubMed2006

metaSHARK: a WWW platform for interactive exploration of metabolic networks.

The metaSHARK (metabolic search and reconstruction kit) web server offers users an intuitive, fully interactive way to explore the KEGG metabolic network via a WWW browser. Metabolic reconstruction information for specific organisms, produced by our automated SHARKhunt tool or from other programs or genome annotations, may be uploaded to the website and overlaid on the generic network. Additional data from gene expression experiments can also be incorporated, allowing the visualization of differential gene expression in the context of the predicted metabolic network. metaSHARK is available at http://bioinformatics.leeds.ac.uk/shark/.

Animals↗

PubMed2000

Real-time teleneuropathology for a second opinion of neurooncological cases.

A teleneuropathology system directed by Java programs through a standard Internet browser was evaluated in the present study. Assessment of neurooncological cases was done by remote microscope through the "Case Study" Web page at the Department of Pathology Web site (http:¿ampat.amu.edu.pl). The site was used to control a remote automatic microscope, the Axioplan 2 (Zeiss), which was connected to a computer that acts as an Internet server. The Java program for the control of the microscope server is automatically downloaded and started if the user selects the Web site of the corresponding microscope server. The microscope server receives microscope operation commands from the telemicroscopy clients, executes them, and distributes the new microscope image to all of the connected telemicroscopy clients. Fifteen cases were evaluated over several weeks. The percentage of correctly classified cases sent by remote consultation was 100%. Since the system does not require specialized software for the remote side and since the number of possible discussion partners is unlimited, this system may help to overcome obstacles to the practice of teleneuropathology.

Adenoma↗

PubMed2006

Current bioinformatics tools in genomic biomedical research (Review).

On the advent of a completely assembled human genome, modern biology and molecular medicine stepped into an era of increasingly rich sequence database information and high-throughput genomic analysis. However, as sequence entries in the major genomic databases currently rise exponentially, the gap between available, deposited sequence data and analysis by means of conventional molecular biology is rapidly widening, making new approaches of high-throughput genomic analysis necessary. At present, the only effective way to keep abreast of the dramatic increase in sequence and related information is to apply biocomputational approaches. Thus, over recent years, the field of bioinformatics has rapidly developed into an essential aid for genomic data analysis and powerful bioinformatics tools have been developed, many of them publicly available through the World Wide Web. In this review, we summarize and describe the basic bioinformatics tools for genomic research such as: genomic databases, genome browsers, tools for sequence alignment, single nucleotide polymorphism (SNP) databases, tools for ab initio gene prediction, expression databases, and algorithms for promoter prediction.

Computational Biology↗

PubMed2002

Web-enabled Glazer surface electromyographic protocol for the remote, real-time assessment and rehabilitation of pelvic floor dysfunction in vulvar vestibulitis syndrome. A case report.

BACKGROUND: The browser-based software for the Glazer pelvic floor muscle surface electromyography (sEMG) protocol can be used for remote, real-time assessment and treatment over the Internet. CASE: The initial application of this system is reported for a patient meeting clinical diagnostic criteria for vulvar vestibulitis syndrome. The patient underwent pelvic floor muscle sEMG evaluation in the Washington, D.C., office of the second author, remotely controlled by the first author from his office in New York City. Pelvic muscle sEMG findings were consistent with previous reports on vestibulitis patients, and rehabilitative exercises were prescribed. Follow-up evaluations and home training normalized the sEMG and resulted in elimination of pain. CONCLUSION: Remote, real-time pelvic floor muscle sEMG in the diagnosis and treatment of vulvar vestibulitis is a novel application of telemedicine with demonstrated efficacy, permitting this technology to be available to all practitioners.

Computer Communication Networks↗

PubMed2005

SynBrowse: a synteny browser for comparative sequence analysis.

MOTIVATION: The recent efforts of various sequence projects to sequence deeply into various phylogenies provide great resources for comparative sequence analysis. A generic and portable tool is essential for scientists to visualize and analyze sequence comparisons. RESULTS: We have developed SynBrowse, a synteny browser for visualizing and analyzing genome alignments both within and between species. It is intended to help scientists study macrosynteny, microsynteny and homologous genes between sequences. It can also aid with the identification of uncharacterized genes, putative regulatory elements and novel structural features of a species. SynBrowse is a GBrowse (the Generic Genome Browser) family software tool that runs on top of the open source BioPerl modules. It consists of two components: a web-based front end and a set of relational database back ends. Each database stores pre-computed alignments from a focus sequence to reference sequences in addition to the genome annotations of the focus sequence. The user interface lets end users select a key comparative alignment type and search for syntenic blocks between two sequences and zoom in to view the relationships among the corresponding genome annotations in detail. SynBrowse is portable with simple installation, flexible configuration, convenient data input and easy integration with other components of a model organism system. AVAILABILITY: The software is available at http://www.gmod.org CONTACT: vbrendel@iastate.edu

Algorithms↗

PubMed2001

JavaScript and interactive web pages in radiology.

Web publishing is becoming a more common method of disseminating information. JavaScript is an object-orientated language embedded into modern browsers and has a wide variety of uses. The use of JavaScript in radiology is illustrated by calculating the indices of sensitivity, specificity, and predictive values from a table of true positives, true negatives, false positives, and false negatives. In addition, a single line of JavaScript code can be used to annotate images, which has a wide variety of uses.

Humans↗

PubMed1997

Design of a Web interface for anatomical images.

Interactive documents for use with the World Wide Web have been developed for viewing multi-dimensional radiographic and visual images of human anatomy, derived from the Visible Human Project. Emphasis has been placed on user-controlled features and selections. The purpose was to develop an interface which was independent of host operating system and browser software which would allow viewing of information by multiple users. The interfaces were implemented using HyperText Markup Language (HTML) forms, C programming language and Perl scripting language. Images were pre-processed using ANALYZE and stored on a Web server in CompuServe GIF format. Viewing options were included in the document design, such as interactive thresholding and two-dimensional slice direction. The interface is an example of what may be achieved using the World Wide Web. Key applications envisaged for such software include education, research and accessing of information through internal databases and simultaneous sharing of images by remote computers by health personnel for diagnostic purposes.

Anatomy, Cross-Sectional↗

PubMed1997

HOSEpipe--a WWW-hosted data management and analysis system for STS content mapping projects.

We have developed a data management system, 'HOSEpipe' (High Output STS Evaluation pipeline) to aid sample tracking and data analysis in STS content mapping projects. The system is based around a World Wide Web (WWW) server that provides a number of pages including forms for sample processing and data entry accessible via a standard WWW browser application. The system is split into two main modules: firstly, a sequence evaluation and annotation module that takes de novo sequence for a potential STS, screens it against existing STSs and DNA sequence databases, followed by appropriate primer sequence design; secondly, a module that handles YAC library STS screening and includes facilities for both sample tracking and experimental data analysis. We present the design and rationale of the HOSEpipe system and its development to support a whole chromosomal physical mapping project. This software and design approach is potentially applicable to physical mapping projects of varying sizes and resolution and to similar projects, such as sample sequencing and the construction of sequence-ready maps.

Animals↗

PubMed1999

Worldwide telemedicine services based on distributed multimedia electronic patient records by using the second generation Web server hyperwave.

A distributed multimedia electronic patient record (EPR) is a central component of a medicine-telematics application that supports physicians working in rural areas of South America, and offers medical services to scientists in Antarctica. A Hyperwave server is used to maintain the patient record. As opposed to common web servers--and as a second generation web server--Hyperwave provides the capability of holding documents in a distributed web space without the problem of broken links. This enables physicians to browse through a patient's record by using a standard browser even if the patient's record is distributed over several servers. The patient record is basically implemented on the "Good European Health Record" (GEHR) architecture.

Antarctic Regions↗

PubMedDate not supplied

Use of and satisfaction with a browser-based nurse teaching tool in a surgical intensive care unit.

Our goal was to determine if a computerized teaching tool is an effective teaching method for nurses in a high-stress fast-paced intensive care unit. We also measured the level of satisfaction with this method of instruction. Thirty-six surgical intensive care nurses used a Web-based Microsoft PowerPoint presentation located on the intranet at nursing stations located on the surgical intensive care unit (SICU). The presentation was designed to provide instruction regarding the methodology and use of APACHE III prior to its implementation. Paired t-tests were performed to compare the results of a pretest and posttest. The questions were divided into two types: methodology and use. After the nurses completed their training sessions, they were asked to complete a questionnaire. The questionnaire questions were rated one a 1 to 5 scale. The average scores were higher on the posttest compared to the pretest (63.2% vs. 69.1%, p = 0.03). The methodology scores were higher on the posttest (74.3% vs. 88.2%, p = 0.001), while the use scores remained the same at 78.1% vs. 75.0%. Our Web-based teaching tool is an effective way to train nurses to understand the APACHE III medical system. The tool was effective at conveying the APACHE III medical systems methodology but was not effective in explaining the usefulness of the system. Most important, the nurses thought the browser-based teaching tool was easily accessible and an effective way to communicate new material to the medical staff.

APACHE↗

PubMed2006

The UCSC genome browser database: update 2007.

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

Animals↗

PubMed2003

An open Internet platform to distributed image processing applied to dermoscopy.

Proprietary systems for dermoscopy images analysis are available to improve the diagnosis and follow-up of the pigmented skin lesions. Their performance seems comparable with that of a human expert. Progress in computer-aided classification of melanocytic lesions depends notably on judicious choices of the algorithms dedicated to the extraction of signs from the dermoscopy images and of the method which combines these signs to classify the lesions. To allow the researcher's community to benefit from their large set of elementary algorithms already available for dermoscopy, we set up a system accessible through the Internet which: allows the engineers to register their algorithms while preserving their secrecy: their programs run on their own server; lets a user to define its own sequence of image analysis and to apply it to its images: the system automatically calls the appropriate remote programs; makes possible and stimulates the synergy of worldwide researchers in order to validate algorithms of images analysis best suited to achieve the correct diagnosis and to track the malignant melanoma; makes these techniques available to the greatest number of users through the Web and thus to support a mass screening; reduces the maintenance of the system to the minimum: it requires users only an Internet browser and engineers to follow a simple widespread standardised interface for distributed programs. Various problems should be addressed: the lack of standardisation of images acquisition: algorithms based on relative colours are best suited to this system; the copyrights on images and algorithms; charging the use of remote computer resources. This system allows for an international collaborative work in the fight against the malignant melanoma by offering a conceptual and technical platform of teledermoscopy. It is intended to support synergy between the engineers and the users implied in the diagnosis and teaching of dermoscopy.

Algorithms↗

PubMedDate not supplied

RSS feeds: what are they and why should I care?

Really simple syndication (RSS) feeds and aggregators are indispensable tools for clinicians who need to stay abreast of the latest clinical research, public health publications, and economic factors that might affect their practice. RSS enables clinicians with a compatible browser, such as Mozilla Firefox, or other desktop aggregator, to view headlines and journal article titles from dozens or even hundreds of disparate Web sites of their choosing. Instead of wasting time visiting each Web site, dealing with pop-ups and advertising, and parsing new data from old, aggregators provide a single, simple window into the information. Setting up a desktop aggregator to manage and display RSS feeds is straightforward and, thanks to open source applications, imminently affordable.

Education, Continuing↗