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At least 73 records · Page 4Linked to original sources

PubMed1999

WebCIS: large scale deployment of a Web-based clinical information system.

WebCIS is a Web-based clinical information system. It sits atop the existing Columbia University clinical information system architecture, which includes a clinical repository, the Medical Entities Dictionary, an HL7 interface engine, and an Arden Syntax based clinical event monitor. WebCIS security features include authentication with secure tokens, authorization maintained in an LDAP server, SSL encryption, permanent audit logs, and application time outs. WebCIS is currently used by 810 physicians at the Columbia-Presbyterian center of New York Presbyterian Healthcare to review and enter data into the electronic medical record. Current deployment challenges include maintaining adequate database performance despite complex queries, replacing large numbers of computers that cannot run modern Web browsers, and training users that have never logged onto the Web. Although the raised expectations and higher goals have increased deployment costs, the end result is a far more functional, far more available system.

Clinical Medicine↗

PubMed2005

Web-based virtual microscopy in teaching and standardizing Gleason grading.

Gleason grading forms the basis of prognostic and therapeutic assessment in prostatic carcinoma despite its subjective nature and substantial interobserver variation. The accuracy of Gleason grading can be improved by the use of educational tools such as reference images. However, conventional microscopy images are of limited educational value because it is neither possible to view the sample at different magnifications nor to navigate into different areas of the specimen. This limitation can be overcome by the use of virtual microscopy, which allows viewing entire digitized microscope slides. We created an interactive Web site ( www.webmicroscope.net/gleason ) featuring a comprehensive set of prostatic needle biopsies as virtual slides, which can be viewed with a standard Web browser (Internet Explorer or Netscape). To evaluate the validity of Web-based virtual microscopy for Gleason grading, an experienced uropathologist (TK) scored a series of 62 biopsies from the original glass slides and 6 weeks later from virtual slides on the Web site using an ordinary desktop computer. The intraobserver agreement was excellent, with identical Gleason scores found in 48 of the 62 cases ( kappa = 0.73). The 14 remaining scores differed only by 1 point on the Gleason scale (2-10). The virtual slides were viewed by 2 other uropathologists (PM and HH), with interobserver kappa coefficients ranging from 0.55 to 0.62, which is within the range of previously reported studies using glass slides. The 3 uropathologists' Gleason scores were included as reference scores on the Web site, which now serves as a publicly open platform for self-testing and learning of Gleason grading. We conclude that Web-based virtual microscopy is a promising new tool for teaching and standardizing Gleason grading.

Biopsy, Needle↗

PubMed1996

What is the Internet learning about you while you are learning about the Internet?

Privacy, confidentiality, and security are largely taken for granted in physicians' offices. However, increasingly, physicians and insurance providers will be obtaining and exchanging information through the sophisticated resources available on the Internet and the World Wide Web (WWW, or the Web). Some of these resources will maintain the same privacy experienced in the office of a trusted clinician or in the reading room of a great library, but more often than not, while people are learning from the Web, the Web will be learning about them. The author describes a new type of file used by Web browsers (the "cookies" file) that may enable users to browse the Web more efficiently but that may also compromise the user's privacy. He then discusses exactly how abuses might occur if information obtained through cookies files is misused, particularly by health insurance providers. Finally, he considers privacy and confidentiality issues raised by computer-based medical records, and the role of the health care provider in maintaining confidential and helpful doctor-patient relationships in the face of rapid technological change and the pressures of managed care.

Computer Communication Networks↗

PubMed2004

A data management system for structural genomics.

BACKGROUND: Structural genomics (SG) projects aim to determine thousands of protein structures by the development of high-throughput techniques for all steps of the experimental structure determination pipeline. Crucial to the success of such endeavours is the careful tracking and archiving of experimental and external data on protein targets. RESULTS: We have developed a sophisticated data management system for structural genomics. Central to the system is an Oracle-based, SQL-interfaced database. The database schema deals with all facets of the structure determination process, from target selection to data deposition. Users access the database via any web browser. Experimental data is input by users with pre-defined web forms. Data can be displayed according to numerous criteria. A list of all current target proteins can be viewed, with links for each target to associated entries in external databases. To avoid unnecessary work on targets, our data management system matches protein sequences weekly using BLAST to entries in the Protein Data Bank and to targets of other SG centers worldwide. CONCLUSION: Our system is a working, effective and user-friendly data management tool for structural genomics projects. In this report we present a detailed summary of the various capabilities of the system, using real target data as examples, and indicate our plans for future enhancements.

Journal Article↗

PubMedDate not supplied

A browser based image bank, useful tool or expensive toy?

DIBS, the Digital Image Banking System, is a web browser based environment for depositing and withdrawing generic medical images. These can be annotated or modified on an individual's computer for use in talks and lectures. DIBS is programmed in 'C', to query and update a database as well as producing web pages on the 'fly'. Images are deposited using an interactive form, minimizing data entry and are received in a digital format or are digitized on demand. Three interfaces allow DIBS to be searched; an image map of the human body presents a simple graphical interface, whilst more specific searches can be performed by selecting categories from predefined scrolling menus or using a full text search. When a DIBS search is performed, preview thumbnail images and descriptions are provided, linked to the full size images that can be saved locally along with the text description. DIBS offers fast and convenient access to a wide range of medical images, eliminating the time consuming process of producing one's own slides or borrowing from colleagues. It is proving to be a useful tool within our Medical School but some copyright, ethical and image security issues still need to be resolved.

Computer Graphics↗

PubMed2006

[The design and realization of Web-view PACS browser].

This article analyses the system structure and realization model of Web-view PACS browser in combination with the characteristic of PACS, and presents the realizing process of the web-view PACS browser using JSP mode and B/S model.

Computer Communication Networks↗

PubMed1997

Implementation of an electronic teaching file using web technology.

The implementation of an electronic teaching file using web technology is discussed in this article. A web client server model is used for a standard web browser capable of displaying joint photographic Experts Group (JPEG) compression images. Like other web-based teaching files, this teaching file in a similar way uses a database containing information. This database section of the teaching file allows flexible database querying and viewing of pages generated by hypertext markup language (HTML). Because the browser client is so flexible, images types such as video and 3D representations with virtual reality markup language (VRML) can be displayed.

Computer Communication Networks↗

PubMed2006

Systematic analysis of Arabidopsis organelles and a protein localization database for facilitating fluorescent tagging of full-length Arabidopsis proteins.

Cells are organized into a complex network of subcellular compartments that are specialized for various biological functions. Subcellular location is an important attribute of protein function. To facilitate systematic elucidation of protein subcellular location, we analyzed experimentally verified protein localization data of 1,300 Arabidopsis (Arabidopsis thaliana) proteins. The 1,300 experimentally verified proteins are distributed among 40 different compartments, with most of the proteins localized to four compartments: mitochondria (36%), nucleus (28%), plastid (17%), and cytosol (13.3%). About 19% of the proteins are found in multiple compartments, in which a high proportion (36.4%) is localized to both cytosol and nucleus. Characterization of the overrepresented Gene Ontology molecular functions and biological processes suggests that the Golgi apparatus and peroxisome may play more diverse functions but are involved in more specialized processes than other compartments. To support systematic empirical determination of protein subcellular localization using a technology called fluorescent tagging of full-length proteins, we developed a database and Web application to provide preselected green fluorescent protein insertion position and primer sequences for all Arabidopsis proteins to study their subcellular localization and to store experimentally verified protein localization images, videos, and their annotations of proteins generated using the fluorescent tagging of full-length proteins technology. The database can be searched, browsed, and downloaded using a Web browser at http://aztec.stanford.edu/gfp/. The software can also be downloaded from the same Web site for local installation.

Arabidopsis↗

PubMed1996

Implementing a distributed intranet-based information system.

The article discusses Internet and intranet technologies and describes how to install an intranet-based information system using the Merle language facility and other readily available components. Merle is a script language designed to support decentralized medical record information retrieval applications on the World Wide Web. The goal of this work is to provide a script language tool to facilitate construction of efficient, fully functional, multipoint medical record information systems that can be accessed anywhere by low-cost Web browsers to search, retrieve, and analyze patient information. The language allows legacy MUMPS applications to function in a Web environment and to make use of the Web graphical, sound, and video presentation services. It also permits downloading of script applets for execution on client browsers, and it can be used in standalone mode with the Unix, Windows 95, Windows NT, and OS/2 operating systems.

Computer Communication Networks↗

PubMed2002

Asynchronous web-based patient-centered home telemedicine system.

A web-based system for asynchronous multimedia messaging between shoulder replacement surgery patients at home and their surgeons was developed and tested. A web browser plug-in simplifies the process of capturing video and transferring it to a web site for novice computer users. The design of the video capture plug-in can be reused to acquire and securely transfer any type of data over the web. For example, readings from home biosensor instruments (e.g., glucometers and spirometers) that can be connected to a personal computer can be transferred to a home telemedicine web site. Both patients and doctors can access this web site to monitor health status longitudinally. Six patients, whose familiarity with computers ranged from no experience to expert users, used the system. All of the subjects were able to use the system to check treatment reminders and to send at least one message with video to their surgeons. The surgeons monitored the system regularly and always responded to messages within 24 h during the six-month trial period.

Arthroplasty, Replacement↗

PubMed2003

Internet resources for neurologists.

This fourth and final review in the JNNP internet series summarises the essential internet resources for adult and paediatric clinical neurology, neuroradiology, and neurophysiology. This article is freely available on the JNNP website (www.jnnp.com), where-within seconds-the complete list of recommended websites can be easily downloaded and incorporated into your web browser as a Bookmark/Favorite file. The further progress of clinical neurology on the world wide web will be monitored in JNNP Neuronline fillers and JNNP Neurology in Practice supplements.

Evidence-Based Medicine↗

PubMed1997

W.W.W. cooperative multimedia interface in medicine.

The World Wide Web is now the most used multimedia information system on Internet allowing, by means of Web browsers such as Netscape Navigator or Mosaic, distribution or consultation of hypermedia documents. Although the Web has appeared only recently, the growth of its use has generated the emergence of numerous information and knowledge bases in the medical field. We suggest to investigate extended functionalities in order to introduce cooperative activities in our medical information system. These new activities allow asynchronous exchange of records and synchronous cooperation for a better coordination of the work within and between hospitals.

Computer Communication Networks↗

PubMed2001

Real time information from bedside monitors as part of a web-based patient record.

Traditional paper-based Medical Records, and even most of their digital counterparts, represent historical patient information. On the other hand new generations of Point-of-Care devices can be connected to standard networks and deliver streams of real time data through an Intranet, or even the Internet. Vital signs provided by IP-based devices can then be viewed at remote stations. Merging both worlds, real time and historical, in the pursuit of a comprehensive EPR is the main challenge of the present project. The basic infra-structure is composed of three main components: an existing Web-based EPR viewing station1 (Web-EPR); a fully integrated HIS/PACS system1; and a monitoring network (Siemens Infinity Network 2). Communication between the components was obtained by developing interfaces based on both HL7 and Siemens protocols the later only for waveforms. For the graphical display a web-browser-based application of the streamed signals was developed and integrated into the existing Web-EPR. This addition expanded the Web-EPR capabilities providing means to include real time signals and calculated parameters on the set of information already available. Some extra features of this project include: one-way SMS messaging of the parameters, interactive WAP access and a DICOM compliant storage of signal waveforms.

Computer Security↗

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↗

PubMed2003

Development of computerized Kana Pick-out Test for the neuropsychological examination.

The Kana Pick-out Test, which was developed in Japan and done with paper and pencil, is said to be suitable for inspecting higher-order brain function and to be a good method for screening persons with mild or slight dementia. We have developed a computerized version of the Kana Pick-out Test, which runs on a stand-alone computer, intended to be utilized for mass screening and self-administration. The program was developed with Microsoft Visual Basic 6.0 and runs under the Windows operating system on any IBM PC compatible computer. In this study, all subjects could use the system by interacting with the computer and it was found that the system seemed to have the capability of detecting cognitive status equal to the paper-based Kana Pick-out Test. Besides this, we developed a network-based Kana Pick-out game software which was intended to attract user's notice. The game program was written in JAVA language and runs on a web-browser supporting JAVA on any operating system. The program, a so called applet, is located on our web site (http://environ.med.tottori-u.ac.jp) and anyone can use the applet by accessing our homepage.

Adult↗

PubMed2004

The physiology constant database of teen-agers in Beijing.

Physiology constants of adolescents are important to understand growing living systems and are a useful reference in clinical and epidemiological research. Until recently, physiology constants were not available in China and therefore most physiologists, physicians, and nutritionists had to use data from abroad for reference. However, the very difference between the Eastern and Western races casts doubt on the usefulness of overseas data. We have therefore created a database system to provide a repository for the storage of physiology constants of teen-agers in Beijing. The several thousands of pieces of data are now divided into hematological biochemistry, lung function, and cardiac function with all data manually checked before being transferred into the database. The database was accomplished through the development of a web interface, scripts, and a relational database. The physiology data were integrated into the relational database system to provide flexible facilities by using combinations of various terms and parameters. A web browser interface was designed for the users to facilitate their searching. The database is available on the web. The statistical table, scatter diagram, and histogram of the data are available for both anonym and user according to queries, while only the user can achieve detail, including download data and advanced search.

Adolescent↗

PubMedDate not supplied

Improving the interactivity and functionality of Web-based radiology teaching files with the Java programming language.

Java is a programming language that runs on a "virtual machine" built into World Wide Web (WWW)-browsing programs on multiple hardware platforms. Web pages were developed with Java to enable Web-browsing programs to overlay transparent graphics and text on displayed images so that the user could control the display of labels and annotations on the images, a key feature not available with standard Web pages. This feature was extended to include the presentation of normal radiologic anatomy. Java programming was also used to make Web browsers compatible with the Digital Imaging and Communications in Medicine (DICOM) file format. By enhancing the functionality of Web pages, Java technology should provide greater incentive for using a Web-based approach in the development of radiology teaching material.

Computer Communication Networks↗

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↗