Datum vypracování: 2004-10-21



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Abstract: Analyses of the relationships and synergy between Bioinformatics (BI) and Medical Informatics (MI) show that there is a great potential for synergy between both disciplines with a view on continuity and individualisation of healthcare, but that a collaborative effort is needed to bridge the current gap between them. Biomedical Informatics (BMI) is the emerging discipline that aims to put these two worlds together so that the discovery and creation of novel diagnostic and therapeutic methods is fostered. The INFOBIOMED network is a new approach that aims to set a durable structure for this collaborative strategy in Europe, mobilising the critical mass of resources necessary for enabling the consolidation of BMI as a crucial scientific discipline for future healthcare. The specific objectives of INFOBIOMED aim at enabling systematic progress in clinical and genetic data interoperability and integration and advancing the exchange and interfacing of methods, tools and technologies used in both MI and BI. Moreover, it intends to enable pilot applications in particular fields that demonstrate the benefits of a synergetic approach in BMI, as well as to create a robust framework for education, training and mobility of involved researchers in BMI for the creation of a solid European BMI research capacity.

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Biomedical ontologies in post-genomic information systems
Perez-Rey, D.; Maojo, V.; Garcia-Remesal, M.; Alonso-Calvo, R.
Artificial Intelligence Laboratory School of Computer Science Polytechnic University of Madrid, Boadilla del Monte, 28660 Madrid, Spain
Conference: Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 , Taichung, Taiwan , 20040519-20040521 , (Sponsor: IEEE Computer Society; IEEE Neural Networks Society; Taichung Healthcare and Management University, Taiwan; Ministry of Education, Taiwan; National Sciences Council, Taiwan; Institute for Information Industry, Taiwan)
Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 2004. , 2004
Language: English

Abstract: After the completion of the Human Genome Project, a new, post genomic era, is beginning to analyze and interpret the huge amount of genomic information. Information methods and techniques from areas such as database integration, information retrieval, knowledge discovery in databases (KDD) and decision support systems (DSS) are needed. These systems should take into account idiosyncratic differences between these two interacting fields, medicine and biology. Their correspondent medical informatics (MI) and bioinformatics (BI) should also interact and there is a need for a point to support the communication. Biomedical ontologies can be used to enhance biomedical information systems, providing a knowledge sharing framework. However, ontology tools are still in its infancy and there is a need of standards, services, automatic management tools, etc... to be able to properly apply this technology environment. Nevertheless, ontologies are just the technical framework the most important issue is the content and the use policy.

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GeneWebEx: Gene annotation web extraction, aggregation, and updating from web-based biomolecular databanks
Masseroli, Marco; Stella, Andrea; Meani, Natalia; Alcalay, Myriam; Pinciroli, Francesco
Bioengineering Department Politecnico di Milano, I-20133 Milano, Italy
Conference: Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 , Taichung, Taiwan , 20040519-20040521 , (Sponsor: IEEE Computer Society; IEEE Neural Networks Society; Taichung Healthcare and Management University, Taiwan; Ministry of Education, Taiwan; National Sciences Council, Taiwan; Institute for Information Industry, Taiwan)
Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 2004. , 2004
Language: English

Abstract: Numerous genomic annotations are currently stored in different web-accessible databanks that scientists need to mine with user-defined queries and in a batch mode to orderly integrate the diverse mined data in suitable user-customizable working environments. Unfortunately, to date, most accessible databanks can be interrogated only for a single gene or protein at a time and generally the data retrieved are available in HTML page format only. We developed GeneWebEx to effectively mine data of interest in different HTML pages of web-based databanks, and organize extracted data for further analyses. GeneWebEx utilizes user-defined templates to identify data to extract, and aggregates and structures them in a database designed to allocate the various extractions from distinct biomolecular databanks. Moreover, a template-based module enables automatic updating of extracted data. Validations performed on GeneWebEx allowed us to efficiently gather relevant annotations from various sources, and comprehensively query them to highlight significant biological characteristics.

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Design of specie-specific primers for virus diagnosis in plants with PCR
Rocha, K.; Medeiros, C.; Monteiro, M.; Goncalves, L.; Marinho, P.
Univ. Federal do Rio Grande do Norte DCA-CT-UFRN, CEP. 59. 072-970, Natal, RN, Brazil
Conference: Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 , Taichung, Taiwan , 20040519-20040521 , (Sponsor: IEEE Computer Society; IEEE Neural Networks Society; Taichung Healthcare and Management University, Taiwan; Ministry of Education, Taiwan; National Sciences Council, Taiwan; Institute for Information Industry, Taiwan)
Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 2004. , 2004
Language: English

Abstract: We propose a specialist software to diagnose viral disease in plants. Our strategy is to align nucleotide sequences of plant virus to discover specie-specific regions of genes of the viral genomes, so as to design a primer. The program designs oligo-nucleotide primers used for polymerase chain reaction (PCR), a very cheap diagnosis technique. The user can specify (or use default) constraints for primer and amplified product lengths, as percentage of G+C, absolute or relative melting temperatures, and primer 3 prime nucleotides. The program screens candidate primer sequences with displayed user-specifiable parameters in order to help minimizing nonspecific priming and primer secondary structure. We tested this tool by designing two specific primers which were used to amplify known viral species, then used to perform a virus diagnosis.

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Using distributed computing platform to solve high computing and huge data processing problems in bioinformatics
Chen, Shih-Nung; Tsai, Jeffrey J.P.; Huang, Chih-Wei; Chen, Rong-Ming; Lin, Raymond C.K.
Conference: Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 , Taichung, Taiwan , 20040519-20040521 , (Sponsor: IEEE Computer Society; IEEE Neural Networks Society; Taichung Healthcare and Management University, Taiwan; Ministry of Education, Taiwan; National Sciences Council, Taiwan; Institute for Information Industry, Taiwan)
Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 2004. , 2004
Language: English

Abstract: Since the problems in bioinformatics are related to massive computing and massive data. In recent years, due to distributed computing is gaining recognition. The task originally requiring high computing power does not only rely on supercomputer. Distributed computing used off-the-shelf PC with high speed network can offer low cost and high performance computing power to handle the task. Therefore, the purpose of this paper is to implement a complete distributed computing platform based on peer-to-peer file sharing technology. The platform integrated scheduling, load balancing, file sharing, maintenance of data integrity, and user-friendly interface etc. functions. Through the platform can assist bioinformaticists in massive computing and massive data problems. Besides, the platform is easier use, more reliable, and more helpful than others for researchers to conduct bioinformatics research.

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An effective approach for constructing the phylogenetic tree on a grid-based architecture
Liu, Damon Shing-Min; Wu, Che-Hao
Department of Computer Science National Chung Cheng University, Chiayi, 621, Taiwan
Conference: Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 , Taichung, Taiwan , 20040519-20040521 , (Sponsor: IEEE Computer Society; IEEE Neural Networks Society; Taichung Healthcare and Management University, Taiwan; Ministry of Education, Taiwan; National Sciences Council, Taiwan; Institute for Information Industry, Taiwan)
Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 2004. , 2004
Language: English

Abstract: In biological research, scientists often need to use the information of the species to infer the evolutionary relationship among them. The evolutionary relationships are generally represented by a labeled binary tree, called the evolutionary tree (or phylogenetic tree). Reconstructing evolutionary tree is a major research problem in biology, and this problem is often known as phylogeny problem. The difficulty of such problem is that the number of possible evolutionary trees is very large. As the number of species increases, exhaustive enumeration of all possible relationships is not feasible. The quantitative nature of species relationships therefore requires the development of more rigorous methods for tree construction. The phylogeny problem is computationally intensive, thus it is suitable for distributed computing environment. Grid Computing (or Computational Grid) is a new concept to integrate the CPU power, the storage and other resources via Internet in order to get overall computing power. Nowadays, many bioinformaticists are developing the BioGrid technology in order to solve the challenges that need intensive computing in biology. In this paper, we design and develop a Grid-based system, and propose an efficient method based on the concept of quartet for solving the phylogeny problem on this architecture.

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Towards Ubiquitous Bio-Information Computing: Data protocols, middleware, and web services for heterogeneous biological information integration and retrieval
Hong, Pengyu; Zhong, Sheng; Wong, Wing H.
Conference: Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 , Taichung, Taiwan , 20040519-20040521 , (Sponsor: IEEE Computer Society; IEEE Neural Networks Society; Taichung Healthcare and Management University, Taiwan; Ministry of Education, Taiwan; National Sciences Council, Taiwan; Institute for Information Industry, Taiwan)
Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 2004. , 2004
Language: English

Abstract: Biological information computing is rapidly advancing from homogeneous data computation to large-scale heterogeneous data computation. However, the development of data specification protocols, software middleware, and Web services, which support large-scale heterogeneous data exchange, integration, and computation, generally falls behind data expansion rates and bioinformatics demands. The Ubiquitous Bio-Information Computing (UBIC**2) project aims to disseminate software packages to assist the development of heterogeneous bio-information computing applications that are interoperable and may run distributedly. UBIC**2 lays down the software architecture for integrating, retrieving, and manipulating heterogeneous biological information so that data behave like being stored in a unified database. UBIC**2 programming library implements the software architecture and provides application programming interfaces (APIs) to facilitate the development of heterogeneous bio-information computing applications. To achieve interoperability, UBIC**2 Web services use XML-based data communication means, which allow distributed applications to consume heterogeneous bio-information regardless of platforms. The documents and software package of UBIC**2 are available at http://www.ubic2.org.

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