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At least 433 records · Page 24Linked to original sources
PubMed1998

Classification of retinal damage by a neural network based system.

The objective of this research is to provide an ophthalmologist with a helpful system, capable of classifying a degree of patients' retinal hemorrhage. The system is composed of four modules: (a) data acquisition module, (b) image Database module, (c) image processing module, (d) image classification module. The system was trained with a modular neural network on a set of 25 images, and tested on a set of 160 images. A training performance of greater than 95% was achieved. The classifying part of the system showed 79% recognition accuracy. Since the testing images were taken from independent sources, we assume that the system should also provide an accurate classification of other image types.

Algorithms↗
PubMed2003

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments.

A control system for high-throughput protein crystallography experiments has been developed based on a multilevel secure (SSL v2/v3) UNIX socket under the Linux operating system. Main features of protein crystallography experiments (purification, crystallization, loop preparation, data collecting, data processing) are dealt with by the software. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data, that are stored in Network File Server) in a relational database (MySQL). The system consists of several servers and clients. TCP/IP secure UNIX sockets with four predefined behaviors [(a) listening to a request followed by a reply, (b) sending a request and waiting for a reply, (c) listening to a broadcast message, and (d) sending a broadcast message] support communications between all servers and clients allowing one to control experiments, view data, edit experimental conditions and perform data processing remotely. The usage of the interface software is well suited for developing well organized control software with a hierarchical structure of different software units (Gaponov et al., 1998), which will pass and receive different types of information. All communication is divided into two parts: low and top levels. Large and complicated control tasks are split into several smaller ones, which can be processed by control clients independently. For communicating with experimental equipment (beamline optical elements, robots, and specialized experimental equipment etc.), the STARS server, developed at the Photon Factory, is used (Kosuge et al., 2002). The STARS server allows any application with an open socket to be connected with any other clients that control experimental equipment. Majority of the source code is written in C/C++. GUI modules of the system were built mainly using Glade user interface builder for GTK+ and Gnome under Red Hat Linux 7.1 operating system.

Crystallography↗
PubMedDate not supplied

Knowledge precepts for design and evaluation of information visualizations.

The design and evaluation of most current information visualization systems descend from an emphasis on a user's ability to "unpack" the representations of data of interest and operate on them independently. Too often, successful decision-making and analysis are more a matter of serendipity and user experience than of intentional design and specific support for such tasks; although humans have considerable abilities in analyzing relationships from data, the utility of visualizations remains relatively variable across users, data sets, and domains. In this paper, we discuss the notion of analytic gaps, which represent obstacles faced by visualizations in facilitating higher-level analytic tasks, such as decision-making and learning. We discuss support for bridging these gaps, propose a framework for the design and evaluation of information visualization systems, and demonstrate its use.

Algorithms↗
PubMed2004

RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.

MOTIVATION: Gene expression array technology has become increasingly widespread among researchers who recognize its numerous promises. At the same time, bench biologists and bioinformaticians have come to appreciate increasingly the importance of establishing a collaborative dialog from the onset of a study and of collecting and exchanging detailed information on the many experimental and computational procedures using a structured mechanism. This is crucial for adequate analyses of this kind of data. RESULTS: The RNA Abundance Database (RAD; http://www.cbil.upenn.edu/RAD) provides a comprehensive MIAME-supportive infrastructure for gene expression data management and makes extensive use of ontologies. Specific details on protocols, biomaterials, study designs, etc. are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format (e.g. ArrayExpress). RAD is part of a more general Genomics Unified Schema (http://www.gusdb.org), which includes a richly annotated gene index (http://www.allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. This infrastructure enables a large variety of queries that incorporate visualization and analysis tools and have been tailored to serve the specific needs of projects focusing on particular organisms or biological systems.

Abstracting and Indexing↗
PubMed1994

Medical office automation integrated into the distributed architecture of a hospital information system.

Patient histories, discharge summaries, and medical consultant reports are made up of written texts. Therefore, the gathering and archiving of these texts in machine-readable form has many characteristics of computer-based medical records. In Geneva, approximately 1,540 PCs are connected to the Hospital Information System DIOGENE 2, with the possibility of accessing all the functions offered by the system without losing any of their MS-DOS word processing capabilities. The UNIDOC system, presented in this paper, takes all these features into account, a real marriage of technologies between the MS-DOS environment and the distributed client-server architecture. The INGRES database management system supports the entire archiving process of the medical patient texts, structured by prelabelled paragraphs and automatically indexed. Both the quality and accessibility of the records are enhanced, while the archiving capacity is neither too limited nor too expensive.

Archives↗
PubMed2005

DVI System International: software assisting in the Thai tsunami victim identification process.

DVI System International is software that operates on the PC-Windows platform. It is capable of managing aspects of identification in day-to-day cases and major disasters, where it has particular advantages when victims of several nationalities are involved. The system uses Interpol forms as standard protocols for input and transfer of antemortem and postmortem information. Following the Thai Tsunami Disaster of 26 December 2004, Interpol recommended that its member country Thailand use DVI System International software, as it is one of the few internationally approved systems. This paper focuses on the concepts upon which the dental forms, F1 and F2, of the DVI System International are designed, describes how it works and some of the adjustments implemented during the ongoing Thai Tsunami Victim Identification process.

Database Management Systems↗
PubMed1992

MUSC information system ARIADNE: a consistent tool for support of experiment planning, execution and scientific evaluation of microgravity-experiments.

One of the main tasks of DLR-MUSC (Microgravity User Support Center) is to accompany an experiment's complete life-cycle, thus supporting the investigators. This task starts with the preparation of experiments, continues with their execution and finally leads to the evaluation of the respective measurement results. A computer-based information system facilitates these tasks. Considerable effort has been taken in order to make a detailed as well as modular design--as a result the system can now be applied for any mission. ARIADNE mainly supports three phases, all using the same consistent database. 1. The first phase of experiment preparation is supported by--the acquisition and maintenance of general and basic data by user entries into the database, and the support of the integration of partially similar experiment proposals into a timeline as planned which is composed by activities. 2. The support during experiment execution consists of--real-time data acquisition and control (i.e. on-line database generation and display after processing) including experiment monitoring, enabling of fast replanning. 3. The support ARIADNE provides for experiment evaluation includes--the selection of series of measurements belonging to the specified experiment (parts), further processing and evaluation of the collected data, which must partly be done in real-time and partly post-mission and, creation of back-up's of the processing results. The ARIADNE database consists of a relational ORACLE-part (for numerical and character data), a bibliographic part, a program-library, and a realtime-part (BAPAS). The open design of ARIADNE allows interfaces to stored special data (such as graphics, images, archives) as well as several interfaces to other systems, such as CUIS, MARS-MDB, EXPRES, etc.

Aerospace Medicine↗
PubMed1999

Motif-based searching in TOPS protein topology databases.

MOTIVATION: TOPS cartoons are a schematic ion of protein three-dimensional structures in two dimensions, and are used for understanding and manual comparison of protein folds. Recently, an algorithm that produces the cartoons automatically from protein structures has been devised and cartoons have been generated to represent all the structures in the structural databank. There is now a need to be able to define target topological patterns and to search the database for matching domains. RESULTS: We have devised a formal language for describing TOPS diagrams and patterns, and have designed an efficient algorithm to match a pattern to a set of diagrams. A pattern-matching system has been implemented, and tested on a database derived from all the current entries in the Protein Data Bank (15,000 domains). Users can search on patterns selected from a library of motifs or, alternatively, they can define their own search patterns. AVAILABILITY: The system is accessible over the Web at http://tops.ebi.ac.uk/tops

Algorithms↗
PubMed1994

Developing and implementing a user-driven departmental database system--implications for the Royal College of Radiologists' COIN proposal.

With the increasing availability of computers, more departments are using word processors in place of typewriters. In the course of typing patient discharge summaries and letters, a large amount of information of potential use for audit or research purposes is entered into the computer but in a form inaccessible for analysis. We have developed a data-base system, based on information entered by departmental staff in the course of their work, rather than by designated data managers. The aim of the system is to replace word-processed clinical summaries. We describe the design, implementation and possible advantages and disadvantages of such a system and implications for the COIN proposal of the Royal College of Radiologists.

Computer Communication Networks↗
PubMed2004

ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems.

MOTIVATION: Complex biological functions emerge from interactions between proteins in stable supra-molecular assemblies and/or through transitory contacts. Most of the time protein partners of the assemblies are composed of one or several domains which exhibit different biochemical functions. Thus the study of cellular process requires the identification of different functional units and their integration in an interaction network; such complexes are referred to as integrated systems. In order to exploit with optimum efficiency the increased release of data, automated bioinformatics strategies are needed to identify, reconstruct and model such systems. For that purpose, we have developed a knowledge warehouse dedicated to the representation and acquisition of bacterial integrated systems involved in the exchange of the bacterial cell with its environment. RESULTS: ISYMOD is a knowledge warehouse that consistently integrates in the same environment the data and the methods used for their acquisition. This is achieved through the construction of (1) a domain knowledge base (DKB) devoted to the storage of the knowledge about the systems, their functional specificities, their partners and how they are related and (2) a methodological knowledge base (MKB) which depicts the task layout used to identify and reconstruct functional integrated systems. Instantiation of the DKB is obtained by solving the tasks of the MKB, whereas some tasks need instances of the DKB to be solved. AROM, an object-based knowledge representation system, has been used to design the DKB, and its task manager, AROMTasks, for developing the MKB. In this study two integrated systems, ABC transporters and two component systems, both involved in adaptation processes of a bacterial cell to its biotope, have been used to evaluate the feasibility of the approach.

ATP-Binding Cassette Transporters↗
PubMed1995

A national computer-based surveillance system for tuberculosis notification in Singapore.

SETTING: The notification rate of tuberculosis (TB) among residents in Singapore has been declining at a mean rate of 5.6% per annum, from 307 cases per 100,000 population in 1960 to 54 cases per 100,000 population in 1992. A National TB Notification Registry was set up in 1958 using a manual card system, and was captured into a computer database from 1986. OBJECTIVE: To monitor epidemiological trends of TB in Singapore with more speed, versatility and analytical capabilities, a new microcomputer-based surveillance system was developed in 1993. DESIGN: The main software programmes used in this system were DBase IV (version 1.5) and Epi Info (version 5). These versions could use base memory interchangeably and were therefore incorporated into a single application DBase programme. Security features were incorporated into the programme. The TB database was linked to the National HIV Notification Registry to enhance surveillance of combined TB and human immunodeficiency virus infection (HIV). RESULTS: The system was able to track notifications and TB culture results, address letters and analyze data and enabled prompt dissemination of information. CONCLUSION: The authors believe that this system would enhance surveillance and provide timely information for national TB control programmes. However, the effectiveness of this system is dependent on an established notification structure with notifications for tuberculosis of sufficient completeness.

Database Management Systems↗
PubMed1999

Thinking combinatorially.

Biopolymers and chemical compounds with novel functions can be selected or screened from randomized libraries. Recently, it has become possible to augment the functions of biopolymers via the conjugation or incorporation of unnatural chemical moieties. In the future, it should prove possible to engineer systems that can self-evolve and thereby reveal unexpected emergent properties.

Biopolymers↗
PubMed2002

Clustering of proximal sequence space for the identification of protein families.

MOTIVATION: The study of sequence space, and the deciphering of the structure of protein families and subfamilies, has up to now been required for work in comparative genomics and for the prediction of protein function. With the emergence of structural proteomics projects, it is becoming increasingly important to be able to select protein targets for structural studies that will appropriately cover the space of protein sequences, functions and genomic distribution. These problems are the motivation for the development of methods for clustering protein sequences and building families of potentially orthologous sequences, such as those proposed here. RESULTS: First we developed a clustering strategy (Ncut algorithm) capable of forming groups of related sequences by assessing their pairwise relationships. The results presented for the ras super-family of proteins are similar to those produced by other clustering methods, but without the need for clustering the full sequence space. The Ncut clusters are then used as the input to a process of reconstruction of groups with equilibrated genomic composition formed by closely-related sequences. The results of applying this technique to the data set used in the construction of the COG database are very similar to those derived by the human experts responsible for this database. AVAILABILITY: The analysis of different systems, including the COG equivalent 21 genomes are available at http://www.pdg.cnb.uam.es/GenoClustering.html.

Algorithms↗