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At least 181 records · Page 10Linked to original sources

Web-based Simulation for Contrast Transfer Function and Envelope Functions.

We have implemented a Web-based simulation program for the contrast transfer function and envelope functions in Java and JavaScript. The simulation provides interactive controls of all the parameters in those functions. In addition to the predefined functions, users can easily define new functions that use any of the parameters in the preset functions. The most useful feature of this new simulation program is the convenient, universal accessibility through Web browsers on any computer platform that supports Java, such as Netscape and Internet Explorer.

Journal Article↗

Database of C-glycosylporphyrins in Web fashion.

The aim of this work was to organize chemical data in a client-server environment using Database Management System and Web fashion for the client interface. To solve this ancient problem (for us) merging text data, reaction schemes, tridimensional structures, and NMR, CD, and UV spectra images, we have based our implementation on a few fundamental points: no cost for the user, availability of data via the Internet, standard and freeware software, and a Web browser for the database inquiry. These functions are delivered in a platform-independent manner via the Internet and are used by computational experts and nonexperts alike. C-Glycosylporphyrins is the class of compounds chosen to test our applications. These results can be exportable for many other classes of chemical compounds.

Databases, Factual↗

JChemTidy: a tool for converting chemical Web document collections to an XHTML representation.

A robot-based procedure is described for traversing a collection of hyperlinked documents written in HTML and converting these to the XML-compliant and well-formed XHTML representation. Transcluded chemical content invoked using or HTML calls are converted to the XHTML recommended form. Additional attributes such as title or derived chemical attributes such as a SMILES descriptor are added to improve the indexing of the resulting document collection. Conformance tests for the popular Web browsers are reported.

Journal Article↗

Computational Science and Engineering Online (CSE-Online): a cyber-infrastructure for scientific computing.

With the expansion of the Internet and World Wide Web (or the Web), research environments have changed dramatically. As a result, the need to be able to efficiently and securely access information and resources from remote computer systems is becoming even more critical. This paper describes the development of an extendable integrated Web-accessible simulation environment for computational science and engineering called Computational Science and Engineering Online (CSE-Online; http://cse-online.net). CSE-Online is based on a unique client-server software architecture that can distribute the workload between the client and server computers in such a way as to minimize the communication between the client and server, thus making the environment less-sensitive to network instability. Furthermore, the new software architecture allows the user to access data and resources on one or more remote servers as well as on the computing grid while having the full capability of the Web-services collaborative environment. It can be accessed anytime and anywhere from a Web browser connected to the network by either a wired or wireless connection. It has different modes of operations to support different working environments and styles. CSE-Online is evolving into middleware that can provide a framework for accessing and managing remote data and resources including the computing grid for any domain, not necessarily just within computational science and engineering.

Engineering↗

AstexViewer: a visualisation aid for structure-based drug design.

AstexViewer is a Java molecular graphics program that can be used for visualisation in many aspects of structure-based drug design. This paper describes its functionality, implementation and examples of its use. The program can run as an Applet in a web browser allowing structures to be displayed without installing additional software. Applications of its use are described for visualisation and as part of a structure based design platform. The software is being made freely available to the community and may be downloaded from http://www.astex-technology.com/AstexViewer.

Computer Graphics↗

Project management system for structural and functional proteomics: Sesame.

A computing infrastructure (Sesame) has been designed to manage and link individual steps in complex projects. Sesame is being developed to support a large-scale structural proteomics pilot project. When complete, the system is expected to manage all steps from target selection to data-bank deposition and report writing. We report here on the design criteria of the Sesame system and on results demonstrating successful achievement of the basic goals of its architecture. The Sesame software package, which follows the client/server paradigm, consists of a framework, which supports secure interactions among the three tiers of the system (the client, server, and database tiers), and application modules that carry out specific tasks. The framework utilizes industry standards. The client tier is written in Java2 and can be accessed anywhere through the Internet. All the development on the server tier is also carried out in Java2 so as to accommodate a wide variety of computer platforms. The database tier employs a commercial database management system. Each Sesame application module consists of a simple user interface in the client tier, corresponding objects in the server tier, and relevant data stored in the centralized database. For security, access to stored data is controlled by access privileges. The system facilitates both local and remote collaborations. Because users interact with the system using Java Web Start or through a web browser, access is limited only by the availability of an Internet connection. We describe several Sesame modules that have been developed to the point where they are being utilized routinely to support steps involved in structural and functional proteomics. This software is available to parties interested in using it and assisting to guide its further development.

Database Management Systems↗

Data management and analysis for gene expression arrays.

Microarray technology makes it possible to simultaneously study the expression of thousands of genes during a single experiment. We have developed an information system, ArrayDB, to manage and analyse large-scale expression data. The underlying relational database was designed to allow flexibility in the nature and structure of data input and also in the generation of standard or customized reports through a web-browser interface. ArrayDB provides varied options for data retrieval and analysis tools that should facilitate the interpretation of complex hybridization results. A sampling of ArrayDB storage, retrieval and analysis capabilities is available (www.nhgri.nih.gov/DIR/LCG/15K/HTML/ ), along with information on a set of approximately 15,000 genes used to fabricate several widely used microarrays. Information stored in ArrayDB is used to provide integrated gene expression reports by linking array target sequences with NCBI's Entrez retrieval system, UniGene and KEGG pathway views. The integration of external information resources is essential in interpreting intrinsic patterns and relationships in large-scale gene expression data.

Computer Communication Networks↗

Quicktime virtual reality technology in light microscopy to support medical education in pathology.

The new computer-based interactive technologies in medicine, such as virtual reality (VR), have revolutionized education. The use of virtual microscopic images would be invaluable in the training of cyto-histopathologists. However, due to the vast amount of digital information on a scanned, conventional cyto-histological slide, which is enormous by current data storage standards, these systems are expensive and not widely used in pathological medicine. The authors propose an inexpensive system based on quicktime virtual reality (QTVR) technology (by Apple Computers Inc.), which accommodates a wide area of a slide at high magnification, generating a 'virtual slide' which makes it possible to navigate by conventional input devices. Commercial softwares that stitch consecutive, adjacent images of cyto-histological preparations onto a QTVR panorama were used. QTVR files have the ability to stand on their own as self-contained, multimedia applications and also have the ability to generate multinode scenes by means of 'hot spots'. QTVR 'movies' can be played on Macintosh or Windows platforms, and on major web browsers. Virtual slides by QTVR is an inexpensive system of high educational value, which allows the creation of multimedia databases of cyto-histological preparations that can exist on an internet server or can be distributed on removable media.

Databases as Topic↗

The Wisdom Project: virtual education in primary care.

This article examines the development of the Wisdom Project, a pilot for the teaching of informatics to primary health care professionals, using an original educational model based on e-mail and Web pages. The article begins by placing the development of the Wisdom Project in the context of changes in medical education and training. The aims and objectives of Wisdom are outlined, and the methodologies for setting up and evaluating the project are described. The article then presents the results of the evaluation, including the identification of significant improvements in knowledge of CD ROMs (P = 0.01), e-mail (P = 0.03), Medline (P = 0.02), operating systems (P = 0.02), Web browsers (P = 0.003) and word processing (P = 0.03). Improvements in evidence-based practice (EBP) did not reach significance. Finally, a number of conclusions are presented, considering the lessons learnt for the future development of such projects.

Attitude to Computers↗

Diagnosing minimal adenocarcinoma on prostate needle biopsy by real-time dynamic telepathology through the internet: evaluation of an economic technology for remote consultation.

Computer-aided telepathology was introduced about 10 years ago, but has not yet met with worldwide acceptance. Recently, the internet has been used for image transmission in telepathology. We set up an easily assembled system comprising a common microscope, a charge-coupled device (CCD) camera, a personal computer, and a commercial internet surveillance program with internet accessibility. The consultant then views the real-time images using a common web browser at the remote site. The purpose of the study was to assess the ability of the system to transmit images of sufficient quality to achieve high concordance between the diagnoses made at the home base and at the remote site. We chose cases of minimal adenocarcinoma on prostate needle biopsy, because these lesions are liable to be overlooked and, even if discovered, are subject to differences in interpretation due to their limited size and subtle histologic changes. One hundred prostate needle biopsy specimens, including 45 minimal adenocarcinoma, 11 atypical small acinar proliferation, and 44 benign lesions, were tested. Two pathologists, unaware of the final diagnoses, were recruited to provide intra- and interinstitutional consultation. The overall concordance rates between telepathology diagnoses and final diagnoses were 97% and 94% for the two pathologists, respectively. Our results demonstrate that this method is effective for teleconsultation. Similar systems using the internet can be easily set up by ordinary pathology laboratories to facilitate remote consultation.

Adenocarcinoma↗

Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell.

The Virtual Cell is a modeling tool that allows biologists and theorists alike to specify and simulate cell-biophysical models on arbitrarily complex geometries. The framework combines an intuitive, front-end graphical user interface that runs in a web browser, sophisticated server-side numerical algorithms, a database for storage of models and simulation results, and flexible visualization capabilities. In this paper, we present an overview of the capabilities of the Virtual Cell, and, for the first time, the detailed mathematical formulation used as the basis for spatial computations. We also present summaries of two rather typical modeling projects, in order to illustrate the principal capabilities of the Virtual Cell. (c) 2001 American Institute of Physics.

Journal Article↗

Wireless and Web-based medical monitoring in the home.

A remote medical monitoring system is described, which continuously monitors patients' state of health. The system uses the services provided by intranets and the Internet to allow remote supervision of patients, who may be domiciled in their own home. A hardware/software prototype system has been constructed to demonstrate the use of non-invasive and minimally intrusive sensors attached to patients. Continuous real-time data is acquired, stored and processed. A wireless system or wires connect these monitor devices to the World Wide Web and, on request, information is delivered to authorized medical staff via a web browser or Wireless Application Protocol-enabled mobile telephones. Medical staff may examine real-time data or graphical information and make comparisons with historical data. Parameters may be set to select and control the data acquisition devices. The potential exists for augmentation of patient health by development of novel sensors and low-power electronic circuitry, and this research continues.

Aged↗

ReproMED on the Internet today and tomorrow.

ReproMED comprises a range of projects applying and researching the role of information technology to support clinical care, education and research in reproductive medicine. This article traces the development of ReproMED on the Internet and concludes by speculating on the future. The project started with a critical evaluation of the infertility information needs of general practitioners and the role of hypertext in meeting those needs, leading to the production of a ReproMED CD-Rom. However, as the project was under development in 1995, Microsoft launched its first web browser amid major expansions of the Internet, thus the project switched to a series of websites and played host to national bodies including the British Fertility Society and the British Andrology Society. After a critical evaluation of the role of the Internet in supporting postgraduate medical education in the southwest region, reproductive medicine training over the Internet was piloted. This pilot was followed by a series of similar training programmes for junior doctors, specialists and general practitioners, leading to the establishment of a formal MSc delivered principally over the Internet. In addition to professional education and research, the ReproMED websites provide patients with extensive interactive information. The future holds many exciting possibilities with rapid technological developments and ever-increasing information needs.

Computer-Assisted Instruction↗

Real-time volume rendered MRI for interventional guidance.

Volume renderings from magnetic resonance imaging data can be created and displayed in real-time with user interactivity. This can provide continuous 3D feedback to assist in guiding an interventional procedure. A system is presented which can produce real-time volume renderings from 2D multi-slice or 3D MR pulse sequences. Imaging frame rates up to 30 per second have been demonstrated with a latency of approximately one-third of a second, depending on the image matrix size. Several interactive capabilities have been implemented to enhance visualization such as cut planes, individual channel scaling and color highlighting, view sharing, saturation preparation, complex subtraction, gating control, and choice of alpha blending or MIP rendering. The system is described and some interventional application examples are shown. To view movies of some of the examples, enter the following address into a web browser: http://nhlbi.nih.gov/labs/papers/lce/guttman/rtvolmri/index/htm.

Animals↗

Using a multi-user desktop-based virtual reality system to recreate the São Miguel das Missões ruins.

This paper presents a project initiated back in 1999, in which Virtual Reality is applied in order to create a virtual community over the Internet. The desktop-based multi-user virtual reality system recreates a three-dimensional environment based on photogrammetric maps from the São Miguel das Missões church ruins. The ruins correspond to one of the Jesuit Mission (settlement) which was active in the south of Brazil in the 17th and 18th centuries. It has a great importance to the local region in terms of cultural, historic, and tourist aspects. It has also been inscribed in the UNESCO's world heritage list since 1983. This electronic mock-up allows several interactive operations such as community chats, electronic message exchanging, message boards, walking-through, discussion groups, and embedding of other media such as movies, sound, and html pages. The only requirement necessary to access the community is a web browser powered with any Virtual Reality Modeling Language (VRML) plug-in freely available over the Internet. It is expected that such a solution improves the conservation and dissemination of the Brazilian historic patrimony, congregating history, art, and tourist information in one place on the Internet.

Humans↗

Opportunities on the Internet for child and adolescent psychopharmacologists: net access and mailing lists.

The Internet, a system linking computers around the world, provides clinical and research psychopharmacologists with a convenient and efficient way to exchange information and offers a growing number of services to facilitate patient care. These opportunities are not theoretical, not in the future, and not for a select few. Many patients are already benefitting from practitioners who have sought guidance for their clinical work on the Internet. This article describes, for the novice user, how to begin the Internet journey. It also discusses psychopharmacology-related mailing lists, including a site that specializes in child and adolescent psychopharmacology. Subsequent articles will (1) show how to use Medlines to conduct literature searches and retrieve abstracts and articles from the computer screen, (2) describe ways to enter and traverse the World Wide Web (the "multimedia" portion of Internet), and (3) survey the use of "Web browsers" to find specialized psychopharmacology resources and databases, electronic journals, pertinent bulletin boards, and support services for patients and families-all with an emphasis on direct benefits to the practicing psychopharmacologist.

Computer Communication Networks↗

Clinical-oriented collaboration over the Web during interventional radiology procedures.

Multidisciplinary collaboration is a key requirement in several contemporary interventional radiology procedures (IRPs). We proposed a hybrid system (NetAngio) to enable "on the fly" heterogeneous collaboration to support IRP providing intraoperating essential services, and investigate its feasibility and effectiveness in a referral medical center. We have developed a Web-based, cost-effective structure, able to support real-time mentoring, image manipulation, and education services beyond the boundaries of the single institution and potentially allow sub specialists to participate in opinion and decision making in more complex cases. Supported services based on a Motion Joint Photographic Experts Group (MJPEG) coder/decoder (CODEC) can be easily accessible by authorized collaborators, within a user-friendly interface by using a typical Web-browser. Ten interventional radiologists, two vascular surgeons and two medical physicists participated in 33 "fully collaborative" cases during a 13-month period from January 2004 to February 2005. In addition, fifteen 90-minute open seminars and finally, 75 expert's module activations, and 255 learner's module activations were performed during the evaluation period. Collaborative procedures are able to enhance outcomes performance especially in more complex cases where the simultaneous presence of a remote expert interventionist and a medical physicist or a surgeon is required. Further research is needed to promote integration of additional data sources and services.

Education, Medical↗

WebBLAST 2.0: an integrated solution for organizing and analyzing sequence data.

SUMMARY: WebBLAST is a suite of programs intended to assist in organizing sequencing data and to provide first-pass sequence analysis in an automated fashion. Data processing is fully automated, with end-users being presented both graphical and tabular summaries of data that can be viewed using any Web browser. AVAILABILITY: The program is free and available at http://genome.nhgri.nih. gov/webblast.

Base Sequence↗