ENFIN--A European network for integrative systems biology.

Integration of biological data of various types and the development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both the generation of new bioinformatics tools and the experimental validation of computational predictions. With the aim of bridging the gap existing between standard wet laboratories and bioinformatics, the ENFIN Network runs integrative research projects to bring the latest computational techniques to bear directly on questions dedicated to systems biology in the wet laboratory environment. The Network maintains internally close collaboration between experimental and computational research, enabling a permanent cycling of experimental validation and improvement of computational prediction methods. The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet.

Assessing pragmatic interoperability of information systems from a semiotic perspective

Most of studies on interoperability of systems integration focus on technical and semantic levels, but hardly extend investigations on pragmatic level. Our past work has addressed pragmatic interoperability, which is concerned with the relationship between signs and the potential behaviour and intention of responsible agents. We also define the pragmatic interoperability as a level concerning with the aggregation and optimisation of various business processes for achieving intended purposes of different information systems. This paper, as the extension of our previous research, is to propose an assessment method for measuring pragmatic interoperability of information systems. We firstly propose interoperability analysis framework, which is based on the concept of semiosis. We then develop pragmatic interoperability assessment process from two dimensions including six aspects (informal, formal, technical, substantive, communication, and control). We finally illustrate the assessment process in an example.

Pragmatic oriented data interoperability for smart healthcare information systems

Smart healthcare is a complex domain for systems integration due to human and technical factors and heterogeneous data sources involved. As a part of smart city, it is such a complex area where clinical functions require smartness of multi-systems collaborations for effective communications among departments, and radiology is one of the areas highly relies on intelligent information integration and communication. Therefore, it faces many challenges regarding integration and its interoperability such as information collision, heterogeneous data sources, policy obstacles, and procedure mismanagement. The purpose of this study is to conduct an analysis of data, semantic, and pragmatic interoperability of systems integration in radiology department, and to develop a pragmatic interoperability framework for guiding the integration. We select an on-going project at a local hospital for undertaking our case study. The project is to achieve data sharing and interoperability among Radiology Information Systems (RIS), Electronic Patient Record (EPR), and Picture Archiving and Communication Systems (PACS). Qualitative data collection and analysis methods are used. The data sources consisted of documentation including publications and internal working papers, one year of non-participant observations and 37 interviews with radiologists, clinicians, directors of IT services, referring clinicians, radiographers, receptionists and secretary. We identified four primary phases of data analysis process for the case study: requirements and barriers identification, integration approach, interoperability measurements, and knowledge foundations. Each phase is discussed and supported by qualitative data. Through the analysis we also develop a pragmatic interoperability framework that summaries the empirical findings and proposes recommendations for guiding the integration in the radiology context.

System Integration in a UAS design. An example of undergraduate student's tasks.

Systems integration is the origin of most major difficulties found in the engineering design of aeronautical vehicles. The whole design team must assure that each subsystem accomplishes its particular goals and that, together with the rest of the systems, they all meet the general aircraft requirements.Design and building of UAS is a field of actuation to which leading Universities, research Centers and Aeronautical designers have dedicated a lot of effort. In recent years, a team of students, lecturers and professors at the Escuela Universitaria de Ingeniería Técnica Aeronáutica (EUITA) have been working on the design and building of a UAS for civil observation. The design of multi-mission Unmanned Aerial Vehicles (UAVs) has seen a rapid progress in the last years. A wide variety of designs and applications, some of them really ingenious, have been proposed. The project, which has been going on as a teamwork experience for the last ten years, consists of the design and building of a UAV, and its peculiarity is that it has been carried out entirely by undergraduate students, as part of their Final Research Project. The students face a challenge that includes all the features and stages of an authentic engineering project. We present the current moment of evolution in the process, together with a description of the main difficulties the project has undergone, as a global experience in engineering design and development.

Integrated manufacturing systems design in a multi-product company

Using a hydraulic equipment manufacturing plant as the case study, this work explores the problems of systems integration in manufacturing systems design, stressing the behavioural aspects of motivation and participation, and the constraints involved in the proper consideration of the human sub-system. The need for a simple manageable modular organisation structure is illustrated, where it is shown, by reference to systems theory, how a business can be split into semi-autonomous operating units. The theme is the development of a manufacturing system based on an analysis of the business, its market, product, technology and constraints, coupled with a critical survey of modern management literature to develop an integrated systems design to suit a specific company in the current social environment. Society currently moves through a socio-technical revolution with man seeking higher levels of motivation. The transitory environment from an autocratic/paternalistic to a participative operating mode demands systems parameters only found to a limited extent in manufacturing systems today. It is claimed, that modern manufacturing systems design needs to be based on group working, job enrichment, delegation of decision making and reduced job monotony. The analysis shows how negative aspects of cellular manufacture such as lack of flexibility and poor fixed asset utilisation are relatively irrelevant and misleading in the broader context of the need to come to terms with the social stresses imposed on a company operating in the industrial environment of the present and the immediate future.

Integration Principles of Russian and Japanese Databases on Inorganic Materials

The methods and software for integration of databases (DBs) on inorganic material and substance properties have been developed. The information systems integration is based on known approaches combination: EII (Enterprise Information Integration) and EAI (Enterprise Application Integration). The metabase - special database that stores data on integrated DBs contents is an integrated system kernel. Proposed methods have been applied for DBs integrated system creation in the field of inorganic chemistry and materials science. Important developed integrated system feature is ability to include DBs that have been created by means of different DBMS using essentially various computer platforms: Sun (DB "Diagram") and Intel (other DBs) and diverse operating systems: Sun Solaris (DB "Diagram") and Microsoft Windows Server (other DBs).

Distributed process execution in collaborative networks

Processes are a central entity in enterprise collaboration. Collaborative processes need to be executed and coordinated in a distributed Computational platform where computers are connected through heterogeneous networks and systems. Life cycle management of such collaborative processes requires a framework able to handle their diversity based on different computational and communication requirements. This paper proposes a rational for such framework, points out key requirements and proposes it strategy for a supporting technological infrastructure. Beyond the portability of collaborative process definitions among different technological bindings, a framework to handle different life cycle phases of those definitions is presented and discussed. (c) 2007 Elsevier Ltd. All rights reserved.

Service-oriented architecture for device lifecycle support in industrial automation

Dissertação para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores Especialidade: Robótica e Manufactura Integrada

Framework for the semantic alignment of enterprise’s domain knowledge

Nowadays, the consumption of goods and services on the Internet are increasing in a constant motion. Small and Medium Enterprises (SMEs) mostly from the traditional industry sectors are usually make business in weak and fragile market sectors, where customized products and services prevail. To survive and compete in the actual markets they have to readjust their business strategies by creating new manufacturing processes and establishing new business networks through new technological approaches. In order to compete with big enterprises, these partnerships aim the sharing of resources, knowledge and strategies to boost the sector’s business consolidation through the creation of dynamic manufacturing networks. To facilitate such demand, it is proposed the development of a centralized information system, which allows enterprises to select and create dynamic manufacturing networks that would have the capability to monitor all the manufacturing process, including the assembly, packaging and distribution phases. Even the networking partners that come from the same area have multi and heterogeneous representations of the same knowledge, denoting their own view of the domain. Thus, different conceptual, semantic, and consequently, diverse lexically knowledge representations may occur in the network, causing non-transparent sharing of information and interoperability inconsistencies. The creation of a framework supported by a tool that in a flexible way would enable the identification, classification and resolution of such semantic heterogeneities is required. This tool will support the network in the semantic mapping establishments, to facilitate the various enterprises information systems integration.

Benchmarking therapeutic drug monitoring software: A review of available computer tools

Therapeutic drug monitoring (TDM) aims to optimize treatments by individualizing dosage regimens based on the measurement of blood concentrations. Dosage individualization to maintain concentrations within a target range requires pharmacokinetic and clinical capabilities. Bayesian calculations currently represent the gold standard TDM approach but require computation assistance. In recent decades computer programs have been developed to assist clinicians in this assignment. The aim of this survey was to assess and compare computer tools designed to support TDM clinical activities. The literature and the Internet were searched to identify software. All programs were tested on personal computers. Each program was scored against a standardized grid covering pharmacokinetic relevance, user friendliness, computing aspects, interfacing and storage. A weighting factor was applied to each criterion of the grid to account for its relative importance. To assess the robustness of the software, six representative clinical vignettes were processed through each of them. Altogether, 12 software tools were identified, tested and ranked, representing a comprehensive review of the available software. Numbers of drugs handled by the software vary widely (from two to 180), and eight programs offer users the possibility of adding new drug models based on population pharmacokinetic analyses. Bayesian computation to predict dosage adaptation from blood concentration (a posteriori adjustment) is performed by ten tools, while nine are also able to propose a priori dosage regimens, based only on individual patient covariates such as age, sex and bodyweight. Among those applying Bayesian calculation, MM-USC*PACK© uses the non-parametric approach. The top two programs emerging from this benchmark were MwPharm© and TCIWorks. Most other programs evaluated had good potential while being less sophisticated or less user friendly. Programs vary in complexity and might not fit all healthcare settings. Each software tool must therefore be regarded with respect to the individual needs of hospitals or clinicians. Programs should be easy and fast for routine activities, including for non-experienced users. Computer-assisted TDM is gaining growing interest and should further improve, especially in terms of information system interfacing, user friendliness, data storage capability and report generation.

A modular approach for integrative analysis of large-scale gene-expression and drug-response data

High-throughput technologies are now used to generate more than one type of data from the same biological samples. To properly integrate such data, we propose using co-modules, which describe coherent patterns across paired data sets, and conceive several modular methods for their identification. We first test these methods using in silico data, demonstrating that the integrative scheme of our Ping-Pong Algorithm uncovers drug-gene associations more accurately when considering noisy or complex data. Second, we provide an extensive comparative study using the gene-expression and drug-response data from the NCI-60 cell lines. Using information from the DrugBank and the Connectivity Map databases we show that the Ping-Pong Algorithm predicts drug-gene associations significantly better than other methods. Co-modules provide insights into possible mechanisms of action for a wide range of drugs and suggest new targets for therapy

MyHits: a new interactive resource for protein annotation and domain identification.

The MyHits web server (http://myhits.isb-sib.ch) is a new integrated service dedicated to the annotation of protein sequences and to the analysis of their domains and signatures. Guest users can use the system anonymously, with full access to (i) standard bioinformatics programs (e.g. PSI-BLAST, ClustalW, T-Coffee, Jalview); (ii) a large number of protein sequence databases, including standard (Swiss-Prot, TrEMBL) and locally developed databases (splice variants); (iii) databases of protein motifs (Prosite, Interpro); (iv) a precomputed list of matches ('hits') between the sequence and motif databases. All databases are updated on a weekly basis and the hit list is kept up to date incrementally. The MyHits server also includes a new collection of tools to generate graphical representations of pairwise and multiple sequence alignments including their annotated features. Free registration enables users to upload their own sequences and motifs to private databases. These are then made available through the same web interface and the same set of analytical tools. Registered users can manage their own sequences and annotations using only web tools and freeze their data in their private database for publication purposes.

Ongoing and future developments at the Universal Protein Resource.

The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.

MyHits: improvements to an interactive resource for analyzing protein sequences.

The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to improve the usability of the service. The MySQL schema and its associated API were revamped and the database engine (HitKeeper) was separated from the web interface. This paper summarizes the current status of the server, with an emphasis on the new services.

Experiencias de interoperabilidad entre CRIS y repositorios en Catalunya

Toni Prieto, Técnico IC del Servicio de Bibliotecas y Documentación (SBD) de la UPC, en su presentación 'Experiencias de interoperabilidad entre CRIS y repositorios en Catalunya', describió la integración del repositorio UPCommons y del CRIS DRAC (Descriptor de la Recerca i l'Activitat Acadèmica) de la UPC. El resultado de esta integración es un esquema integrado de archivo CRIS/IR en dos fases, envío y revisión, en el que los metadatos se introducen en DRAC -para posteriormente ser transferidos, validados y enriquecidos si procede- y el archivo de texto completo asociado se realiza en UPCommons. De manera similar funciona la integración de GIR (Gestió Integral de la Recerca, basado en Universitas XXI Investigación) y el repositorio O2 en la UOC, permitiendo la asignación del identificador handle de un ítem en O2 a una referencia en GIR. Ambos sistemas, DRAC en la UPC y GIR en la UOC, están integrados en el Proyecto CVN de generación de CVs normalizados. Se mencionaron asimismo experiencias posteriores de integración CRIS/IR actualmente en curso en la Universitat de Barcelona y en la U Pompeu Fabra, y se mostró el impacto significativo de la estrategia de integración de sistemas sobre el ritmo de incorporación de contenidos a UPCommons.