A new way to classify and retrieve reusable components: the finder metaphor

Our research group ISRI (InCormation Syslems Reuse on Internet) is working in a new classification scheme for reusable software (assets) based on the idea of hyper-spherical finders. The Finder metaphor deals with a multidimensional space where the components are positioned according to its functional description. and vision fields. hiper-spheres, which can move in space and see the components. Our approach has some advantages over other techniques and methodologies, for example: we start with an empty space (the universe) and automatically fill it with reusable assets, which describe the application domain, but the space itself is dynamically generated as components are inserted; furthermore, we can build different finders, alter its radius or its kind of movement, without the need of reclassifying the repository, allowing a dynamical classification. We developed and tested a simple but practical method to compute similarities, allowing to locate assets in this kind of universe, generating finders and modifying them, querying the universe and retrieving similar components. The tested values of recall and precision were similar or better than other known methods but ours is by far easier to implement and maintain. An extensive list of references about reuse and classificationlretrieval problem. where interested readers can investigate more deeply is offered.Eje: Ingeniería del software. Computación gráfica y visualizaciónRed de Universidades con Carreras en Informática (RedUNCI

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Peptidome, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov

A new way to classify and retrieve reusable components: the finder metaphor

Our research group ISRI (InCormation Syslems Reuse on Internet) is working in a new classification scheme for reusable software (assets) based on the idea of hyper-spherical finders. The Finder metaphor deals with a multidimensional space where the components are positioned according to its functional description. and vision fields. hiper-spheres, which can move in space and see the components. Our approach has some advantages over other techniques and methodologies, for example: we start with an empty space (the universe) and automatically fill it with reusable assets, which describe the application domain, but the space itself is dynamically generated as components are inserted; furthermore, we can build different finders, alter its radius or its kind of movement, without the need of reclassifying the repository, allowing a dynamical classification. We developed and tested a simple but practical method to compute similarities, allowing to locate assets in this kind of universe, generating finders and modifying them, querying the universe and retrieving similar components. The tested values of recall and precision were similar or better than other known methods but ours is by far easier to implement and maintain. An extensive list of references about reuse and classificationlretrieval problem. where interested readers can investigate more deeply is offered.Eje: Ingeniería del software. Computación gráfica y visualizaciónRed de Universidades con Carreras en Informática (RedUNCI

Computer-aided research in natural sciences

Diese Magisterarbeit beschäftigt sich mit den Möglichkeiten, die der Computer den Scientific Communities bietet. Schwerpunkte sind die Verbreitung von Wissen durch das Internet, Politik, Portale, Suchmaschinen und die digitale Rekonstruktion von Organismen.This master thesis concentrates on the possibilities for the scientific communities caused by the computer. Main topics are the propagation of knowledge by the Internet, politics, portals, search engines and digital reconstruction of organisms

An application in bioinformatics : a comparison of affymetrix and compugen human genome microarrays

The human genome microarrays from Compugen® and Affymetrix® were compared in the context of the emerging field of computational biology. The two premier database servers for genomic sequence data, the National Center for Biotechnology Information and the European Bioinformatics Institute, were described in detail. The various databases and data mining tools available through these data servers were also discussed. Microarrays were examined from a historical perspective and their main current applications-expression analysis, mutation analysis, and comparative genomic hybridization-were discussed. The two main types of microarrays, cDNA spotted microarrays and high-density spotted microarrays were analyzed by exploring the human genome microarray from Compugen® and the HGU133 Set from Affymetrix® respectively. Array design issues, sequence collection and analysis, and probe selection processes for the two representative types of arrays were described. The respective chip design of the two types of microarrays was also analyzed. It was found that the human genome microarray from Compugen 0 contains probes that interrogate 1,119,840 bases corresponding to 18,664 genes, while the HG-U133 Set from Affymetrix® contains probes that interrogate only 825,000 bases corresponding to 33,000 genes. Based on this, the efficiency of the 25-mer probes of the HG-U133 Set from Affymetrix® compared to the 60-mer probes of the microarray from Compugen® was questioned