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At least 487 records · Page 27Linked to original sources

PubMed2005

ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs.

RT-PCR is one of the most powerful and direct methods to detect transcript variants due to alternative splicing (AS) that increase transcript diversity significantly in vertebrates. ASePCR is an efficient web-based application that emulates RT-PCR in various tissues. It estimates the amplicon size for a given primer pair based on the transcript models identified by the reverse e-PCR program of the NCBI. The tissue specificity of each PCR band is deduced from the tissue information of expressed sequence tag (EST) sequences compatible with each transcript structure. The output page shows PCR bands like a gel electrophoresis in various tissues. Each band in the output picture represents a putative isoform that could happen in a tissue-specific manner. It also shows the EST alignment and tissue information in the genome browser. Furthermore, the user can compare the AS patterns of orthologous genes in other species. The ASePCR, available at http://genome.ewha.ac.kr/ASePCR/, supports the transcriptome models of the RefSeq, Ensembl, ECgene and AceView for human, mouse, rat and chicken genomes. It will be a valuable web resource to explore the transcriptome diversity associated with different tissues and organs in multiple species.

Algorithms↗

PubMed1996

Challenges and opportunities of the Internet for medical oncology.

PURPOSE: The internet, and in particular the world wide web (www), has a rapidly increasing potential to provide information for oncologists and their patients about cancer biology and treatment. A brief overview of this environment is given along with examples of how easily the information is accessed as a means of introducing the web page of the American Society of Clinical Oncology (ASCO), ASCO OnLine. METHODS: Oncology information sources on the www were accessed from the author's home using a 14.4 kbs modem, Netscape browser (Netscape communications Corp, Mountain View, CA), and the locations recorded for tabulation and discussion. RESULTS: Overwhelming amounts of oncology-related information are now available via the Internet. CONCLUSION: Oncology as a subspecialty is ideally suited to apply the newest information technology to traditional needs in areas of education, research, and patient care. Oncologists will increasingly act as information guides rather than information resources for patients and their families with cancer.

Computer Communication Networks↗

PubMed2000

Oral medicine and surgery interests on the Internet.

The Internet is a global network which link millions of people via the information highway. The internet use for dentistry is growing rapidly. This has been accelerated by the use of many browsers. There has been a very rapid increase in the number of media resources and the quality of information over the internet has improved. Many universities, institutions and dental suppliers are establishing web pages. The resources is getting vast and in this paper, we explore the usefulness of the internet. This paper serve as a guide to the oral surgery, oral pathology and oral medicine resources and forums available on the information highway.

Information Storage and Retrieval↗

PubMed2005

Web GIS in practice II: interactive SVG maps of diagnoses of sexually transmitted diseases by Primary Care Trust in London, 1997 - 2003.

BACKGROUND: The rates of Sexually transmitted diseases (STDs) in England have been rising steadily since the mid 1990s, making them a major public health concern. In 2003, 672,718 people were diagnosed with an STD in England, and around one third of those cases were diagnosed in London. RESULTS: Using GeoReveal v1.1 for Windows, we produced Web-based interactive choropleth maps of diagnoses of STDs by Primary Care Trust (PCT) in London for the years from 1997 to 2003 http://healthcybermap.org/PCT/STDs/. These maps are in Scalable Vector Graphics (SVG) format and require a freely available Adobe SVG browser plug-in to be displayed. They are based on data obtained from the House of Commons Hansard Written Answers for 15 October 2004. They show steadily rising rates of STDs in London over the covered seven-year period. Also, one can clearly see on the maps that PCTs located in central London had the highest numbers of STD diagnoses throughout the mapped seven years. A companion bar chart allows users to instantly compare the STD figure of a given PCT for a given year against the average figure for all 25 mapped PCTs for the same year, and also compare those figures across all seven years. The maps offer users a rich set of useful features and functions, including the ability to change the classification method in use, the number of ranges in the map, and the colour theme, among others. CONCLUSIONS: Wizard-driven tools like GeoReveal have made it very easy to transform complex raw data into valuable decision support information products (interactive Web maps) in very little time and without requiring much expertise. The resultant interactive maps have the potential of further supporting health planners and decision makers in their planning and management tasks by allowing them to graphically interrogate data, instantly spot trends, and make quick and effective visual comparisons of geographically differentiated phenomena between different geographical areas and over time.SVG makes an ideal format for such maps. SVG is a World Wide Web Consortium non-proprietary, XML-based vector graphics format, and is an extremely powerful alternative to Macromedia(R) Flash and bitmap graphics.

Journal Article↗

PubMed2026

eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation-gene expression associations through across 11 tissues and 4 diseases.

MOTIVATION: Epigenome-wide association studies (EWAS) have identified numerous DNA methylation (DNAm) CpG sites associated with complex traits and diseases, but interpretation of those CpG sites remains challenging because in EWAS, CpGs are mostly linked to nearby genes based only on genomic proximity. Expression quantitative trait methylation (eQTM) analyses connect DNAm CpGs with statistically associated gene expression levels. However, a comprehensive, searchable resource integrating eQTMs across diverse tissues and disease contexts has been lacking. RESULTS: We developed the eQTM Atlas, a web-based resource that manually curates more than 11 million DNAm-gene expression associations from eight cohorts, covering 11 tissue types, four broad disease contexts, 173,886 unique CpG probes and 20,231 unique genes. The Atlas supports gene- or CpG- searches by tissue or disease type and finding associated CpG or genes, visualization of cis- and trans-eQTMs through genome browser, heatmap interfaces across various tissues, and cohort-level data downloads. By integrating eQTM results with EWAS resources, the eQTM Atlas enables users to connect disease- or trait-associated CpGs to statistically associated genes rather than relying solely on proximity-based gene annotation, supporting functional interpretation of EWAS findings and generation of disease-specific regulatory hypotheses. AVAILABILITY AND IMPLEMENTATION: The eQTM Atlas is freely available at https://shiny.crc.pitt.edu/eqtm_browser/. The web interface is implemented in R Shiny and hosted through the University of Pittsburgh Center for Research Computing (CRC). Source code is available at https://github.com/ads303/eQTM-Atlas.

DNA methylation↗

PubMed2005

BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser.

The growing amount of information resulting from the increasing number of publicly available genomes and experimental results thereof necessitates the development of comprehensive systems for data processing and analysis. In this paper, we describe the current state and latest developments of our BRIGEP bioinformatics software system consisting of three web-based applications: GenDB, EMMA and ProDB. These applications facilitate the processing and analysis of bacterial genome, transcriptome and proteome data and are actively used by numerous international groups. We are currently in the process of extensively interconnecting these applications. BRIGEP was developed in the Bioinformatics Resource Facility of the Center for Biotechnology at Bielefeld University and is freely available. A demo project with sample data and access to all three tools is available at https://www.cebitec.uni-bielefeld.de/groups/brf/software/brigep/. Code bundles for these and other tools developed in our group are accessible on our FTP server at ftp.cebitec.uni-bielefeld.de/pub/software/.

Bacterial Proteins↗

PubMed2004

ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection.

The ORFDB (http://orf.invitrogen.com/) represents an ongoing effort at Invitrogen Corporation to integrate relevant scientific data with an evolving collection of human and mouse Open Reading Frame (ORF) clones (Ultimate ORF Clones). The ORFDB serves as a central data warehouse enabling researchers to search the ORF collection through its web portal ORFBrowser, allowing researchers to find the Ultimate ORF clones by blast, keyword, GenBank accession, gene symbol, clone ID, Unigene ID, LocusLink ID or through functional relationships by browsing the collection via the Gene Ontology (GO) Browser. As of October 2003, the ORFDB contains 6200 human and 2870 mouse Ultimate ORF clones. All Ultimate ORF clones have been fully sequenced with high quality, and are matched to public reference protein sequences. In addition, the cloned ORFs have been extensively annotated across six categories: Gene, ORF, Clone Format, Protein, SNP and Genomic links, with the information assembled in a format termed the ORFCard. The ORFCard represents an information repository that documents the sequence quality, alignment with respect to public protein sequences, and the latest publicly available information associated with each human and mouse gene represented in the collection.

Animals↗

PubMed1997

[Construction of an MRI reporting system using the Internet].

Out university hospital, includes a LAN (Local Area Network) and uses network services such as WWW(World Wide Web). We have constructed an MRI diagnostic reporting system on the Internet in which interactive date management was established on WWW by using CGI (Common Gateway Interface) software. Linking database information such as MRI reports with WWW browsers using by CGI provides easy data access to the database and offers hypertext and searching. This system suggests the possibility of creating a cheaper and more flexible network using Internet technology.

Computer Communication Networks↗

PubMed2002

Storage and distribution of pathology digital images using integrated web-based viewing systems.

CONTEXT: Health care providers have expressed increasing interest in incorporating digital images of gross pathology specimens and photomicrographs in routine pathology reports. OBJECTIVE: To describe the multiple technical and logistical challenges involved in the integration of the various components needed for the development of a system for integrated Web-based viewing, storage, and distribution of digital images in a large health system. DESIGN: An Oracle version 8.1.6 database was developed to store, index, and deploy pathology digital photographs via our Intranet. The database allows for retrieval of images by patient demographics or by SNOMED code information. SETTING: The Intranet of a large health system accessible from multiple computers located within the medical center and at distant private physician offices. RESULTS: The images can be viewed using any of the workstations of the health system that have authorized access to our Intranet, using a standard browser or a browser configured with an external viewer or inexpensive plug-in software, such as Prizm 2.0. The images can be printed on paper or transferred to film using a digital film recorder. Digital images can also be displayed at pathology conferences by using wireless local area network (LAN) and secure remote technologies. CONCLUSIONS: The standardization of technologies and the adoption of a Web interface for all our computer systems allows us to distribute digital images from a pathology database to a potentially large group of users distributed in multiple locations throughout a large medical center.

Computer Storage Devices↗

PubMed2006

ArrayFusion: a web application for multi-dimensional analysis of CGH, SNP and microarray data.

UNLABELLED: ArrayFusion annotates conventional CGH results and various types of microarray data from a range of platforms (cDNA, expression, exon, SNP, array-CGH and ChIP-on-chip) and converts them into standard formats which can be visualized in genome browsers (Affymetrix Integrated Genome Browser and GBrowse in the HapMap Project). Converted files can then be imported simultaneously into a single genome browser to benefit a collective interpretation between different array results. ArrayFusion therefore provides a new type of tool facilitating the integration of CGH and array results to provide new experimental directions. AVAILABILITY: http://microarray.ym.edu.tw/tools/arrayfusion

Algorithms↗

PubMed2003

Rapid deployment of physician order entry using web-based, disease-specific order sets.

Computerized physician order entry (POE) is a disruptive technology that holds great promise to reduce medical errors and improve workflow. However, Studies have reported significant physician resistance. This presentation will describe a two-pronged strategy to build broad support for POE: To build a secure, open source, browser-based platform to support POE and create a large number of disease-specific order-sets for immediate use. This presentation will demonstrate the conceptual framework and implementation requirements for such an endeavor.

Attitude of Health Personnel↗

PubMed2004

Isotopica: a tool for the calculation and viewing of complex isotopic envelopes.

The web application Isotopica has been developed as an aid to the interpretation of ions that contain naturally occurring isotopes in a mass spectrum. It allows the calculation of mass values and isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. In addition, Isotopica takes modifications of the input molecule into consideration using a simple and flexible language as a straightforward extension of the molecular formula syntax. This function is especially useful for biomolecules, which are often subjected to additional modifications other than normal constituents, such as the frequently occurring post-translational modification in proteins. The isotopic distribution of any molecule thus defined can be calculated by considering full widths at half maximum or mass resolution. The combined envelope of several overlapping isotopic distributions of a mixture of molecules can be determined after specifying each molecule's relative abundance. The results can be displayed graphically on a local PC using the Isotopica viewer, a standalone application that is downloadable from the sites below, as a complement to the client browser. The m/z and intensity values can also be obtained in the form of a plain ASCII text file. The software has proved to be useful for peptide mass fingerprinting and validating an observed isotopic ion distribution with reference to the theoretical one, even from a multi-component sample. The web server can be accessed at http://bioinformatica.cigb.edu.cu/isotopica and http://coco.protein.osaka-u.ac.jp/isotopica [correction].

Amino Acid Sequence↗

PubMed1997

A guide to finding and evaluating best practices health care information on the Internet: the truth is out there?

BACKGROUND: The advent of virtually free Internet access has opened large vistas of health care information to those willing to invest a small amount of time and energy learning how to perform searches using browser software. Health care providers, organizations, and professional associations, among many others, publish "best practices" information for both administrative and clinical audiences, making these recommendations among the fastest-growing types of health care information appearing on the World Wide Web. The problem is how to find best practices among the wealth of resources on the Internet and then how to separate the proverbial wheat from the chaff. WHO IS SEEKING BEST PRACTICES ON THE INTERNET? Best practice describes a process or technique whose employment results in improved patient and/or organizational outcomes. Health care providers, managed care organizations, administrators, payers, and policy analysts are all interested in improving the quality of health care and are likely to be customers of best practices informational resources. HOW TO EVALUATE THE QUALITY OF BEST PRACTICES INFORMATION? Once the information is available on the Internet, the problem for the searcher shifts from one of quantity to quality. The best practices information seeker should stop and ask a number of questions about the quality of information, its sources, and the methods used to obtain it. CONCLUSION: The "truth" may be out there some-where in cyberspace, but locating best practices information and evaluating its quality require new skills and patience and time to practice and develop them to the point of efficiency.

Authorship↗

PubMed2005

Alternative Web Access toolKit for impairEd users.

Although navigation through the World Wide Web (WWW) may seem pretty straightforward to most of us, a large group of individuals exists for whom it is not quite as easy. We are referring to people with disabilities. This paper is a proposal for an Internet user agent (browser) designed to help people with severe physical impairments to navigate the http://WWW. It utilizes a single switch as an input device and scanning as a selection method.

Communication Devices for People with Disabilities↗

PubMed2006

Making the procedure manual come alive: A prototype relational database and dynamic website model for the management of nursing information.

The nursing procedural manual is an essential resource for clinical practice, yet insuring its currency and availability at the point of care remains an unresolved information management challenge for nurses. While standard HTML-based web pages offer significant advantage over paper compilations, employing emerging computer science tools offers even greater promise. This paper reports on the creation of a prototypical dynamic web-based nursing procedure manual driven by a relational database. We created a relational database in MySQL to manage, store, and link the procedure information, and developed PHP files to guide content retrieval, content management, and display on demand in browser-viewable format. This database driven dynamic website model is an important innovation to meet the challenge of content management and dissemination of nursing information.

Information Management↗

PubMed2024

A fast comparative genome browser for diverse bacteria and archaea.

Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast.genomics, that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast.genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast.genomics is available at https://fast.genomics.lbl.gov.

Archaea↗

PubMed1999

A dynamic two-dimensional polyacrylamide gel electrophoresis database: the mycobacterial proteome via Internet.

Proteome analysis by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry, in combination with protein chemical methods, is a powerful approach for the analysis of the protein composition of complex biological samples. Data organization is imperative for efficient handling of the vast amount of information generated. Thus we have constructed a 2-D PAGE database to store and compare protein patterns of cell-associated and culture-supernatant proteins of different mycobacterial strains. In accordance with the guidelines for federated 2-DE databases, we developed a program that generates a dynamic 2-D PAGE database for the World-Wide-Web to organise and publish, via the internet, our results from proteome analysis of different Mycobacterium tuberculosis as well as Mycobacterium bovis BCG strains. The uniform resource locator for the database is http://www.mpiib-berlin.mpg.de/2D-PAGE and can be read with a Java compatible browser. The interactive hypertext markup language documents displayed are generated dynamically in each individual session from a rational data file, a 2-D gel image file and a map file describing the protein spots as polygons. The program consists of common gateway interface scripts written in PERL, minimizing the administrative workload of the database. Furthermore, the database facilitates not only interactive use, but also worldwide active participation of other scientific groups with their own data, requiring only minimal computer hardware and knowledge of information technology.

Bacterial Proteins↗

PubMed2001

Measurable models of abdominal aortic aneurysm on the Web.

In this paper we describe a method for 3D reconstruction and web distribution of vessel structures specifically designed to allow the remote measurement of parameters of surgical interest. Deformable models are used for segmentation, while VRML and ECMA scripting are used to obtain 3D models that are not only viewable from any VRML97 enabled browser, but that also allow users to interact with the model, navigate along the vessel lumen and perform guided measurements of distances and angles.

Aortic Aneurysm, Abdominal↗