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Bioinformatics brings computational methods to the analysis and processing of genomic data. Bioinformatics: Databases and Systems focuses on the issues of system building and data curation that dominate the day-to-day concerns of bioinformatics practitioners. Included are chapters by many of today's leading bioinformatics practitioners, describing most of the current paradigms of system building and curation, including both their strengths and weaknesses. Biological topics covered include sequence databases, metabolic pathways, phenotypes, variety collections, gene expression atlases and neuroinformatics. Species range from bacteria to mammals to plants. Software systems and technologies covered include OPM, CORBA, SRS, KLEISLI, ACEDB, Web-based integration and laboratory workflow.
Bioinformatics: Databases and Systems provides a valuable introduction for newcomers to the field, and a useful reference for veterans.
Introduction; S. Letovsky. Databases. 1. NCBI: Integrated Data for Molecular Biology Research; K. Sirotkin. 2. Hovergen: Comparative Analysis of Homologous Vertebrate Genes; L. Duret, et al. 3. WIT/WIT2: Metabolic Reconstruction Systems; R. Overbeek, et al. 4. EcoCyc: The Resource and the Lessons Learned; P.D. Karp, M. Riley. 5. KEGG: From Genes to Biochemical Pathways; M. Kanehisa. 6. OMIM: Online Mendelian Inheritance in Man; A.F. Scott, et al. 7. GDB: Integrating Genomic Maps; S. Letovsky. 8. HGMD: The Human Gene Mutation Database; M. Krawczak, et al. 9. Senselab: Modeling Heterogenous Data on the Nervous System; P. Nadkarni, et al. 10. The Mouse Genome Database and The Gene Expression Database: Genotype to Phenotype; J.T. Eppig, et al. 11. The Edinburgh Mouse Atlas: Basic Structure and Informatics; R.A. Baldock, et al. 12. FlyBase: Genomic and Post-Genomic Viewpoints; The FlyBase Consortium. 13. MaizeDB: The Maize Genome Database; M. Polacco, E. Coe. 14. AGIS: Using the Agricultural Genome Information System; S.M. Beckstrom-Sternberg, D.C. Jamison. 15. CGSC: The E. coli Genetic Sk Center Database; M.K.B. Berlyn. Systems. 16. OPM: Object-Prool Model Data Management Tools '97; V.M. Markowitz, et al. 17. BioKleisli: Integrating Biomedical Data and Analysis Packages; S.B. Davidson, et al. 18. SRS: Analyzing and Using Data from Heterogenous Textual Databanks; P. Carter, et al. 19. Biology Workbench: A Computing and Analysis Environment for the Biological Sciences; R. Unwin, et al. 20. EBI: CORBA and the EBI Databases; K. Jungfer, et al. 21. Biowidgets: Reusable Visualization Components for Bioinformatics; J. Crabtree, et al. 22. ACEDB: The ACE Database Manager; J. Thierry-Mieg, et al. 23. LABBASE: Data and Workflow Management for Large Scale Biological Research; N. Goodman, et al. Index.
Overview
Bioinformatics brings computational methods to the analysis and processing of genomic data. Bioinformatics: Databases and Systems focuses on the issues of system building and data curation that dominate the day-to-day concerns of bioinformatics practitioners. Included are chapters by many of today's leading bioinformatics practitioners, describing most of the current paradigms of system building and curation, including both their strengths and weaknesses. Biological topics covered include sequence databases, ...