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At least 109 records · Page 6Linked to original sources
PubMed2005

Shoestring budgets, band-AIDS, and team work: challenges and motivators in the development of a Web-based resource for undergraduate clinical skills teaching.

BACKGROUND: Learning how to conduct a medical interview and perform a physical examination is fundamental to the practice of medicine; however, when this project began, the methods used to teach these skills to medical students at the University of Toronto (U of T) had not changed significantly since the early 1990s despite increasing outpatient care, shorter hospital stays, and heavy preceptor workloads. In response, a Web-based clinical skills resource was developed for the first-year undergraduate medical course-The Art and Science of Clinical Medicine I (ASCM I). OBJECTIVES: This paper examines our experiences with the development of the ASCM I website and details the challenges and motivators inherent in the production of a Web-based, multimedia medical education tool at a large Canadian medical school. METHODS: Interviews and a focus group were conducted with the development team to discover the factors that positively and negatively affected the development process. RESULTS: Motivating factors included team attributes such as strong leadership and judicious use of medical students and faculty volunteers as developers. Other motivators included a growing lack of instructional equivalency across diverse clinical teaching sites and financial and resource support by the Faculty of Medicine. Barriers to development included an administrative environment that did not yet fully incorporate information technology into its teaching vision and framework, a lack of academic incentive for faculty participation, and inadequate technical support, space, and equipment. CONCLUSIONS: The success of electronic educational resources such as the ASCM I website has caused a significant cultural shift within the Faculty of Medicine, resulting in the provision of more space, resources, and support for IT endeavours in the undergraduate medical curriculum.

Budgets↗
PubMed2004

A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication.

We propose a freely accessible web-based pipeline, which processes raw microarray scan data to obtain experimentally consolidated gene expression values. The tool MADSCAN, which stands for MicroArray Data Suites of Computed ANalysis, makes a practical choice among the numerous methods available for filtering, normalizing and scaling of raw microarray expression data in a dynamic and automatic way. Different statistical methods have been adapted to extract reliable information from replicate gene spots as well as from replicate microarrays for each biological situation under study. A carefully constructed experimental design thus allows to detect outlying expression values and to identify statistically significant expression values, together with a list of quality controls with proposed threshold values. The integrated processing procedure described here, based on multiple measurements per gene, is decisive for reliably monitoring subtle gene expression changes typical for most biological events.

Data Interpretation, Statistical↗
PubMed2006

Terrorism preparedness: Web-based resource management and the TOPOFF 3 exercise.

BACKGROUND: The bombings of London on July 7, 2005 highlight the need for continued vigilance and readiness to respond to terrorist attacks. Trauma centers need to be at the core of preparedness activities. The State of Connecticut has taken a lead in preparedness and was selected as a site for the US Department of Homeland Security's Top Officials Three Exercise (TOPOFF 3), the largest and most extensive antiterrorism drill ever conducted. METHODS: All 32 acute care hospitals in Connecticut took part in the drill. The simulated attacks were designed to test all aspects of emergency preparedness including the ability of hospitals to treat large numbers of victims and effectively monitor and implement mechanisms for surge capacity. In Connecticut, TOPOFF 3 tested the Bioterrorism Preparedness Web Application that was designed to be the primary communication and resource management tool during a terrorist event or public health emergency. This paper describes: 1) the impetus for the State of Connecticut Department of Public Health's Bioterrorism Preparedness Web Application; 2) the strategies used to ensure its readiness and appropriate utilization during a public health emergency; and 3) its use for communication and resource management by the Department of Public Health and the acute care hospitals during TOPOFF 3. RESULTS: The Bioterrorism Preparedness Web Application was successfully implemented and used during TOPOFF 3 to assess surge capacity and other resources. CONCLUSIONS: Careful development and implementation of the Web application, or any communication system, as well as training and regular practice are required to ensure effective use during a public health emergency.

Bioterrorism↗
PubMed2001

Professional toxicology societies: web based resources.

The number of digital tools available for use by researchers continues to rapidly increase as does the quantity of information available on the web. However, judging the reliability, quality and timeliness of this information is not always easy. One source of information about the profession of toxicology comes from the web sites of the various professional organizations that exist in this field. Given the broad nature of toxicology, there are a large number of such organizations. Some serve broader segments of the profession, while others have a more narrow focus. The web sites they have created are similarly variable, although there are some consistencies in the type of information that is provided. These include mission statements, information on joining the organization, and details on their annual meetings. There is also a consistent decision by these sites not to provide toxicologic information per se, although links to sites that do contain such information are occasionally provided. Overall, the information and tools provided by professional toxicology societies around the world appears to be similar in both quantity and quality to other scientific organizations. It is also apparent that this information is rapidly evolving and will likely be much different within the next 5 years.

Certification↗
PubMed2006

Towards pathogenomics: a web-based resource for pathogenicity islands.

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at http://www.gem.re.kr/paidb.

Bacteria↗
PubMed2005

Congenital melanocytic nevus and the Internet: an evaluation of available web-based resources.

The Internet has become an increasingly used tool for patient education and the coordination of support groups. For families with children diagnosed with congenital melanocytic nevus, this is also the case. To evaluate the quality of congenital melanocytic nevus-related information on the Internet, a standardized assessment of web sites was used. The overall Internet informational and support resources regarding congenital melanocytic nevus were found to be accurate and user friendly but limited. The authors recommend practitioners direct patient families to www.nevusnetwork.org as a starting point, and supplement an interest in pictures and information regarding support groups with visits to www.dermatlas.org and http://groups.MSN.com/AussieNevusSupportGroup.

Child↗
PubMed1998

Web-based resources for clinical protocol management.

The data monitoring regulatory procedures, and administrative tasks associated with protocol management have become increasingly complex. Relational database technology and Internet-based connectivity offer resources to improve the quality and efficiency of protocol operations. At Fox Chase Cancer Center, we have developed a suite of database applications for protocol management and tracking of patient accrual. All data transactions and reporting occur through a graphical web browser interface using standard Internet technology. Security and confidentiality have been addressed through encryption, user authentication, address restriction, and database authority. Database management has been tightly integrated with protocol operations to avoid duplication of resources and effort. Data query functions also extend to other institutional resources, such as tumor registry and the hospital clinical laboratory, to further reduce the need for redundant data storage. Newer components, such as chemotherapy orders and toxicity reporting, have been incorporated in a modular fashion. Although custom software development can be expensive and time-consuming, it offers the best opportunity for successful integration with existing resources, staff, and procedures, as well as collaboration with other institutions.

Clinical Protocols↗
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↗
PubMed2005

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.

BACKGROUND: Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic sequence. Apart from often being computationally expensive, this approach is vulnerable to several problems--hence the need to develop novel strategies. RESULTS: We propose a method, based on a novel multiple genome-EST alignment algorithm, for the detection of splice sites. To avoid limitations of splice sites prediction (mainly, over-predictions) due to independent single EST alignments to the genomic sequence our approach performs a multiple alignment of transcript data to the genomic sequence based on the combined analysis of all available data. We recast the problem of predicting constitutive and alternative splicing as an optimization problem, where the optimal multiple transcript alignment minimizes the number of exons and hence of splice site observations. We have implemented a splice site predictor based on this algorithm in the software tool ASPIC (Alternative Splicing PredICtion). It is distinguished from other methods based on BLAST-like tools by the incorporation of entirely new ad hoc procedures for accurate and computationally efficient transcript alignment and adopts dynamic programming for the refinement of intron boundaries. ASPIC also provides the minimal set of non-mergeable transcript isoforms compatible with the detected splicing events. The ASPIC web resource is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility. CONCLUSION: Extensive bench marking shows that ASPIC outperforms other existing methods in the detection of novel splicing isoforms and in the minimization of over-predictions. ASPIC also requires a lower computation time for processing a single gene and an EST cluster. The ASPIC web resource is available at http://aspic.algo.disco.unimib.it/aspic-devel/.

Algorithms↗
PubMed2000

A new generation of tools for search, recovery and quality evaluation of World Wide Web medical resources.

Although the Internet is already a valuable information resource in medicine, there are important challenges to be faced before physicians and general users will have extensive access to this information. As a result of a research effort to compile a health-related Internet directory, new tools and strategies have been developed to solve key problems derived from the explosive growth of medical information on the Net and the great concern over the quality of such critical information. The current Internet search engines lack some important capabilities. We suggest using second generation tools (client-side based) able to deal with large quantities of data and to increase the usability of the records recovered. We tested the capabilities of these programs to solve health-related information problems, recognising six groups according to the kind of topics addressed: Z39.50 clients, downloaders, multisearchers, tracing agents, indexers and mappers. The evaluation of the quality of health information available on the Internet could require a large amount of human effort. A possible solution may be to use quantitative indicators based on the hypertext visibility of the Web sites. The cybermetric measures are valid for quality evaluation if they are derived from indirect peer review by experts with Web pages citing the site. The hypertext links acting as citations need to be extracted from a controlled sample of quality super-sites.

Documentation↗
PubMed2006

Functional annotation of the Arabidopsis P450 superfamily based on large-scale co-expression analysis.

Cytochrome P450 mono-oxygenases play prominent roles in a diverse set of metabolic pathways, but the function of most of these enzymes remains obscure. A bottleneck in the functional genomics of this superfamily constitutes hypothesis generation to identify potential substrates (or substrate classes) individual P450s may act on. We used publicly available large-scale expression data to perform co-expression analysis comparing the expression matrix of each P450 with those from more than 4000 selected genes across thousands of microarrays. Based on functional annotations of co-expressed genes from a diverse set of databases, co-expressed pathways were thus identified for each P450. Using this approach, most P450s with known functions were placed into their respective pathways, thereby proofing the concept. As examples, pathway mapping results identifying novel P450s potentially acting on flower-specific monoterpenes and root-specific triterpenes are described. Co-expression results for all Arabidopsis P450s will be presented as a web resource on the 'CYPedia' web pages (http://ibmp.u-strasbg.fr/CYPedia/).

Arabidopsis↗
PubMed2005

T1DBase, a community web-based resource for type 1 diabetes research.

T1DBase (http://T1DBase.org) is a public website and database that supports the type 1 diabetes (T1D) research community. The site is currently focused on the molecular genetics and biology of T1D susceptibility and pathogenesis. It includes the following datasets: annotated genome sequence for human, rat and mouse; information on genetically identified T1D susceptibility regions in human, rat and mouse, and genetic linkage and association studies pertaining to T1D; descriptions of NOD mouse congenic strains; the Beta Cell Gene Expression Bank, which reports expression levels of genes in beta cells under various conditions, and annotations of gene function in beta cells; data on gene expression in a variety of tissues and organs; and biological pathways from KEGG and BioCarta. Tools on the site include the GBrowse genome browser, site-wide context dependent search, Connect-the-Dots for connecting gene and other identifiers from multiple data sources, Cytoscape for visualizing and analyzing biological networks, and the GESTALT workbench for genome annotation. All data are open access and all software is open source.

Animals↗
PubMedDate not supplied

The Community Tool Box: a Web-based resource for building healthier communities.

Building healthier cities and communities requires an array of community-building skills that are not always taught in formal education. The Community Tool Box (http://ctb.ukans.edu) is an Internet-based resource for practical, comprehensive, accessible, and user-friendly information on community-building, which both professionals and ordinary citizens can use in everyday practice. It connects people, ideas, and resources, offering more than 200 how-to sections and more than 5,000 pages of text.

Community Health Planning↗