A real-time and dynamic biological information retrieval and analysis system (BIRAS)

The aim of this study is to design a biological information retrieval and analysis system (BIRAS) based on the Internet. Using the specific network protocol, BIRAS system could send and receive information from the Entrez search and retrieval system maintained by National Center for Biotechnology Information (NCBI) in USA. The literatures, nucleotide sequence, protein sequences, and other resources according to the user-defined term could then be retrieved and sent to the user by pop up message or by E-mail informing automatically using BIRAS system. All the information retrieving and analyzing processes are done in real-time. As a robust system for intelligently and dynamically retrieving and analyzing on the user-defined information, it is believed that BIRAS would be extensively used to retrieve specific information from large amount of biological databases in now days. The program is available on request from the corresponding author.     

Grammatic representation of beat sequences for fuzzy arrhythmia diagnosis

The final stage of a system for automatic monitoring of cardiac arrhythmias is the diagnosis of the rhythm or arrhythmia present in the patient during the monitoring process. In this paper we approach the detection process by means of the analysis of the electrocardiographic signal (ECG) on a surface lead produced by those arrhythmias which can be recognized by identifying specific beat sequences and taking into account contextual information, mainly rhythm information. We have developed a diagnosis process for arrhythmias which uses a fuzzy classification of beats according to their etiology or focus of origin. The process we describe permits a more adequate consideration by the user of the arrhythmias diagnosed by the system, mainly in those cases in which the information derived from ECG analysis is not determinant.     

The DIMA web resource--exploring the protein domain network

Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. Availability: http://mips.gsf.de/genre/proj/dima     

An ensemble approach for healthcare application and diagnosis using natural language processing

Integration of healthcare records into a single application is still a challenging process There are additional issues when data becomes heterogeneous, and its application based on users does not appear to be the same. Hence, we propose an application called MEDSHARE which is a web-based application that integrates the data from various sources and helps the patient to access all their health records in a single point of source. Apart just from the collection of data, this portal enables the process of diagnosis using Natural language processing. The process is carried out by fuzzy logic ruleset which is generated by using NLP packages. The resulted information is given to the SVM classifier which helps in the prediction of diseases resulting in 89% of accuracy and standing the best compared to other classifiers. Finally, the observations resulted are sent to the front end application and the concerned user mobile through text message in their own native language for which translation package is been used.     

Extracting human protein interactions from MEDLINE using a full-sentence parser

MOTIVATION: The living cell is a complex machine that depends on the proper functioning of its numerous parts, including proteins. Understanding protein functions and how they modify and regulate each other is the next great challenge for life-sciences researchers. The collective knowledge about protein functions and pathways is scattered throughout numerous publications in scientific journals. Bringing the relevant information together becomes a bottleneck in a research and discovery process. The volume of such information grows exponentially, which renders manual curation impractical. As a viable alternative, automated literature processing tools could be employed to extract and organize biological data into a knowledge base, making it amenable to computational analysis and data mining. RESULTS: We present MedScan, a completely automated natural language processing-based information extraction system. We have used MedScan to extract 2976 interactions between human proteins from MEDLINE abstracts dated after 1988. The precision of the extracted information was found to be 91%. Comparison with the existing protein interaction databases BIND and DIP revealed that 96% of extracted information is novel. The recall rate of MedScan was found to be 21%. Additional experiments with MedScan suggest that MEDLINE is a unique source of diverse protein function information, which can be extracted in a completely automated way with a reasonably high precision. Further directions of the MedScan technology improvement are discussed. AVAILABILITY: MedScan is available for commercial licensing from Ariadne Genomics, Inc.     

Grid computing in image analysis

Diagnostic surgical pathology or tissue–based diagnosis still remains the most reliable and specific diagnostic medical procedure. The development of whole slide scanners permits the creation of virtual slides and to work on so-called virtual microscopes. In addition to interactive work on virtual slides approaches have been reported that introduce automated virtual microscopy, which is composed of several tools focusing on quite different tasks. These include evaluation of image quality and image standardization, analysis of potential useful thresholds for object detection and identification (segmentation), dynamic segmentation procedures, adjustable magnification to optimize feature extraction, and texture analysis including image transformation and evaluation of elementary primitives. Grid technology seems to possess all features to efficiently target and control the specific tasks of image information and detection in order to obtain a detailed and accurate diagnosis. Grid technology is based upon so-called nodes that are linked together and share certain communication rules in using open standards. Their number and functionality can vary according to the needs of a specific user at a given point in time. When implementing automated virtual microscopy with Grid technology, all of the five different Grid functions have to be taken into account, namely 1) computation services, 2) data services, 3) application services, 4) information services, and 5) knowledge services. Although all mandatory tools of automated virtual microscopy can be implemented in a closed or standardized open system, Grid technology offers a new dimension to acquire, detect, classify, and distribute medical image information, and to assure quality in tissue–based diagnosis.     

A visual data flow environment for macromolecular crystallographic computing

This article describes the integration of programs from the widely used CCP4 macromolecular crystallography package into a modern data flow visualization environment (application visualization system [AVS]), which provides a simple graphical user interface, a visual programming paradigm, and a variety of 1-, 2-, and 3-D data visualization tools for the display of graphical information and the results of crystallographic calculations, such as electron density and Patterson maps. The CCP4 suite comprises a number of separate Fortran 77 programs, which communicate via common file formats. Each program is encapsulated into an AVS macro module, and may be linked to others in a data flow network, reflecting the nature of many crystallo-graphic calculations. Named pipes are used to pass input parameters from a graphical user interface to the program module, and also to intercept line printer output, which can be filtered to extract graphical information and significant numerical parameters. These may be passed to downstream modules, permitting calculations to be automated if no user interaction is required, or giving the user the opportunity to make selections in an interactive manner.     

An computer information system for genetic engineering

The article describes the vectors data base and the software for its use (the VECTOR-PC system). At present the prototype versions of data base and VECTOR-PC exist and are in test exploitation. The original data base entry format contains 17 main fields for specific genetic engineering information. The VECTOR-PC system includes programs for data base search and support, and also the "genetic engineering designer", which allows the user to design his own hypothetic structures from the objects of data base and to receive detailed information about them. The system is destined for IBM PC or compatible computers.     

Semi-automated fluorimetric method for the estimation of urinary catecholamines using high-performance liquid chromatography

A high-performance liquid chromatographic method for the quantitation of adrenaline and noradranaline in urine is described, using fluorescence detection. The effluent from the liquid chromatograph is led directly into an analyser to produce the fluorescent trihydroxyindoles from the catecholamines. The method is more reliable and specific than conventional fluorescence techniques. Both catecholamines can be detected at levels of 0.5 ng on the column.     

A Supervisory Control Approach for Execution Control of an FMC

This paper presents a generic methodology based on formal language theory for the modeling and control of flexible manufacturing cell (FMC) systems. The motivating idea behind the overall approach stems from the supervisory control theory under the framework of Ramadge and Wonham. Essentially, we characterize the asynchronous and dynamic behavior of an FMC as a regular language and formulate the control logic generation problem as a sublanguage calculation problem, which requires the resulting language to satisfy at least two properties: maximal permissiveness and controllability. Then an algorithm for resolving the problem is presented. Based on the solution of the problem called supervisor, we propose a controller architecture that guarantees coordinated operation of an FMC through the regulation of occurrences of events. An adaptive control policy that regenerates supervisors on changes in task configurations is presented and a dynamic equation that describes the evolution of the control logic along time is derived. Then, we show that the proposed maximally permissive adaptive control policy has a number of preferred properties, including computational efficiency and consistency between the successive supervisors. Finally, a controller for an example FMC is implemented, using the object-oriented software modules. Our procedure has the merit of mathematical soundness, modular design, and systematic implementation.     

A flexible online metadata editing and management system

Our team developed a metadata editing and management system employing state of the art XML technologies initially aimed at the environmental sciences but with the potential to be useful across multiple domains. We chose a modular and distributed design for scalability, flexibility, options for customizations, and the possibility to add more functionality at a later stage. The system consists of a desktop design tool that generates code for the actual online editor, a native XML database, and an online user access management application. A Java Swing application that reads an XML schema, the design tool provides the designer with options to combine input fields into online forms with user-friendly tags and determine the flow of input forms. Based on design decisions, the tool generates XForm code for the online metadata editor which is based on the Orbeon XForms engine. The design tool fulfills two requirements: First data entry forms based on a schema are customized at design time and second the tool can generate data entry applications for any valid XML schema without relying on custom information in the schema. A configuration file in the design tool saves custom information generated at design time. Future developments will add functionality to the design tool to integrate help text, tool tips, project specific keyword lists, and thesaurus services.Cascading style sheets customize the look-and-feel of the finished editor. The editor produces XML files in compliance with the original schema, however, a user may save the input into a native XML database at any time independent of validity. The system uses the open source XML database eXist for storage and uses a MySQL relational database and a simple Java Server Faces user interface for file and access management. We chose three levels to distribute administrative responsibilities and handle the common situation of an information manager entering the bulk of the metadata but leave specifics to the actual data provider.     

Geneious plugins for the access of PlasmoDB and PiroplasmaDB databases

The bioinformatics software, Geneious, provides a useful platform for researchers to retrieve and analyse genomic and functional genomics information. However, the main databases that the software is able to access are hosted by NCBI (National Center for Biotechnology Information). The databases of EuPathDB (Eukaryotic Pathogen Database Resources), such as PlasmoDB and PiroplasmaDB, collect more specific and detailed information about eukaryotic pathogens than those kept in NCBI databases. Two plugins for Geneious, one for PlasmaDB and one for PiroplasmaDB were developed. When installed, users can use search facilities to find and import gene and protein sequences from the EuPathDB databases. Users can then use the functions of Geneious to process the sequence information. When information unique to PlasmoDB and PiroplasmaDB is required, the user can access results linked with the gene/protein sequence via the default web browser. The plugins are freely available from the Victorian Bioinformatics Consortium website. The plugins can be modified to access any of the databases of EuPathDB.     

Calorimetric method for the monitoring and control of biocatalysed reactions

A method for determining the reactant concentration and biocatalyst activity during a biocatalysed reaction is described. The analyser functions by monitoring the temperature change of a sample of reaction mixture which is held under adiabatic conditions. Details are given of the successful application of the analyser to the monitoring and control of a fed-batch bioconversion by Rhodococcus ruber NCIMB 40757 of acrylonitrile to 42% (w/w) (4.37 M) ammonium acrylate and the wider application of the analyser to other bioconversions is considered.     

Remote health monitoring for elderly through interactive television

ABSTRACT: BACKGROUND: Providing remote health monitoring to specific groups of patients represents an issue of great relevance for the national health systems, because of the costs related to moving health operators, the time spent to reach remote sites, and the high number of people needing health assistance. At the same time, some assistance activities, like those related to chronical diseases, may be satisfied through a remote interaction with the patient, without a direct medical examination. METHODS: Moving from this considerations, our paper proposes a system architecture for the provisioning of remote health assistance to older adults, based on a blind management of a network of wireless medical devices, and an interactive TV Set Top Box for accessing health related data. The selection of TV as the interface between the user and the system is specifically targeted to older adults. Due to the private nature of the information exchanged, a certified procedure is implemented for data delivery, through the use of non conditional smart cards. All these functions may be accomplished through a proper design of the system management, and a suitable interactive application. RESULTS: The interactive application acting as the interface between the user and the system on the TV monitor has been evaluated able to help readability and clear understanding of the contents and functions proposed. Thanks to the limited amount of data to transfer, even a Set Top Box equipped with a traditional PSTN modem may be used to support the proposed service at a basic level; more advanced features, like audio/video connection, may be activated if the Set Top Box enables a broadband connection (e.g. ADSL). CONCLUSIONS: The proposed layered architecture for a remote health monitoring system can be tailored to address a wide range of needs, according with each patient's conditions and capabilities. The system exploits the potentialities offered by Digital Television receivers, a friendly MHP interface, and the familiar remote control, to make the service effective and easy to use also for elderly people.     

SBML export interface for the systems biology toolbox for MATLAB

In this application note, we present an Systems biology markup language (SBML) export interface for the Systems Biology Toolbox for MATLAB. This interface allows modelers to automatically convert models, represented in the toolbox's own format (SBmodels) to SBML files. Since SBmodels do not explicitly contain all the information that is required to generate SBML, the necessary information is gathered by parsing SBmodels. The export can be done in two different ways. First, it is possible to call the export from the command line, thereby directly converting a model to an SBML file. The second option is to inspect and edit the conversion results with the help of a graphical user interface and to subsequently export the model to SBML. Availability: The SBML export interface has been integrated into the Systems Biology Toolbox for MATLAB, which is open source and freely available from http://www.sbtoolbox.org. The website also contains a tutorial, extensive documentation and examples.     

Recombinant DNA laboratory data manager using DBASE III+

The use of recombinant DNA technology in clinical and research laboratories involves diverse information management functions such as keeping track of patient samples, blot membranes, polymerase chain reaction products and test results. We report here the use of a PC-based database manager (DBASE III+, Ashton-Tate) for the coordinated maintenance of these functions. We have implemented a menu driven interface, developed using DBASE's programming language, which provides a data entry and maintenance system. The system is easily learned by technologists and saves time and reduces data handling errors compared to a manual method. The system can rapidly look up data and produce customized worksheets or reports correlating all available clinical and laboratory information. We will provide a copy of the program disc to interested parties.     

BioDataServer: a SQL-based service for the online integration of life science data

Regarding molecular biology, we see an exponential growth of data and knowledge. Among others, this fact is reflected in more than 300 molecular databases which are readily available on the Internet. The usage of these data requires integration tools capable of complex information fusion processes. This paper will present a novel concept for user specific integration of life science data. Our approach is based on a mediator architecture in conjunction with freely adjustable data schemes. The implemented prototype is called BioDataServer and can be accessed on the Internet: http://integration.genophen.de. To realize a comfortable usage of the resulted data sets of the integration process, a SQL-based query language and a XML data format were developed and implemented.     

BCDB - A database for breast cancer research and information

In pursuit of a better updated source including 'omics' information for breast cancer, Breast Cancer Database (BCDB) has been developed to provide the researcher with the quick overview of the Breast cancer disease and other relevant information. This database comprises of myriad of information about genes involved in breast cancer, its functions and drug molecules which are currently being used in the treatment of breast cancer. The data available in BCDB is retrieved from the biomedical research literature. It facilitates the user to search information on gene, its location in chromosome, functions and its importance in cancer diseases. Broadly, this can be queried by giving gene name, protein name and drug name. This database is platform independent, user friendly and freely accessible through internet. The data present in BCDB is directly linked to other on-line resources such as NCBI, PDB and PubMed. Hence, it can act as a complete web resource comprising gene sequences, drug structures and literature information related to breast cancer, which is not available in any other breast cancer database. AVAILABILITY: The database is freely available at http://122.165.25.137/bioinfo/breastcancerdb/