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PubMed2003

SDAP: database and computational tools for allergenic proteins.

SDAP (Structural Database of Allergenic Proteins) is a web server that provides rapid, cross-referenced access to the sequences, structures and IgE epitopes of allergenic proteins. The SDAP core is a series of CGI scripts that process the user queries, interrogate the database, perform various computations related to protein allergenic determinants and prepare the output HTML pages. The database component of SDAP contains information about the allergen name, source, sequence, structure, IgE epitopes and literature references and easy links to the major protein (PDB, SWISS-PROT/TrEMBL, PIR-ALN, NCBI Taxonomy Browser) and literature (PubMed, MEDLINE) on-line servers. The computational component in SDAP uses an original algorithm based on conserved properties of amino acid side chains to identify regions of known allergens similar to user-supplied peptides or selected from the SDAP database of IgE epitopes. This and other bioinformatics tools can be used to rapidly determine potential cross-reactivities between allergens and to screen novel proteins for the presence of IgE epitopes they may share with known allergens. SDAP is available via the World Wide Web at http://fermi.utmb.edu/SDAP/.

Allergens↗

PubMed1996

WWW-query: an on-line retrieval system for biological sequence banks.

We have developed a World Wide Web (WWW) version of the sequence retrieval system Query: WWW-Query. This server allows to query nucleotide sequence banks in the EMBL/GenBank/DDBJ formats and protein sequence banks in the NBRF/PIR format. WWW-Query includes all the features of the on-line sequences browsers already available: possibility to build complex queries, integration of cross-references with different data banks, and access to the functional zones of biological interest. It also provides original services not available elsewhere: introduction of the notion of re-usable sequence lists, integration of dedicated helper applications for visualizing alignments and phylogenetic trees and links with multivariate methods for studying codon usage or for complementing phylogenies.

Amino Acid Sequence↗

PubMed2003

ATIDB: Arabidopsis thaliana insertion database.

Insertional mutagenesis techniques, including transposon- and T-DNA-mediated mutagenesis, are key resources for systematic identification of gene function in the model plant species Arabidopsis thaliana. We have developed a database (http://atidb.cshl.org/) for archiving, searching and analyzing insertional mutagenesis lines. Flanking sequences from approximately 10 500 insertion lines (including transposon and T-DNA insertions) from several tagging programs in Arabidopsis were mapped to the genome sequence through our annotation system before being entered into the database. The database front end provides World Wide Web searching and analyzing interfaces for genome researchers and other biologists. Users can search the database to identify insertions in a particular gene or perform genome-wide analysis to study the distribution and preference of insertions. Tools integrated with the database include a graphical genome browser, a protein search function, a graphical representation of the insertion distribution and a Blast search function. The database is based on open source components and is available under an open source license.

Amino Acid Sequence↗

PubMed2006

EasyExonPrimer: automated primer design for exon sequences.

UNLABELLED: EasyExonPrimer is a web-based software that automates the design of PCR primers to amplify exon sequences from genomic DNA. EasyExonPrimer is written in Perl and uses Primer3 to design PCR primers based on the genome builds and annotation databases available at the University of California, Santa Cruz (UCSC) Genome Browser database (http://genome.ucsc.edu/). It masks repeats and known single nucleotide polymorphism (SNP) sites in the genome and designs standardised primers using optimised conditions. Users can input genes by RefSeq mRNA ID, gene name or keyword. The primer design is optimised for large-scale resequencing of exons. For exons larger than 1 kb, the user has the option of breaking the exon sequence down into overlapping smaller fragments. All primer pairs are then verified using the In-Silico PCR software to test for uniqueness in the genome. We have designed >1000 pairs of primers for 90 genes; 95% of the primer pairs successfully amplified exon sequences under standard PCR conditions without requiring further optimisation. AVAILABILITY: EasyExonPrimer is available from http://129.43.22.27/~primer/. The source code is also available upon request. CONTACT: Xiaolin Wu (forestwu@mail.nih.gov).

Algorithms↗

PubMedDate not supplied

ArQiologist: an integrated decision support tool for lead optimization.

This paper describes ArQiologist, a Web-based tool that integrates chemical, analytical, biological, and computational data to facilitate decision support for lead optimization at ArQule. It features an easy-to-use graphical query builder that allows queries to be saved, reused, and shared by researchers. Query results can be viewed with built-in data browsers or exported with structures to external applications such as Microsoft Excel or Spotfire for further analysis.

Journal Article↗

PubMed1997

Special considerations for WEB-based clinical database applications.

The Hospital Information System at the University of Missouri-Columbia Veterinary Medical Teaching Hospital is implementing a web-based interface to the existing Hospital Information System. The "stateless" nature of HTML forms introduces a number of special considerations that, though not immediately obvious, nevertheless apply to any multi-user database application. Problems including identifying sessions and users, dealing with abandoned sessions or use of the "Back" arrow on the browser, record locking across multiple forms, state variables, and flow through "utility" forms. General solutions to each of these problems have been devised and are presented here.

Animals↗

PubMed2006

TFBScluster web server for the identification of mammalian composite regulatory elements.

Identification of transcriptional regulatory elements represents a critical step in our ability to reconstruct transcriptional regulatory networks from gene expression profiling datasets. To facilitate computational identification of candidate gene regulatory elements from whole genome sequences, we have developed the TFBScluster web server that integrates several tools for the genome-wide identification and subsequent characterization of transcription factor binding site clusters that are conserved in multiple mammalian species. Either the human or mouse genomes can be used as the reference sequence with direct links from the search results to the ENSEMBL and UCSC genome browsers. Moreover, TFBScluster provides seamless integration of transcription factor binding site searches with genome annotation and gene expression profiling data, to allow prioritising computational predictions for subsequent experimental validation. TFBScluster is publicly available at http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.html.

Animals↗

PubMed2005

Future directions for depicting credibility in health care web sites.

OBJECTIVES: The purpose of the paper was to determine appropriate terminology, criteria, implementation, and develop a theoretical framework by which credibility in health care web sites can be depicted. Future research directions for evaluating credibility in health care web sites was also discussed. METHOD: A comprehensive literature review of published articles, policy papers, and grey literature using relevant search terms was conducted. Sources for articles reviewed included MEDLINE (from 1966 to present), PsycINFO (from 1840 to present), ERIC (from 1966 to present), and the Association for Computing Machinery (ACM) databases. The Web of Science citation service was continuously searched using a subscription service from 2002 to 2004. The search engine Google was also implemented. RESULTS: A common term, credibility, was purposed for use in this context. A comprehensive set of credibility criteria, presented within a theoretical framework was also developed. Implementation by means of a browser-based graphic icon was purposed. CONCLUSIONS: Relevancy and readiness of the purposed common terminology, criteria, and implementation within the theoretical framework must be further researched. More knowledge of consumers' behaviour regarding use of online health content and collaboration with others when implementing such information should be considered in future research.

Canada↗

PubMed1998

[Management and delivery of radiation dose distribution images using the Internet].

Dose distribution images play important roles in the management of cancer patients. To date hard copies of these images have been stored and referred to by radiation oncologists as needed. In most cases, these images were not available to medical personnel outside the radiation oncology department. We have developed a mechanism in the hospital to access these dose distribution images via WWW (World Wide Web). A screen snapshot of a dose distribution image on the CRT of a treatment planning machine is copied to the WWW server and converted to a GIF image. Similarly, we can register dose volume histograms and digitally reconstructed radiographs on the WWW. Medical personnel throughout the hospital can access the images through the WWW browser. As a result, radiation oncologists are given detailed information on target definition in treatment planning by expert physicians. The system also helps co-medical staff in understanding dose distributions and predicting radiation injuries. At the same time, it actualizes an electronic archive of dose distribution images, which is a database for quick and reliable review, evaluation and comparison of treatment plans. This technique also furthers a close relationship among radiation oncologists, physicians, and co-medical personnel.

Computer Communication Networks↗

PubMedDate not supplied

Clinical usefulness of the management and delivery of radiation dose-distribution images using the Internet.

Dose distribution images in radiation therapy play important roles in the management of cancer patients. To date, hard copies of these images have been stored for referral by radiation oncologists as needed. In most cases, these images are not available to medical personnel outside the radiation oncology department. We have developed a means to access these dose distribution images from the hospital via the World-Wide Web (WWW). A screen snapshot of a dose distribution image on the CRT of a treatment planning unit is copied to the WWW server and converted to a GIF (graphic interchange format) image. Similarly, we can register dose volume histograms and digitally reconstructed radiographs (DRR) on the WWW. Medical personnel can view these images through the WWW browser from anywhere in the hospital. As a result, radiation oncologists are given detailed information on target definition in treatment planning by expert physicians. The system also helps co-medical personnel in understanding dose distribution and predicting radiation injury. At the same time, it actualizes an electronic archive of dose distribution images, which is a database for quick and reliable review, evaluation, and comparison of treatment plans. This technique also fosters closer relationships among radiation oncologists, physicians, and co-medical personnel.

Humans↗

PubMed2000

Architecture of an image capable, Web-based, electronic medical record.

With each medical center department creating and maintaining its own patient care-related data, nursing and house staff may find it confusing to log into all the information systems necessary to achieve a global perspective of the patient's state. The Medical Information Network Database application provides a logically centralized Worldwide Web viewing application for the physically distributed data. In addition to coordinating data displays for histories, laboratories, pathology, radiology, and discharge summaries, the application can be configured to apply rule sets to the data and remind caregivers of follow-up tests or of possible reactions to treatment protocols. The viewing client runs on any HTML 2.0-compliant browser, although certain applet enhancements (notably for viewing radiological images) require a browser with Java abilities. With this "thin client" approach, the application can be configured to coexist with other applications (such as a PACS viewer), thus centralizing information and reducing the overall number of computers in the medical center.

Computer Systems↗

PubMed2003

Culture differences in design of portal sites.

Two experiments were carried out to examine the effects of cultural differences between the Chinese and the US people on the perceived usability and search performance of World Wide Web (WWW) portal sites. Chinese users in Taiwan and US users in Chicago were recruited to perform searching tasks on two versions of Yahoo! portal site: the standard Yahoo! and Yahoo! Chinese. The layout of Yahoo! Chinese is the same as the layout of Yahoo!, and categories on Yahoo! Chinese have been translated from its US counterpart. A special browser was programmed to record all the keystroke data and participants were asked to fill out a satisfaction questionnaire after finishing the tasks. Significant differences of satisfaction and steps to perform some tasks were found between the two groups. The experiment results also provided more detailed insights into the cultural differences between the Chinese and the US users.

Adult↗

PubMed2006

HOLLYWOOD: a comparative relational database of alternative splicing.

RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective databases to support experimental and computational investigations of alternative splicing (AS) is a significant challenge. In an effort to integrate accurate exon and splice site annotation with current knowledge about splicing regulatory elements and predicted AS events, and to link information about the splicing of orthologous genes in different species, we have developed the Hollywood system. This database was built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags, and links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. Hollywood was implemented as a relational database and currently contains comprehensive information for human and mouse. It is accompanied by a web query tool that allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A streamlined graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser. The database is accessible at http://hollywood.mit.edu.

Alternative Splicing↗

PubMed2000

A centralized dose calculation system for radiation therapy.

Centralization of treatment planning in a radiation therapy department is a realistic strategy to achieve an integrated and quality-controlled planning system, especially for institutions with numerous affiliations. The rapid evolution of computer hardware and software technology makes this a distinct possibility. However, the procedure of three-dimensional treatment planning involves a number of steps, such as: (1) input of patient computed tomography (CT) images and contour information; (2) interactions with local devices such as a film digitizer; and (3) output of beam information to be integrated with the record and verify the system. A full-fledged realization of the web-based centralized three-dimensional treatment planning system will require an extensive commercial development effort. We have developed and incorporated a web-based Timer/Monitor Unit (MU) program as a first step towards the full implementation of a centralized treatment planning system. The software application was developed in JAVA language. It uses the internet server and client technology. With one server that can handle multiple threads, it is a simple process to access the application anywhere on the network with an internet browser. Both the essential data needed for the calculation and the results are stored on the server, which centralizes the maintenance of the software and the storage of patient information.

Computer Systems↗

PubMed2004

PTGL--a web-based database application for protein topologies.

Protein Topology Graph Library (PTGL) is a database application for the representation and retrieval of protein topologies. Protein topologies are based on a graph-theoretical protein model at secondary structure level. Different views on protein topology are given by four linear notations for their characterization. Protein topologies can be derived at different description levels considering alpha- and beta-structures. The on-line search tool is based on an object-relational database and provides a query browser for data interrogation by string patterns, keyword queries and sequence similarity. Protein topologies are represented both as schematic diagrams and as three-dimensional images.

Computer Graphics↗

PubMed2004

GDPC: connecting researchers with multiple integrated data sources.

UNLABELLED: The goal of this project is to simplify access to genomic diversity and phenotype data, thereby encouraging reuse of this data. The Genomic Diversity and Phenotype Connection (GDPC) accomplishes this by retrieving data from one or more data sources and by allowing researchers to analyze integrated data in a standard format. GDPC is written in JAVA and provides (1) data sources available as web services that transfer XML formatted data via the SOAP protocol; (2) a JAVA API for programmatic access to data sources; and (3) a front-end application that allows users to manage data sources, retrieve data based on filters, sort/group data based on property values and save/open the data as XML files. AVAILABILITY: The source code, compiled code, documentation and GDPC Browser are freely available at: www.maizegenetics.net/gdpc/index.html the current release of GDPC is version 1.0, with updated releases planned for the future. Comments are welcome.

Database Management Systems↗

PubMed2000

The EMBL nucleotide sequence database.

The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (http://www.ebi.ac. uk/embl/index.html ) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank (USA). Data is exchanged amongst the collaborative databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. WEBIN is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via Internet and WWW interfaces. EBI's Sequence Retrieval System (SRS) is a network browser for databanks in molecular biology, integrating and linking the main nucleotide and protein databases plus many specialised databases. For sequence similarity searching a variety of tools (e.g., BLITZ, FASTA, BLAST) are available which allow external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

Classification↗

PubMed2025

Tsbrowse: an interactive browser for ancestral recombination graphs.

SUMMARY: Ancestral recombination graphs (ARGs) represent the interwoven paths of genetic ancestry of a set of recombining sequences. The ability to capture the evolutionary history of samples makes ARGs valuable in a wide range of applications in population and statistical genetics. ARG-based approaches are increasingly becoming a part of genetic data analysis pipelines due to breakthroughs enabling ARG inference at biobank-scale. However, there is a lack of visualization tools, which are crucial for validating inferences and generating hypotheses. We present tsbrowse, an open-source, web-based Python application for the interactive visualization of the fundamental building blocks of ARGs, i.e. nodes, edges and mutations. We demonstrate the application of tsbrowse to various data sources and scenarios, and highlight its key features of browsability along the genome, user interactivity, and scalability to very large sample sizes. AVAILABILITY AND IMPLEMENTATION: Tsbrowse is installed as a Python package from PyPI (https://pypi.org/project/tsbrowse/), while a development version is maintained at https://github.com/tskit-dev/tsbrowse. Documentation is available at https://tskit.dev/tsbrowse/docs/. Source code is archived on Zenodo with DOI, https://doi.org/10.5281/zenodo.15683039.

Software↗