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At least 127 records · Page 7Linked to original sources
PubMedDate not supplied

Mining protein data from two-dimensional gels: tools for systematic post-planned analyses.

There is a considerable need to develop comprehensive, systematic mechanisms to analyze the vast number of proteins that orchestrate various cellular functions and to identify proteins associated with disease or that are affected by pharmacological agents. Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) continues to be relied upon to analyze protein constituents of cells and tissues. We have developed a Laboratory Information Processing System (LIPS) as a computer-based tool for capturing quantitative and qualitative changes in thousands of proteins detected in 2-D gels of various types. Protein databases have been developed to serve as a repository for data processing of the basic and derived data and of findings derived from different studies. There have been remarkable advances both in database technology as well as in the computer hardware that have benefited our effort at mining protein data from 2-D gels. We here review our current efforts aimed at improving the performance and features of our 2-D related protein databases, with particular emphasis on the tools we utilize for database mining via a systematic analysis of information known as post-planned analysis.

Acrylic Resins↗
PubMed1993

GeneView: multi-language human gene mapping library with a graphical user interface.

GeneView is a newly developed human gene mapping library system that works on an X-Window platform. This system is designed for researchers who routinely utilize gene mapping data in the laboratory but are unfamiliar with computer technology. GeneView offers various features, including friendly user interface, fast operation and visualization facility. Genetic loci are displayed graphically with an idiogram. This system can be operated in multiple languages. A current version supports Japanese and English, and can be easily expanded to include other languages. A prototype of GeneView is now installed on a SPARC (Sun4) workstation. Because of the X-Window platform, GeneView should be compatible with various types of workstations.

Algorithms↗
PubMed2004

Expression-based monitoring of transcription factor activity: the TELiS database.

MOTIVATION: In microarray studies it is often of interest to identify upstream transcription control pathways mediating observed changes in gene expression. The Transcription Element Listening System (TELiS) combines sequence-based analysis of gene regulatory regions with statistical prevalence analyses to identify transcription-factor binding motifs (TFBMs) that are over-represented among the promoters of up- or down-regulated genes. Efficiency is maximized by decomposing the problem into two steps: (1) a priori compilation of prevalence matrices specifying the number of putative binding sites for a variety of transcription factors in promoters from all genes assayed by a given microarray, and (2) real-time statistical analysis of pre-compiled prevalence matrices to identify TFBMs that are over- or under-represented in promoters of differentially expressed genes. The interlocking JAVA applications namely, PromoterScan and PromoterStats carry out these tasks, and together constitute the TELiS database for reverse inference of transcription factor activity. RESULTS: In two validation studies, TELiS accurately detected in vivo activation of NF-kappaB and the Type I interferon system by HIV-1 infection and pharmacologic activation of the glucocorticoid receptor in peripheral blood mononuclear cells. The population-based statistical inference underlying TELiS out-performed conventional statistical tests in analytic sensitivity, with parametric studies demonstrating accurate identification of transcription factor activity from as few as 20 differentially expressed genes. TELiS thus provides a simple, rapid and sensitive tool for identifying transcription control pathways mediating observed gene expression dynamics.

Algorithms↗
PubMed2004

The Ensembl computing architecture.

Ensembl is a software project to automatically annotate large eukaryotic genomes and release them freely into the public domain. The project currently automatically annotates 10 complete genomes. This makes very large demands on compute resources, due to the vast number of sequence comparisons that need to be executed. To circumvent the financial outlay often associated with classical supercomputing environments, farms of multiple, lower-cost machines have now become the norm and have been deployed successfully with this project. The architecture and design of farms containing hundreds of compute nodes is complex and nontrivial to implement. This study will define and explain some of the essential elements to consider when designing such systems. Server architecture and network infrastructure are discussed with a particular emphasis on solutions that worked and those that did not (often with fairly spectacular consequences). The aim of the study is to give the reader, who may be implementing a large-scale biocompute project, an insight into some of the pitfalls that may be waiting ahead.

Computational Biology↗
PubMedDate not supplied

Real-time optimal adaptation for planetary geometry and texture: 4-8 tile hierarchies.

The real-time display of huge geometry and imagery databases involves view-dependent approximations, typically through the use of precomputed hierarchies that are selectively refined at runtime. A classic motivating problem is terrain visualization in which planetary databases involving billions of elevation and color values are displayed on PC graphics hardware at high frame rates. This paper introduces a new diamond data structure for the basic selective-refinement processing, which is a streamlined method of representing the well-known hierarchies of right triangles that have enjoyed much success in real-time, view-dependent terrain display. Regular-grid tiles are proposed as the payload data per diamond for both geometry and texture. The use of 4-8 grid refinement and coarsening schemes allows level-of-detail transitions that are twice as gradual as traditional quadtree-based hierarchies, as well as very high-quality low-pass filtering compared to subsampling-based hierarchies. An out-of-core storage organization is introduced based on Sierpinski indices per diamond, along with a tile preprocessing framework based on fine-to-coarse, same-level, and coarse-to-fine gathering operations. To attain optimal frame-to-frame coherence and processing-order priorities, dual split and merge queues are developed similar to the Realtime Optimally Adapting Meshes (ROAM) Algorithm, as well as an adaptation of the ROAM frustum culling technique. Example applications of lake-detection and procedural terrain generation demonstrate the flexibility of the tile processing framework.

Algorithms↗
PubMed2000

Automated teaching file and slide database for digital images.

OBJECTIVE: We developed an easy-to-use method for creating a searchable digital teaching file of CT and MR images. CONCLUSION: We describe a method of creating a digital archive of interesting cases that is easy to implement and works on a commercially available workstation. A remote daemon polls for images transferred to the product film tool. It creates a tagged image file format (TIFF) digital archive of these images on any platform supporting file transfer protocol (FTP), operates in the background, and automatically generates a searchable index of case information in the database.

Computer Systems↗
PubMed1994

A clinical database as a component of a diagnostic hematology workstation.

A clinical database was designed as part of a comprehensive workstation for diagnostic laboratory hematology. The database stores coded findings pertinent to hematologic disorders including inherited abnormalities, previous surgery, malignancies, current therapy, and laboratory test results. The workstation includes knowledge-based systems for peripheral blood analysis, flow cytometry studies, and bone marrow morphology. The peripheral blood system renders an interpretive report based on data from a complete blood count with manual review of a blood smear by a technologist. The flow cytometry module interprets the immunophenotyping and DNA content results, and correlates them with the clinical findings and the peripheral blood data. The bone marrow system bases its report on all of the available information including the morphologic review of the bone marrow specimen by a physician, the peripheral blood data, immunophenotype, and clinical/laboratory findings. Before generating an interpretive report, each of the knowledge-based systems automatically searches the clinical database for specific information pertinent to the findings in the case. Since the workstation must function in situations where access to distributed databases is not feasible or not yet practical, a data entry module with a graphical user interface has been created.

Artificial Intelligence↗
PubMed1994

Evolving a legacy system: restructuring the Mendelian Inheritance in Man database.

Mendelian Inheritance in Man (MIM) is an encyclopedia of medical genetics that has been in electronic form for over 30 years. In its lifetime, MIM has undergone many organizational and software changes. In 1994, a major transition was made based on three basic principles: industry standards, open systems architecture, and extensibility. The resulting MIM database allows users to navigate to other genomic databases, permits the delivery of multimedia information, and improves the quality of data. The new MIM database also improved its administration because of 1) an internal format that enforces consistency; 2) a lower maintenance cost of software; and 3) a better ability to migrate MIM content. In addition, the new architecture will allow MIM easily to adopt emergent technologies as they mature.

Computer Systems↗
PubMed1994

The role of object representation in the design of the intelligent radiology workstation.

The paper describes the design of the Intelligent Radiology Workstation (IRW) that is intended to handle heterogeneous radiologic data (text, image, video) and radiologic knowledge in such a way that it is easy to store, access, use, and repurpose. An object-based structure is used to combine the relational database, hybrid knowledge base, and hypermedia within a common framework. Functions such as data entry and retrieval, browsing, and intelligent processing of data are available in the single environment. IRW open architecture allows radiologic digital resources to be used for clinical practice, diagnosis support, education, and research.

Artificial Intelligence↗
PubMed2000

A three-tier clinical information systems design model.

Modern health care institutions are often multi-site organisations that implement heterogeneous information management systems interacting with distributed databases. Advances in treatment modality/technology and rapidly changing information technology create increasing demand for changes/redevelopment of many health information applications. These features spawn the need for solutions to (a) guarantee data exchange across different types of applications and database management systems, and (b) reduce the costs of systems development and modification. This paper explores the concept of 'middleware services' as a solution to achieve these goals. It reports on the successful application of a component-based 3-tier system architecture to develop a computerised clinical pathways management system. The implementation experience confirms a number of significant benefits of the 3-tier structure including, reusability, flexibility, significant reduction in costs and efforts of systems development, and provision of easy, open migration pathway for future change of technology and system redevelopment.

Critical Pathways↗
PubMed1992

The French communicable diseases computer network: a technical view.

This paper describes an information system (IS) established in France in 1984 for the national surveillance of communicable diseases. This IS is based on a videotex server and a relational database management system. The videotex server is the IS front-end. It performs the following functions: interpersonal communications, synthetic information retrieval into an epidemiologic info-base and data entry owing to its specialized applications. The relational database management system allows the user to manage and consult an epidemiologic database updated in quasi-real time. Several specific tools have also been developed in order to enhance data representation and analysis and the decision support capabilities of the IS.

Algorithms↗
PubMedDate not supplied

Design of hospital database systems in a non-relational environment.

The lack of an appropriate, widely accepted, design procedure for use with non-relational database management systems has been a major, common problem in many efforts to develop an integrated hospital database. The availability of such a design procedure is particularly important today since the majority of the database management systems currently in use are non-relational. A database design procedure is proposed which should assist with the design of optimal non-relational hospital database systems. The proposed design procedure is separated into two distinct steps: the development of an appropriate intermediate relational database structure and the subsequent development of an equivalent non-relational one. A set of rules is given for the move from the proposed intermediate relational to the equivalent non-relational structure. An example application from the hospital environment is also included in order to better demonstrate the process.

Computer Communication Networks↗
PubMed2006

BioWarehouse: a bioinformatics database warehouse toolkit.

BACKGROUND: This article addresses the problem of interoperation of heterogeneous bioinformatics databases. RESULTS: We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. CONCLUSION: BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

Computational Biology↗
PubMed2002

A management information system to study space diets.

A management information system (MIS), including a database management system (DBMS) and a decision support system (DSS), was developed to dynamically analyze the variable nutritional content of foods grown and prepared in an Advanced Life Support System (ALSS) such as required for long-duration space missions. The DBMS was designed around the known nutritional content of a list of candidate crops and their prepared foods. The DSS was designed to determine the composition of the daily crew diet based on crop and nutritional information stored in the DBMS. Each of the selected food items was assumed to be harvested from a yet-to-be designed ALSS biomass production subsystem and further prepared in accompanying food preparation subsystems. The developed DBMS allows for the analysis of the nutrient composition of a sample 20-day diet for future Advanced Life Support missions and is able to determine the required quantities of food needed to satisfy the crew's daily consumption. In addition, based on published crop growth rates, the DBMS was able to calculate the required size of the biomass production area needed to satisfy the daily food requirements for the crew. Results from this study can be used to help design future ALSS for which the integration of various subsystems (e.g., biomass production, food preparation and consumption, and waste processing) is paramount for the success of the mission.

Biomass↗