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At least 757 records · Page 42Linked to original sources

PubMed1990

A two-path recursive relational database structure for molecular information systems.

A recursive relational database structure, called the two-path structure, is proposed for holding data about the properties and structure of molecules. The two-path database approach solves certain severe restriction problems by providing two pathways to the structure of complex chemical entities. One pathway permits a fast descent to the atomic structure in terms of correct IUPAC carbon atom occurrence numbers. The other pathway descends through the molecular substructures, which can be referenced at any level in retrievals. The database appears to be capable of faithfully recording the structure of all chemical entities, including proteins and enzymes.

Database Management Systems↗

PubMed2005

MFAML: a standard data structure for representing and exchanging metabolic flux models.

SUMMARY: MFAML is a standard data structure designed for the formal representation and effective exchange of metabolic flux models. It allows for the explicit description of stationary states of a metabolic system by defining environmental/genetic conditions of the system, e.g. flux measurements, balancing constraints and physiological objectives as well as basic information on metabolites and reactions. In addition, a library of MFAML comprising a model parser and a converter provides an open framework for establishing the pipeline from metabolic modeling to metabolic flux analysis. AVAILABILITY: MFAML (version 1) is fully described and available at http://mbel.kaist.ac.kr/mfaml/.

Computer Simulation↗

PubMed2004

FLOSYS--a web-accessible workflow system for protocol-driven biomolecular sequence analysis.

FLOSYS is an interactive web-accessible bioinformatics workflow system designed to assist biologists in multi-step data analyses. FLOSYS allows the user to create complex analysis pathways (protocols) graphically, similar to drawing a flowchart: icons representing particular bioinformatics tools are dragged and dropped onto a canvas and lines connecting those icons are drawn to specify the relationships between the tools. In addition, FLOSYS permits to select input-data, execute the protocol and store the results in a personal workspace. The three-tier architecture of FLOSYS has been implemented in Java and uses a relational database system together with new technologies for distributed and web computing such as CORBA, RMI, JSP and JDBC. The prototype of FLOSYS, which is part of the bioinformatics workbench AnaBench, is accessible on-line at http://malawimonas.bcm.umontreal.ca: 8091/anabench. The entire package is available on request to academic groups who wish to have a customized local analysis environment for research or teaching.

Computational Biology↗

PubMed2004

Data mining challenges in the design of telemedicine platforms.

The evolution of telemedicine information systems involves the general processes of acquiring useful knowledge from medical data sets for diagnosis, intelligent efficient patient record transmission and autonomous adaptation of biomedical devices and their related software environments using quality of service attributes. Knowledge engineering concepts and methods allow application to the design of intelligent telemedicine platforms, satisfying the performance requirements and the quality assurance criteria of each specialized telemedicine application.

Artificial Intelligence↗

PubMed1997

A process model basis for evolving hospital information systems.

Hospitals often invest significant resources in the development of large and complex information systems that must be modified and extended to respond to changing requirements and to exploit the capabilities offered by modern technologies. A disciplined approach of managing the evolution of hospital information systems is then required so that to meet the increasing demands for effective and efficient use of scarce resources. This paper takes a process oriented view of the hospital and presents an approach based on hospital process modeling which aims at assessing the current status of computer support within a hospital and at identifying new opportunities for automation. The approach is illustrated by an example taken from a major Greek hospital.

Clinical Laboratory Information Systems↗

PubMed1992

Three methods of implementing a picture archiving and communication system.

A picture archiving and communication system (PACS) is a system integration of many components, including radiologic image acquisition devices, computers, communication networks, image display workstations, and data base management systems. The author describes three general approaches to implementing a PACS. In the first approach, the department or institution acts as a systems integrator, designing and implementing the PACS. In the second approach, the PACS is planned on the basis of the department's operations and environment and then a manufacturer is contracted to design and build the system. The third approach is to purchase a turnkey system, with some modifications provided by the manufacturer for a specific clinical application. The author provides examples of each approach in the clinical environment and presents the disadvantages and advantages of each.

Computer Systems↗

PubMed1996

Ventures in education: a pipeline to medical education for minority and economically disadvantaged students.

BACKGROUND: Ventures in Education is an independent, nonprofit educational organization established by the Josiah H. Macy, Jr. Foundation to improve the academic achievement of minority and economically disadvantaged students, particularly in science and mathematics. One specific objective has been to increase the number of students who enter schools of the health professions, in particular schools of medicine, which was the focus of this study. METHOD: A search was conducted of the Association of American Medical Colleges' (AAMC's) Student and Applicant Information Management System database, to determine whether any of the 981 graduates in the first five Venture classes (1985 to 1989) of the original five New York City high schools in the program had pursued medical education. RESULTS: The search located 160 of the 981 Ventures graduates, and, of those, 136 had taken the Medical College Admission Test (13.9%), 109 (11.1%) has applied to medical school, 75 (7.6%) had been accepted, and 72 (7.3%) had matriculated into medical school. All of these percentages were significantly higher than the corresponding percentages for the general population. CONCLUSION: The findings have important implications for the AAMC's Project 3000 by 2000, showing that a rigorous academic curriculum with resources for individualized attention can facilitate the entry of minority and economically disadvantage students into medical education, with at least 7.3% of the Ventures graduates entering medical school and nearly 70% of those applying subsequently being accepted.

Achievement↗

PubMed2004

PathAligner: metabolic pathway retrieval and alignment.

MOTIVATION: Analysis of metabolic pathways is a central topic in understanding the relationship between genotype and phenotype. The rapid accumulation of biological data provides the possibility of studying metabolic pathways at both the genomic and the metabolic levels. Retrieving metabolic pathways from current biological data sources, reconstructing metabolic pathways from rudimentary pathway components, and aligning metabolic pathways with each other are major tasks. Our motivation was to develop a conceptual framework and computational system that allows the retrieval of metabolic pathway information and the processing of alignments to reveal the similarities between metabolic pathways. RESULTS: PathAligner extracts metabolic information from biological databases via the Internet and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites etc. It provides an easy-to-use interface to retrieve, display and manipulate metabolic information. PathAligner also provides an alignment method to compare the similarity between metabolic pathways. AVAILABILITY: PathAligner is available at http://bibiserv.techfak.uni-bielefeld.de/pathaligner.

Algorithms↗

PubMed1991

NMINT--introductory courseware for nuclear medicine: database design.

Computer-Aided Instruction (CAI) provides a dynamic and self-paced learning experience to the medical trainee. Microcomputer based hypermedia systems integrate text, graphics, and image information. We present the design of an introductory CAI course for nuclear medicine called NMINT and elaborate on the underlying relational database that contains clinically relevant information and links to local or remote image storage over high speed networks. The IBM PS/2 Windows system uses Toolbook software augmented by C language modules for image and image-overlay database access. The current implementation stores text, graphical lesson material, and image index information on microcomputer magnetic disk; image data are stored on the attached optical disk. The storage architecture is described in detail. We emphasize its multi-access methods and its expandability into department-wide image networks.

Computer Graphics↗

PubMed2002

Osprey: a network visualization system.

We have developed a software platform called Osprey for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale data sets can be readily combined with Osprey for comparison of different methods.

Computational Biology↗

PubMed1999

The assent of a nation: genethics and Iceland.

The Icelandic parliament passed legislation authorizing the establishment of a national health sector database which will be sponsored financially by private enterprises through DeCode Genetics Inc. Health related data will be gathered from patients, without their informed consent, from all points of contact with Icelandic public and private health care providers. A centralized data curator will 'non-personalize' the identity of the subjects in a one-way coding system which the government and DeCode Genetics argue overrides the need for informed consent. This legislation is in conflict with the European Data Protection Act, which requires informed consent for the collection of personal data. The law raises many ethical questions regarding the central tenets of informed consent, the power of government, the rights of the human subject, and finally, the responsibility of the clinician balancing commitments of the patient and research.

Bioethics↗

PubMed1994

Assigning function to CDS through qualified query answering: beyond alignment and motifs.

In this paper, we show how to use qualitative query answering to annotate CDS-to-function relationships with confidence in the score, confidence in the tool, and confidence in the decision about the function. The system, implemented in Prolog, provides users with a powerful tool to analyze large quantities of data that have been produce by multiple sequence analysis programs. Using qualified query answering techniques, users can easily change the criteria for how tools reinforce each other and for how numbers of occurrences of particular functions reinforce each other. They can also alter how different scores for different tools are categorized.

Animals↗

PubMed2002

Genquire: genome annotation browser/editor.

UNLABELLED: We present a software package, Genquire, that allows visualization, querying, hand editing, and de novo markup of complete or partially annotated genomes. The system is written in Perl/Tk and uses, where possible, existing BioPerl data models and methods for representation and manipulation of the sequence and annotation objects. An adaptor API is provided to allow Genquire to display a wide range of databases and flat files, and a plugins API provides an interface to other sequence analysis software. AVAILABILITY: Genquire v3.03 is open-source software. The code is available for download and/or contribution at http://www.bioinformatics.org/Genquire

Chromosome Mapping↗

PubMed2000

MuStaR and other software for locus-specific mutation databases.

As the human genome sequencing project nears completion, there has been a vast increase in the rate at which disease and nondisease associated variant sequences are being sought and detected. This has heightened the need for software with which to accumulate allelic variant (mutation) data, and with which to make the data accessible to the scientific community. Many ad hoc solutions have been developed by those interested in specific genes and diseases, and the creation of central databases which hold data for all genes has provided an alternative repository for some of the locus data. Despite this, few specialised software tools exist for researchers to create their own locus-specific allelic variant databases. This article describes methods available to potential curators, including software systems developed with the sole purpose of generating locus-specific mutation databases. In particular, the authors' own software, MuStaRtrade mark, is described. MuStaRtrade mark allows curators to maintain a database on a laptop computer if desired, while being able to export the data to an automatically generated Website which will run on any cgi compliant Web server. Searching the database and the submission of new mutations are made possible through fill-in Web forms. A number of other software tools which may be of use to curators are also described.

Chromosome Mapping↗

PubMed1991

[Electronic data processing data bank for vascular surgery as a multiple site system with network connection].

A clinical database, using FileMaker Pro and a network of APPLE Macintosh computers, were created for a vascular surgical unit. The databank presented here is based on proven, routine working procedures of the department. An easily learnable entry facility with hands-on, screen-oriented users' guide and help data file provide easy operability and highly efficient databank capability, along with great flexibility. This criterial and user-friendly features make staff acceptance and compliance readily achievable, thus assuring comprehensive data entry.

Computer Communication Networks↗

PubMed2004

VisANT: an online visualization and analysis tool for biological interaction data.

BACKGROUND: New techniques for determining relationships between biomolecules of all types--genes, proteins, noncoding DNA, metabolites and small molecules--are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems. RESULTS: We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology. CONCLUSION: VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at http://visant.bu.edu.

Animals↗

PubMed2005

GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.

BACKGROUND: The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration. RESULTS: GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets. The system provides an underlying data layer for computational analysis tools and visualization tools. GeneKeyDB relies primarily on existing database identifiers derived from community databases (NCBI, GO, Ensembl, et al.) as well as the known relationships among those identifiers. It is a lightweight, portable, and extensible platform for integration with computational tools and analysis environments. CONCLUSION: GeneKeyDB can enable analysis tools and users to manipulate the intersections, unions, and differences among different data sets.

Algorithms↗

PubMed1999

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms.

TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles. In addition to being updated and extended by new features, it has been complemented now by a series of additional database modules. Among them, modules which provide data about signal transduction pathways (TRANSPATH) or about cell types/organs/developmental stages (CYTOMER) are available as well as an updated version of the previously described COMPEL database. The databases are available on the WWW at http://transfac.gbf.de/

Animals↗