PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Web Browser”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources
PubMed2002

Challenges in implementing a knowledge editor for the Arden Syntax: knowledge base maintenance and standardization of database linkages.

CONTEXT: Incorporation of research findings into clinical practice lags behind their dissemination in the medical literature. Arden Syntax is a standard that could be used to encode evidence in a clinical decision support system (CDSS). However, dissemination of knowledge is hampered by lack of standard linkages to clinical databases. OBJECTIVE: To create a knowledge editor that facilitates transfer of knowledge from the medical literature to clinical practice via a CDSS. METHODS: Using a Web browser-based application, we implemented linkages to MEDLINE to permit queries on demand and registration of queries to be executed periodically, with results copied into Arden Medical Logic Modules (MLMs). To facilitate standardization of MLMs, database linkages are encoded using emerging HL7 standards such as a data model (virtual medical record). CONCLUSIONS: A Web-based application can facilitate transfer of knowledge into clinical practice and knowledge base maintenance through periodic queries and deployment of standards for knowledge representation.

Artificial Intelligence↗
PubMed2024

Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.

Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.

User-Computer Interface↗
PubMed2001

From legacy and client/server systems to components in healthcare information systems in Finland.

A strategy and toolset (FixIT) for migrating a specific type of legacy systems--based on the FileMan DBMS of the U.S. Department of Veterans Affairs--to a two-tier client/server and web browser-based architecture was presented in MEDINFO'98. In the current paper we discuss the further migration to a multitier software component architecture. A literature survey and industry contacts were used to specify an open, component-based target architecture for healthcare information systems to be reached by the year 2005, as well as a phased migration strategy from the present FileMan/FixIT-based systems towards the target. The target architecture is based on large-grained business components and accommodates heterogeneous elements on the intra-component, intra-application, intra-organization and inter-organizational levels. Four logical tiers are identified within a business component. Three migration paths are specified for different cases: the tier-by-tier, piece-by-piece, and web-wrapping paths. It is argued that the architecture, supported by off-the-shelf toolsets, application frameworks and a new software development process, makes it possible to turn legacy systems into a valuable asset, split monolithic applications into reusable components, and ultimately replace the legacy parts at a feasible pace

Database Management Systems↗
PubMed2026

VIJB: a companion of the JBROWSE genome browser for the visually impaired people.

MOTIVATION: The availability of touch-sensitive and haptic devices has been a keystone development for the inclusion of visually impaired people (VIPs) in modern, highly digitized work environments. Braille displays have proven efficient and versatile enough to parse large and complex text files, making bioinformatics and text-heavy programming accessible to VIPs. However, the complex graphical objects -combining numerous datasets- typically generated during data integration remain challenging, even with the aid of descriptive AI. This is particularly true in functional genomics. Here, we present VIJB, a simple application that displays the multilayered output of the JBROWSE genome browser on a Braille reader, enabling VIPs to fully participate in data integration in functional genomics. AVAILABILITY AND IMPLEMENTATION: VIJB is programmed in Python and relies on the scientific library NumPy, the braillegraph and pyBigWig libraries, and the TABIX software. The architecture is summarized in Supplementary Material 1, available as supplementary data at Bioinformatics online. VIJB is available for download at the GitHub repository https://GitHub.com/NiBuMNHN/VIJB and is licenced under the GPL 3.0.

Persons with Visual Disabilities↗
PubMed1999

Automated genome sequence analysis and annotation.

MOTIVATION: Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. RESULTS: We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. AVAILABILITY: The GeneQuiz system is publicly available for analysis of protein sequences through a Web server at http://www.sander.ebi.ac. uk/gqsrv/submit

Amino Acid Sequence↗
PubMed2026

Functional Prediction of Epitranscriptome.

N6-methyladenosine (m6A) is one of the most prevalent and well-studied RNA modifications, playing a pivotal role in many biological processes. With the recent advances in high-throughput sequencing technologies, tens of thousands of m6A sites have been reported. However, not all m6A sites are important or functionally significant, highlighting the need to distinguish biologically relevant m6As from non-functional or technically artefactual ones. Here, we describe ConsRM, which is a web-based resource that was designed to evaluate the importance of m6As from an evolutionary perspective. It introduced a novel scoring framework for quantifying the conservation degree of m6As in humans. Its web interface includes a database of 177998 distinct human m6A sites along with their calculated conservation score, and allows users to analyze their own data via the web server. ConsRM is freely accessible at: http://180.208.58.19/conservation/browser.html .

Humans↗
PubMed2026

NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks.

MOTIVATION: Genome-scale metabolic network (GSMN) models enable flux-based metabolite fate discovery, metabolic engineering, drug target identification, and multi-omics integration. However, programming requirements, architectural complexity, and limited visualization support impede its adoption by the broader scientific community. Existing tools exclusively specialize in GSMN analyses or visualization while lacking important features such as pathway-specific views, database-integrated refinement, and comprehensive enrichment and perturbation analyses. RESULTS: Here, we present NAViFluX (metabolic Network Analysis and Visualization of Flux), a visualization-centric, web browser-based tool that unifies native pathway/subsystem map generation, interactive model refinement via KEGG/BiGG, pathway merging and modules for flux computations, topology, and functional enrichment all within network views. Using three independent case studies on Escherichia coli, the utility of NAViFluX for characterization of nutrient-specific metabolic adaptations, enhancing gene essentiality predictions and interpretability, and rational design of an optimized carbon-fixing metabolic state is demonstrated. AVAILABILITY AND IMPLEMENTATION: All source code and supplementary files associated with the case studies are publicly available via Zenodo at https://zenodo.org/records/19107831. NAViFluX can be easily installed as a standalone software through https://github.com/bnsb-lab-iith/NAViFluX.

Metabolic Networks and Pathways↗
PubMed2004

APD: the Antimicrobial Peptide Database.

An antimicrobial peptide database (APD) has been established based on an extensive literature search. It contains detailed information for 525 peptides (498 antibacterial, 155 antifungal, 28 antiviral and 18 antitumor). APD provides interactive interfaces for peptide query, prediction and design. It also provides statistical data for a select group of or all the peptides in the database. Peptide information can be searched using keywords such as peptide name, ID, length, net charge, hydrophobic percentage, key residue, unique sequence motif, structure and activity. APD is a useful tool for studying the structure-function relationship of antimicrobial peptides. The database can be accessed via a web-based browser at the URL: http://aps.unmc.edu/AP/main.html.

Amino Acid Motifs↗
PubMed2016

KERIS: kaleidoscope of gene responses to inflammation between species.

A cornerstone of modern biomedical research is the use of animal models to study disease mechanisms and to develop new therapeutic approaches. In order to help the research community to better explore the similarities and differences of genomic response between human inflammatory diseases and murine models, we developed KERIS: kaleidoscope of gene responses to inflammation between species (available at http://www.igenomed.org/keris/). As of June 2016, KERIS includes comparisons of the genomic response of six human inflammatory diseases (burns, trauma, infection, sepsis, endotoxin and acute respiratory distress syndrome) and matched mouse models, using 2257 curated samples from the Inflammation and the Host Response to Injury Glue Grant studies and other representative studies in Gene Expression Omnibus. A researcher can browse, query, visualize and compare the response patterns of genes, pathways and functional modules across different diseases and corresponding murine models. The database is expected to help biologists choosing models when studying the mechanisms of particular genes and pathways in a disease and prioritizing the translation of findings from disease models into clinical studies.

Animals↗
PubMed2006

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.

Protein crystallization remains one of the bottlenecks in crystallographic analysis of macromolecules. An automated large-scale protein-crystallization system named PXS has been developed consisting of the following subsystems, which proceed in parallel under unified control software: dispensing precipitants and protein solutions, sealing crystallization plates, carrying robot, incubators, observation system and image-storage server. A sitting-drop crystallization plate specialized for PXS has also been designed and developed. PXS can set up 7680 drops for vapour diffusion per hour, which includes time for replenishing supplies such as disposable tips and crystallization plates. Images of the crystallization drops are automatically recorded according to a preprogrammed schedule and can be viewed by users remotely using web-based browser software. A number of protein crystals were successfully produced and several protein structures could be determined directly from crystals grown by PXS. In other cases, X-ray quality crystals were obtained by further optimization by manual screening based on the conditions found by PXS.

Automation↗
PubMed2005

User acceptance of the Web-based distribution of radiology services in regional and remote centres of Western Australia.

A large-scale, Web browser-based radiological information system integrated with a picture archiving and communication system (RIS/PACS) has been installed in regional and remote radiology centres of Western Australia. This provides patients in rural areas with local access to advanced medical imaging. User attitudes to the changes were surveyed in a six-week period starting in March 2005. A total of 53 people completed the survey (62% response rate). Respondents were eight radiologists, 21 medical imaging technologists, 10 administration officers and 14 reception staff. All groups gave average ratings of the system's quality. All staff rated the information quality of the system as good. On-site information technology support was judged to be reliable, professional and empathic towards user concerns. There was a broad range of opinion between groups, but on average they were satisfied. The lack of a modern network, comparable to what is available in the metropolitan areas, has impeded the full potential of RIS/PACS in the smaller rural centres.

Attitude of Health Personnel↗
PubMedDate not supplied

MIPortal: a high capacity server for molecular imaging research.

The introduction of novel molecular tools in research and clinical medicine has created a need for more refined information management systems. This article describes the design and implementation of such a new information platform: the Molecular Imaging Portal (MIPortal). The platform was created to organize, archive, and rapidly retrieve large datasets using Web-based browsers as access points. The system has been implemented in a heterogeneous, academic research environment serving Macintosh, Unix, and Microsoft Windows clients and has been shown to be extraordinarily robust and versatile. In addition, it has served as a useful tool for clinical trials and collaborative multi-institutional small-animal imaging research.

Computational Biology↗
PubMed1999

MediLink: a wearable telemedicine system for emergency and mobile applications.

The practical needs of the medical professional faced with critical care or emergency situations differ from those working in many environments where telemedicine and mobile computing have been introduced and tested. One constructive criticism of the telemedicine initiative has been to question what positive benefits are gained from videoconferencing, paperless transactions, and online access to patient record. With a goal of producing a positive answer to such questions an architecture for multipurpose mobile telemedicine applications has been developed. The core technology is based upon a wearable personal computer with a smart-card interface coupled with speech, pen, video input and wireless intranet connectivity. The TransPAC system with the MedLink software system is designed to provide an integrated solution for a broad range of health care functions where mobile and hands-free or limited-access systems are preferred or necessary and where the capabilities of other mobile devices are insufficient or inappropriate. Structured and noise-resistant speech-to-text interfacing plus the use of a web browser-like display, accessible through either a flatpanel, standard, or headset monitor, gives the beltpack TransPAC computer the functions of a complete desktop including PCMCIA card interfaces for internet connectivity and a secure smartcard with 16-bit microprocessor and upwards of 64K memory. The card acts to provide user access control for security, user custom configuration of applications and display and vocabulary, and memory to diminish the need for PC-server communications while in an active session. TransPAC is being implemented for EMT and ER staff usage.

Emergency Medical Services↗
PubMed2000

Digital health care--the convergence of health care and the Internet.

The author believes that interactive media (the Internet and the World Wide Web) and associated applications used to access those media (portals, browsers, specialized Web-based applications) will result in a substantial, positive, and measurable impact on medical care faster than any previous information technology or communications tool. Acknowledging the dynamic environment, the author classifies "pure" digital health care companies into three business service areas: content, connectivity, and commerce. Companies offering these services are attempting to tap into a host of different markets within the health care industry including providers, payers, pharmaceutical and medical products companies, employers, distributors, and consumers. As the fastest growing medium in history, and given the unique nature of health care information and the tremendous demand for content among industry professionals and consumers, the Internet offers a more robust and targeted direct marketing opportunity than traditional media. From the medical consumer's standpoint (i.e., the patient) the author sees the Internet as performing five critical functions: (1) Disseminate information, (2) Aid informed decision making, (3) Promote health, (4) Provide a means for information exchange and support--the community concept, and (5) Increase self-care and manage demand for health services, lowering direct medical costs. The author firmly submits the Web will provide overall benefits to the health care economy as health information consumers manage their own health problems that might not directly benefit from an encounter with a health professional. Marrying the Internet to other interactive technologies, including voice recognition systems and telephone-based triage lines among others, holds the promise of reducing unnecessary medical services.

Commerce↗
PubMed1996

Entering the "land of the "puter braindead"!

My goal has been to give you a basic understanding of the concepts involved with understanding and exploring the web. By this point you should know: what the Internet is, what the World Wide Web is, what a web site is, what a home page is, what a URL is, what a browser is, what hyperlinks are, and how to use your browser to surf the web. Problems that arise can usually be solved by going to the "Help" icon on your browser or going to the Web Tutorials that all browsers have on their software.

Computer Communication Networks↗
PubMed2003

Reconstruction and web distribution of measurable arterial models.

In this paper a novel framework for the segmentation, 3D reconstruction and web distribution of vessel structures specifically tailored to the assessment of abdominal aortic aneurysms for endovascular surgery planning is presented. Deformable models are used for segmentation, while VRML97 and ECMA scripting are used to obtain models that are not only viewable from any VRML97 enabled browser, but that also allow users to perform, directly from standard web browsers, guided measurements of geometrical parameters, relevant to surgical planning.

Aortic Aneurysm, Abdominal↗