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PubMedDate not supplied

Large-scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases: the example of Escherichia coli.

Knowledge-based molecular modelling of proteins has proven useful in many instances, including the rational design of mutagenesis experiments, but it has generally been limited by the availability of expensive computer hardware and software. To overcome these limitations, we developed the SWISS-MODEL server for automated knowledge-based protein modelling. The SWISS-MODEL server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates protein models for sequences which share significant similarities with at least one protein of known three-dimensional structure. We have now used the software framework of the server to generate large collections of protein models, and established the SWISS-MODEL Repository, a new database for automatically generated and theoretical protein models. This repository is directly integrated with the SWISS-PROT and SWISS-2DPAGE databases through the ExPASy World Wide Web server (URL is http://expasy.hcuge.ch). Here we present an illustration of this process by an application to the Escherichia coli sequences.

Bacterial Proteins↗
PubMed1998

Evaluation of Internet-based oncologic teaching for medical students.

BACKGROUND: Electronic tools with substantial educational applications are now widely available. METHODS: In a prospective, randomized study, the value of Web-based educational tools for teaching second-year medical students was evaluated. The 35-hour, image-intensive multifaculty neoplasia course was selected for the experiment, with 103 students assigned to the control group (C) and 61 to the experimental group (E). Representative password-controlled multimedia course modules, accessible via the Internet, were developed. The E cohort was exposed to both classroom and Web-aided materials, whereas the C group had access to the Web modules only after the experiment was concluded (but before the final examination). Pre- and post-exposure questionnaires assessed computer knowledge, familiarity with the Internet, availability of computer access, and the value of Web-based education for both cohorts. Additionally, pre-and post-exposure tests were administered to both cohorts based on educational materials presented in the Web modules. RESULTS: The overall participation rate was 64% (E = 69%; C = 60%). The post-test showed no major performance difference between the two groups. The questionnaires revealed that: less than 1% of the students had not accessed the Internet previously; less than 5% had not used the Internet for medical education before; 34% felt that computer resources on campus were inadequate; and over 75% found Web-based education to be an important additional educational resource. The major negative aspect was the slow pace of data transfer for modem-based home access. Only 1% of students felt that Web-based education could completely replace traditional teaching. CONCLUSION: The potential for incorporating Web-based education in the medical curriculum is considerable.

Computer Literacy↗
PubMed2003

Quartet mapping and the extent of lateral transfer in bacterial genomes.

Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these studies is that lateral gene transfer (LGT) has blurred prokaryotic phylogenies to such a degree that the darwinian scheme of treelike evolution might be abandoned in favor of a net or web. Here, we focus on one of these methods, quartet mapping, and show that its application can lead to overestimation of the extent of inferred LGT in prokaryotes, particularly when applied to distantly related taxa.

Bacteria↗
PubMed2004

The Gene Ontology (GO) database and informatics resource.

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.

Animals↗
PubMed2005

Australian national strategy for pharmacy preceptor education and support.

OBJECTIVES: (i) To develop a national strategy for pharmacy preceptor education and support, with special consideration for rural and remote practitioners. (ii) To deliver an innovative national core pharmacist preceptor education and support model that could be customised for specific undergraduate programs. DESIGN: A steering committee, with representatives from four Pharmacy Schools in three Australian states, was established to develop an educational curriculum and implementation strategy. SETTING: The project was designed to provide an online educational program for preceptors of Australian pharmacy students, particularly those in rural areas. SUBJECTS: The recipients of this program will primarily be rural pharmacy preceptors but could also be urban practitioners. INTERVENTIONS: After consultation with an advisory group, the steering committee considered the educational content, delivery strategy and adaptability of the package to maintain its currency and links to universities, pharmacy boards and professional organisations: an extensive literature search was conducted; writers and an educational designer were employed. The steering committee reviewed and modified the content before transfer of the program to the worldwide web. MAIN OUTCOME MEASURE: The development of a Pharmacy Preceptor Education Program suitable for national application and able to fulfil the needs of rural preceptors. RESULTS: A Preceptor Education Program has been developed suitable for use in all Australian states and capable of meeting the needs of rural pharmacy preceptors. CONCLUSIONS: Collaboration between four schools of pharmacy and pharmacy professional bodies has resulted in development of a flexible program for preceptors of undergraduate pharmacy students. This program can be developed for use by preceptors of pharmacy graduates, and in other disciplines.

Australia↗
PubMed1997

The promise of the World Wide Web and other telecommunication technologies within deaf education.

The authors summarize a national survey that collected information on instructional technology resources available at schools serving deaf students in the United States. Results indicated that over 70% of these schools have access to the Internet and World Wide Web. The authors also explore innovative uses of the Internet and provide examples of specific applications for deaf students.

Computer Communication Networks↗
PubMed2002

JavaScript DNA translator: DNA-aligned protein translations.

There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

Amino Acid Sequence↗
PubMed2002

The Stanford MediaServer Project: strategies for building a flexible digital media platform to support biomedical education and research.

Medical media collections are growing at a pace that exceeds the value they currently provide as research and educational resources. To address this issue, the Stanford MediaServer was designed to promote innovative multimedia-based application development. The nucleus of the MediaServer platform is a digital media database strategically designed to meet the information needs of many biomedical disciplines. Key features include an intuitive web-based interface for collaboratively populating the media database, flexible creation of media collections for diverse and specialized purposes, and the ability to construct a variety of end-user applications from the same database to support biomedical education and research.

Abstracting and Indexing↗
PubMed2004

Web of science: a unique method of cited reference searching.

The number of times an article is acknowledged as a reference in another article reflects its scientific impact. Citation analysis is one of the parameters for assessing the quality of research published in scientific, technology and social science journals. Web of Science enables users to search current and retrospective multidisciplinary information. Parameters and practical applications evaluating journal and article citation characteristics available through the Science Citation Index are summarized.

Abstracting and Indexing↗
PubMed2005

Anticoagulation monitoring part 1: warfarin and parenteral direct thrombin inhibitors.

OBJECTIVE: To review the availability, mechanisms, limitations, and clinical application of point-of-care (POC) devices used in the management of warfarin and parenteral direct thrombin inhibitors. DATA SOURCES: Scientific articles were identified through a MEDLINE search (1966-August 2004), manufacturer Web sites, additional references listed in articles and Web sites, and abstracts from scientific meetings. STUDY SELECTION AND DATA EXTRACTION: English-language literature from clinical trials was reviewed to evaluate the accuracy, reliability, and clinical application of POC monitoring devices. DATA SYNTHESIS: The prothrombin time expressed as the international normalized ratio (PT-INR) is a well-established test for monitoring warfarin anticoagulation. Multiple devices are available for POC testing. Because there is no universally accepted standard, the performance of each device is typically tested against a standard test performed in a reference laboratory. Performance of currently available devices, as measured by correlations to a standard reference laboratory PT-INR, may be considered very good and acceptable for use in patient care. Utilization of patient self-testing and patient self-monitoring of warfarin anticoagulation using POC devices is increasing. Parenteral direct thrombin inhibitors are typically monitored using a standard laboratory activated partial thromboplastin time. Some research has shown that POC monitoring of direct thrombin inhibitors using the ecarin clotting time is helpful for patients undergoing cardiopulmonary bypass surgery, although that test is not readily available. CONCLUSIONS: POC testing for anticoagulation therapy has been available for >20 years. Multiple POC devices are available to monitor warfarin. There is some variability in results between devices and between reagents used in the same device. Despite these limitations, POC monitoring of warfarin via the PT-INR is an integral part of clinical practice. Additional research evaluating POC monitoring of direct thrombin inhibitors is necessary.

Anticoagulants↗
PubMed2000

Digital library research and application.

The last decade has seen an exponential rise in the amount and the nature of information that is available on the Internet. Internet and World Wide Web technology have raised many technical as well as social and economic issues. The paper begins with a description of the recent digital library research initiative funded by the U.S. federal government. Digital library research addresses a host of informatics issues relevant to the current Internet-based environment. The paper continues with a discussion of some problems in information access, including a discussion of the potential of the Unified Medical Language System for navigating among multiple biomedical information systems. Next, some issues in creating Web-accessible resources for health care consumers are addressed, with a focus on recent work at the National Library of Medicine, including a description of the MEDLINEplus system. The paper ends with a brief discussion of some implications of digital library research for the health informatics community.

Internet↗
PubMed2005

GEMSS: grid-infrastructure for medical service provision.

OBJECTIVES: The European GEMSS Project is concerned with the creation of medical Grid service prototypes and their evaluation in a secure service-oriented infrastructure for distributed on demand/supercomputing. Key aspects of the GEMSS Grid middleware include negotiable QoS support for time-critical service provision, flexible support for business models, and security at all levels in order to ensure privacy of patient data as well as compliance to EU law. METHODS: The GEMSS Grid infrastructure is based on a service-oriented architecture and is being built on top of existing standard Grid and Web technologies. The GEMSS infrastructure offers a generic Grid service provision framework that hides the complexity of transforming existing applications into Grid services. For the development of client-side applications or portals, a pluggable component framework has been developed, providing developers with full control over business processes, service discovery, QoS negotiation, and workflow, while keeping their underlying implementation hidden from view. RESULTS: A first version of the GEMSS Grid infrastructure is operational and has been used for the set-up of a Grid test-bed deploying six medical Grid service prototypes including maxillo-facial surgery simulation, neuro-surgery support, radio-surgery planning, inhaled drug-delivery simulation, cardiovascular simulation and advanced image reconstruction. CONCLUSIONS: The GEMSS Grid infrastructure is based on standard Web Services technology with an anticipated future transition path towards the OGSA standard proposed by the Global Grid Forum. GEMSS demonstrates that the Grid can be used to provide medical practitioners and researchers with access to advanced simulation and image processing services for improved preoperative planning and near real-time surgical support.

Access to Information↗
PubMed2000

An integrated web interface for large-scale characterization of sequence data.

Large-scale genome projects require the analysis of large amounts of raw data. This analysis often involves the application of a chain of biology-based programs. Many of these programs are difficult to operate because they are non-integrated, command-line driven, and platform-dependent. The problem is compounded when the number of data files involved is large, making navigation and status-tracking difficult. To demonstrate how this problem can be addressed, we have created a platform-independent Web front end that integrates a set of programs used in a genomic project analyzing gene function by transposon mutagenesis in Saccharomyces cerevisiae. In particular, these programs help define a large number of transposon insertion events within the yeast genome, identifying both the precise site of transposon insertion as well as potential open reading frames disrupted by this insertion event. Our Web interface facilitates this analysis by performing the following tasks. Firstly, it allows each of the analysis programs to be launched against multiple directories of data files. Secondly, it allows the user to view, download, and upload files generated by the programs. Thirdly, it indicates which sets of data directories have been processed by each program. Although designed specifically to aid in this project, our interface exemplifies a general approach by which independent software programs may be integrated into an efficient protocol for large-scale genomic data processing.

Clinical Laboratory Information Systems↗
PubMed2006

Web-based education in bioprocess engineering.

The combination of web technology, knowledge of bioprocess engineering, and theories on learning and instruction might yield innovative learning material for bioprocess engineering. In this article, an overview of the characteristics of web-based learning material is given, as well as guidelines for the design of learning material from theories of learning and instruction and from the bioprocess engineering domain. A diverse body of learning material is presented, which illustrates the application of these guidelines; this material has been developed during the past six years for different courses, mostly at undergraduate level, and it illustrates how web-based learning material can enable various different approaches to learning objectives that might improve overall learning. Such learning material has been used for several years in education, it has been evaluated with positive results, and is now part of the regular learning material for bioprocess engineering at Wageningen University.

Biomedical Engineering↗
PubMed2003

The UMLS Semantic Network and the Semantic Web.

The Unified Medical Language System is an extensive source of biomedical knowledge developed and maintained by the US National Library of Medicine (NLM) and is being currently used in a wide variety of biomedical applications. The Semantic Network, a component of the UMLS is a structured description of core biomedical knowledge consisting of well defined semantic types and relationships between them. We investigate the expressiveness of DAML+OIL, a markup language proposed for ontologies on the Semantic Web, for representing the knowledge contained in the Semantic Network. Requirements specific to the Semantic Network, such as polymorphic relationships and blocking relationship inheritance are discussed and approaches to represent these in DAML+OIL are presented. Finally, conclusions are presented along with a discussion of ongoing and future work.

Programming Languages↗
PubMedDate not supplied

Comparing Web and touch screen transaction log files.

BACKGROUND: Digital health information is available on a wide variety of platforms including PC-access of the Internet, Wireless Application Protocol phones, CD-ROMs, and touch screen public kiosks. All these platforms record details of user sessions in transaction log files, and there is a growing body of research into the evaluation of this data. However, there is very little research that has examined the problems of comparing the transaction log files of kiosks and the Internet. OBJECTIVES: To provide a first step towards examining the problems of comparing the transaction log files of kiosks and the Internet. METHODS: We studied two platforms: touch screen kiosks and a comparable Web site. For both of these platforms, we examined the menu structure (which affects transaction log file data), the log-file structure, and the metrics derived from log-file records. RESULTS: We found substantial differences between the generated metrics. CONCLUSIONS: None of the metrics discussed can be regarded as an effective way of comparing the use of kiosks and Web sites. Two metrics stand out as potentially comparable and valuable: the number of user sessions per hour and user penetration of pages.

Adolescent↗