SEARCH · PubMed Health

Results for “Web application”

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 1,027 records · Page 57Linked to original sources

PubMed2026

OmicsQ: a user-friendly platform for interactive quantitative omics data analysis.

MOTIVATION: High-throughput omics technologies generate complex datasets with thousands of features that are quantified across multiple experimental conditions, but often suffer from incomplete measurements, missing values, and individually fluctuating variances. This requires analytical tools for accurate, deep and insightful biological interpretation, capable of dealing with a large variety of data properties and different amounts of completeness. Software capable of handling such data complexity and integrating with external applications for downstream analysis remains rare and mostly relies on programming-based environments, limiting accessibility for researchers without computational expertise. RESULTS: We present OmicsQ, an interactive, web-based platform designed to streamline quantitative omics data analysis. OmicsQ provides an intuitive, browser-based visualization interface that integrates established statistical processing tools. Those include robust batch correction, automated experimental design annotation, and handling of missing data without imputation, which maintains data integrity and avoids artifacts from a priori assumptions. OmicsQ seamlessly interacts with external applications (e.g. PolySTest, VSClust, ComplexBrowser) for statistical testing, clustering, analysis of protein complex behavior, and pathway enrichment, offering a comprehensive and flexible workflow from data import to biological interpretation that is broadly applicable across domains. AVAILABILITY AND IMPLEMENTATION: OmicsQ is implemented in R and Shiny and is available at https://computproteomics.bmb.sdu.dk/app_direct/OmicsQ. Source code and installation instructions: https://github.com/computproteomics/OmicsQ, DOI: 10.5281/zenodo.17778420.

Software↗

PubMed2026

Ori-Finder-Arch: An Updated Web Server for the Annotation and Visualization of Archaeal Replication Origins.

Archaea are promising chassis organisms in biotechnology, and the accurate annotation of their chromosomal replication origins (oriCs) is the key to unlocking their full potential. However, the existing Ori-Finder 2 web server suffers from low accuracy, slow speed, and limited scalability. In this study, we present Ori-Finder-Arch, an updated web server for high-performance oriC prediction in archaea. This pipeline integrates HMMER-based replication initiation protein (RIP) annotation, refined consensus motif recognition, and GC profile-based DNA unwinding element (DUE) detection. On a benchmark set of experimentally validated oriCs, Ori-Finder-Arch achieved a recall of 95.6% and a precision of 86.0%, substantially outperforming Ori-Finder 2 (62.2% and 63.6%, respectively), while running 4.75 times faster and supporting diverse assembly levels. When applied to the available archaeal assemblies, it successfully annotated 17,472 oriCs. Meanwhile, the web server provides interactive visualizations at different levels. In conclusion, Ori-Finder-Arch offers an efficient, accurate, and user-friendly platform for advanced studies of archaeal DNA replication initiation and synthetic biology applications, and is freely available at https://tubic.org/Ori-Finder-Arch/ and https://tubic.tju.edu.cn/Ori-Finder-Arch/.

Archaea↗

PubMed1998

Siegfried: System for Interactive Electronic Guidelines with Feedback and Resources for Instructional and Educational Development.

The proliferation of clinical practice guidelines (CPGs) has necessitated computerized solutions for guideline distribution and implementation. In this paper we describe a Web-based system that interactively presents CPGs at the point of care. Our system, known as Siegfried, provides a generalized solution for implementing CPGs by maintaining the guideline knowledge base separate from the application that presents the guidelines. As a result of this design, new CPGs can be easily added and existing CPGs can be expeditiously modified without additional programming. This system also solicits feedback from users regarding guideline recommendations and provides hypertext links to relevant Web-based instructional and educational resources.

Artificial Intelligence↗

PubMed2002

Radtracker: a web-based open-source issue tracking tool.

Radiology departments are besieged with a multitude of information systems, each needing significant technical support. Information systems include the dictation system, the radiology information system (RIS), the picture archiving and communication systems (PACS), and every workstation and acquisition modality along with any dedicated system such as a teleradiology solution or specialized reporting tools. Typical radiology departments have very limited resources available to provide support. The challenges facing technical support are in responding to mission critical applications during a failure, building a knowledge base for each system, and providing clear communication with the users of the system experiencing problems. We have constructed a web-based support method that addresses the 3 main challenges of supporting so many different information systems with a formalized response mechanism. The website allows anyone to easily submit issues by describing the problem and selecting a specific category. Each support person subscribes to categories for which they are qualified. High-priority issues will be sent automatically to the alphanumeric pagers of the support personnel with the description of the problem. Drill down capabilities on the website allow searching of resolved and unresolved problems. Automatic emails are sent out to the person submitting the problem every time an action is taken to keep them in a closed loop. This tool pools the limited resources of the department and formalizes response mechanism to provide optimal support to the users.

Internet↗

PubMed1991

[Clinical application of retrograde island flap from back of the hand].

With the blood vessels filled with dye, 12 fresh specimens of adult human hand were dissected. At web spaces, anastomoses between artereiae palmariae dorsales and arteriae digitalis palmares communes or their branches were always present. The anastomotic branch was 0.4-0.8 mm thick and 11-14 mm long, and was accompanied by 2 veins, lying superficially in the subcutaneous space. With the anastomotic branch as an axis and the arteriae palmares dorsales as pedicle, a retrograde island flap back of the hand was designed and employed to cover skin defect of finger in 11 patients. One of the flaps was transposed together with an extensor tendon. The defect was covered by suturing together the skin edges on both sides and healed nicely. The 11 transpositioned flaps varying from 3.5 x 2.2 cm2 in size were taken successfully. Follow-up examination for 2-10 months after operation revealed fine texture of and good sensation over the flaps, and good function of the transplanted extensor tendon. We conclude that this kind of flap is physiologically sound and easy to be made for the repair of palmar defect and in finger defect.

Adolescent↗

PubMed1999

Transparent image access in a distributed picture archiving and communications system: the Master Database broker.

A distributed design is the most cost-effective system for small-to medium-scale picture archiving and communications systems (PACS) implementations. However, the design presents an interesting challenge to developers and implementers: to make stored image data, distributed throughout the PACS network, appear to be centralized with a single access point for users. A key component for the distributed system is a central or master database, containing all the studies that have been scanned into the PACS. Each study includes a list of one or more locations for that particular dataset so that applications can easily find it. Non-Digital Imaging and Communications in Medicine (DICOM) clients, such as our worldwide web (WWW)-based PACS browser, query the master database directly to find the images, then jump to the most appropriate location via a distributed web-based viewing system. The Master Database Broker provides DICOM clients with the same functionality by translating DICOM queries to master database searches and distributing retrieval requests transparently to the appropriate source. The Broker also acts as a storage service class provider, allowing users to store selected image subsets and reformatted images with the original study, without having to know on which server the original data are stored.

CD-ROM↗

PubMed2006

Visual interaction: models, systems, prototypes. The Pictorial Computing Laboratory at the University of Rome La Sapienza.

This paper reports on the research activities performed by the Pictorial Computing Laboratory at the University of Rome, La Sapienza, during the last 5 years. Such work, essentially is based on the study of humancomputer interaction, spans from metamodels of interaction down to prototypes of interactive systems for both synchronous multimedia communication and groupwork, annotation systems for web pages, also encompassing theoretical and practical issues of visual languages and environments also including pattern recognition algorithms. Some applications are also considered like e-learning and collaborative work.

Academies and Institutes↗

PubMed2006

A data-gathering broker as a future-orientated approach to supporting EPR users.

With the continued expansion of electronic patient record systems ahead of comprehensive evidence, metrics, or future-proofing, health informatics in Europe and beyond is embarking on a faith-driven adventure that also risks data swamping of end-users. An alternative approach is an information broker system, drawing from departmental data sources. A 3-year study in health and social care has produced a first demonstrator which can search for specified information in heterogeneous distributed data stores, with source-specific permission can copy it, and then merge the search results into one integrated picture in a real-time process which is also captured in an audit system. The research project has addressed a number of issues during the study, including updating the concepts of role-based access, semantic interoperability, and harnessing web-based services bound at the time of need. A demonstrator now exists, and provides a platform for further application and development research. This paper summarises how this opens up a viable alternative approach for the next generation of health record systems, enabling record searching and integration as and when it is needed for specific patient-related purposes, whilst being independent of organisations, diagnostic approaches, or service delivery structures, and reducing the risks of data swamping.

Access to Information↗

PubMed2006

A sequence database allowing automated genotyping of Classical swine fever virus isolates.

Classical swine fever (CSF) is a highly contagious viral disease of pigs. According to the OIE classification of diseases it is classified as a notifiable (previously List A) disease, thus having the potential for causing severe socio-economic problems and affecting severely the international trade of pigs and pig products. Effective control measures are compulsory, and to expose weaknesses a reliable tracing of the spread of the virus is necessary. Genetic typing has proved to be the method of choice. However, genotyping involves the use of multiple software applications, which is laborious and complex. The implementation of a sequence database, which is accessible by the World Wide Web with the option to type automatically new CSF virus isolates once the sequence is available is described. The sequence to be typed is tested for correct orientation and, if necessary, adjusted to the right length. The alignment and the neighbor-joining phylogenetic analysis with a standard set of sequences can then be calculated. The results are displayed as a graph. As an example, the determination is shown of the genetic subgroup of the isolate obtained from the outbreaks registered in Russia, in 2005. After registration (Irene.greiser-wilke@tiho-hannover.de) the database including the module for genotyping are accessible under http://viro08.tiho-hannover.de/eg/eurl_virus_db.htm.

Algorithms↗

PubMedDate not supplied

The visible embryo project: embedded program objects for knowledge access, creation and management through the World Wide Web.

We have designed a prototype knowledge management online environment for the biomedical sciences which integrates access to online representations of the scientific literature, bibliographic databases, high-performance visualization technologies, large-scale scientific databases, and tools for authoring new-generation scientific publications. This system will provide widespread access to its resources by using the World Wide Web for its underlying architecture. This system expands upon our Weblet Interactive Remote Visualization (IRV) server technology to produce a set of dedicated Internet "visualization servers" which provide interactive control of real-time visualizations from the Visible Embryo Project database from within Web pages viewed with our WebRouser software package. This system will be used to develop a set of prototype applications for both online education of medical students in developmental anatomy and for an interactive patient education system for expectant parents. We recognize that knowledge represented by these national resource databases is not static, therefore it is essential to include tools for both the creation of new "compound documents" which incorporate embedded objects, as well as for managing the peer-review of scholarly publications, in order to ensure the integrity of new knowledge as it is added to these databases in the future. We have therefore begun to design integrated tools for our system which facilitate both the creation of and the validation of new generations of scientific knowledge.

Anatomy, Cross-Sectional↗

PubMed2004

Globally distributed object identification for biological knowledgebases.

The World-Wide Web provides a globally distributed communication framework that is essential for almost all scientific collaboration, including bioinformatics. However, several limits and inadequacies have become apparent, one of which is the inability to programmatically identify locally named objects that may be widely distributed over the network. This shortcoming limits our ability to integrate multiple knowledgebases, each of which gives partial information of a shared domain, as is commonly seen in bioinformatics. The Life Science Identifier (LSID) and LSID Resolution System (LSRS) provide simple and elegant solutions to this problem, based on the extension of existing internet technologies. LSID and LSRS are consistent with next-generation semantic web and semantic grid approaches. This article describes the syntax, operations, infrastructure compatibility considerations, use cases and potential future applications of LSID and LSRS. We see the adoption of these methods as important steps toward simpler, more elegant and more reliable integration of the world's biological knowledgebases, and as facilitating stronger global collaboration in biology.

Animals↗

PubMed2005

A fractional programming approach to efficient DNA melting temperature calculation.

MOTIVATION: In a wide range of experimental techniques in biology, there is a need for an efficient method to calculate the melting temperature of pairings of two single DNA strands. Avoiding cross-hybridization when choosing primers for the polymerase chain reaction or selecting probes for large-scale DNA assays are examples where the exact determination of melting temperatures is important. Beyond being exact, the method has to be efficient, as these techniques often require the simultaneous calculation of melting temperatures of up to millions of possible pairings. The problem is to simultaneously determine the most stable alignment of two sequences, including potential loops and bulges, and calculate the corresponding melting temperature. RESULTS: As the melting temperature can be expressed as a fraction in terms of enthalpy and entropy differences of the corresponding annealing reaction, we propose to use a fractional programming algorithm, the Dinkelbach algorithm, to solve the problem. To calculate the required differences of enthalpy and entropy, the Nearest Neighbor model is applied. Using this model, the substeps of the Dinkelbach algorithm in our problem setting turn out to be calculations of alignments which optimize an additive score function. Thus, the usual dynamic programming techniques can be applied. The result is an efficient algorithm to determine melting temperatures of two DNA strands, suitable for large-scale applications such as primer or probe design. AVAILABILITY: The software is available for academic purposes from the authors. A web interface is provided at http://www.zaik.uni-koeln.de/bioinformatik/fptm.html

Algorithms↗

PubMed2002

A Web-based geriatrics portfolio to document medical students' learning outcomes.

OBJECTIVE: The University of Michigan Medical School is integrating into its curriculum the attitudes, knowledge, and skills that pertain to the care of older individuals using a defined set of core learning outcomes encompassing all four years. Students will demonstrate proficiency in these outcomes as a graduation requirement. We have developed an individualized, interactive, Web-based geriatrics portfolio to track the acquisition and mastery of these outcomes for students. DESCRIPTION: The required learning outcomes in geriatrics are presented to first-year students in their geriatrics portfolio Web page. The outcomes have been adapted from the recommendations published by the American Geriatrics Society's Education Committee.(1) The portfolio cross-references learning outcomes to specific activities in the curriculum. The activities include content given in lectures, multidisciplinary case discussions, standardized patient instructor (SPI) experiences involving older patients, and specific types of patient encounters during the clinical years. The portfolio allows documentation of completion dates of specific activities and the evaluations the student received. Certain activities such as the SPI experiences will include hyperlinks to their descriptions and the information that should be reviewed prior to each activity. The portfolio is integrated with existing administrative databases. Data entry occurs through links (e.g., exam scores), uploading comment forms from the SPI, and direct student input. One novel example of student input is the ability to upload information concerning encounters with older patients that students are recording in personal data assistant templates such that this information maps directly to the appropriate learning outcomes in their portfolios. The portfolio is designed to encourage students to take responsibility for their geriatrics education. Several types of evaluation data are provided, some that are specific to an activity (e.g., SPI feedback) and others that provide global assessments of learning outcomes (e.g., attitude surveys). The Web page can be displayed by the list of outcomes (categorized by attitudes, knowledge, and skills), by medical school year, and by date of completion. In this way, students can see at a glance how they are performing and whether they are up-to-date with completing the required outcomes. DISCUSSION: The geriatrics portfolio serves to identify and highlight geriatrics-related content across the four years. Its interactive features make it much more dynamic than a written transcript. Requiring proficiency in learning outcomes related to geriatrics for graduation will clearly convey to students that this information is critically important in their training to become physicians. The individualized evaluation summaries will prove useful to the student because self-directed learning opportunities can be targeted to address weak areas. Evaluation of performances will also aid program directors to appropriately modify the curriculum to address any deficiencies. This innovative Web-based approach to capture learning outcomes that are dispersed throughout a four-year curriculum may also find application in similar curricula (e.g., women's health and end-of-life care).

Education, Medical, Undergraduate↗

PubMedDate not supplied

Designing for social data analysis.

The NameVoyager, a Web-based visualization of historical trends in baby naming, has proven remarkably popular. We describe design decisions behind the application and lessons learned in creating an application that makes do-it-yourself data mining popular. The prime lesson, it is hypothesized, is that an information visualization tool may be fruitfully viewed not as a tool but as part of an online social environment. In other words, to design a successful exploratory data analysis tool, one good strategy is to create a system that enables "social" data analysis. We end by discussing the design of an extension of the NameVoyager to a more complex data set, in which the principles of social data analysis played a guiding role.

Computer Graphics↗

PubMed2002

Information technology and medication safety: what is the benefit?

Medication errors occur frequently and have significant clinical and financial consequences. Several types of information technologies can be used to decrease rates of medication errors. Computerized physician order entry with decision support significantly reduces serious inpatient medication error rates in adults. Other available information technologies that may prove effective for inpatients include computerized medication administration records, robots, automated pharmacy systems, bar coding, "smart" intravenous devices, and computerized discharge prescriptions and instructions. In outpatients, computerization of prescribing and patient oriented approaches such as personalized web pages and delivery of web based information may be important. Public and private mandates for information technology interventions are growing, but further development, application, evaluation, and dissemination are required.

Adverse Drug Reaction Reporting Systems↗

PubMed2006

miTarget: microRNA target gene prediction using a support vector machine.

BACKGROUND: MicroRNAs (miRNAs) are small noncoding RNAs, which play significant roles as posttranscriptional regulators. The functions of animal miRNAs are generally based on complementarity for their 5' components. Although several computational miRNA target-gene prediction methods have been proposed, they still have limitations in revealing actual target genes. RESULTS: We implemented miTarget, a support vector machine (SVM) classifier for miRNA target gene prediction. It uses a radial basis function kernel as a similarity measure for SVM features, categorized by structural, thermodynamic, and position-based features. The latter features are introduced in this study for the first time and reflect the mechanism of miRNA binding. The SVM classifier produces high performance with a biologically relevant data set obtained from the literature, compared with previous tools. We predicted significant functions for human miR-1, miR-124a, and miR-373 using Gene Ontology (GO) analysis and revealed the importance of pairing at positions 4, 5, and 6 in the 5' region of a miRNA from a feature selection experiment. We also provide a web interface for the program. CONCLUSION: miTarget is a reliable miRNA target gene prediction tool and is a successful application of an SVM classifier. Compared with previous tools, its predictions are meaningful by GO analysis and its performance can be improved given more training examples.

Algorithms↗

PubMed2002

Medical staff appointment and delineation of pediatric privileges in hospitals.

The review and verification of credentials and the granting of clinical privileges are required of every hospital to ensure that members of the medical staff are competent and qualified to provide specified levels of patient care. The credentialing process involves the following: 1) assessment of the professional and personal background of each practitioner seeking privileges; 2) assignment of privileges appropriate for the clinician's training and experience; 3) ongoing monitoring of the professional activities of each staff member; and 4) periodic reappointment to the medical staff on the basis of objectively measured performance. This statement examines the essential elements of a credentials review for initial and renewed medical staff appointments along with suggested criteria for the delineation of clinical privileges. Sample forms for the delineation of privileges can be found on the American Academy of Pediatrics Web site (http://www.aap.org/visit/cmte19.htm). Because of the differences in individual hospitals, no one method for credentialing is universally applicable. The medical staff of each hospital must, therefore, establish its own process based on the general principles reviewed in this statement. The issues of medical staff membership and credentialing have become very complex, and institutions and medical staffs are vulnerable to legal action. Consequently, it is advisable for hospitals and medical staffs to obtain expert legal advice when medical staff bylaws are constructed or revised.

Child↗

PubMed2003

eHealth for Europe.

eHealth has been defined as "a means of applying new low cost electronic technologies, such as 'web enabled' transactions, advanced networks and new design approaches, to healthcare delivery. In practice, it implies not only the application of new technologies, but also a fundamental re-thinking of healthcare processes based on using electronic communication and computer-based support at all levels and for all functions both within the healthcare service itself and in its dealings with outside suppliers. eHealth is a term which implies a way of working rather than a specific technology of application". As the chairman of the eHealth Working Group of the European Health Telematics Association and as an Honorary Consultant Physician at the Great Ormond Street Hospital for Children as well as a Consultant Paediatrician at the Portland Hospital for Women and Children, the author tries to identify relevant aspects of eHealth for Europe.

Europe↗