Databasing the Brain

Stephen H. Koslow is the Director Office on Neuroinformatics, Associate Director, National Institute of Mental Health, National Institutes of Health. He also coordinates the Human Brain Project, a multi government agency informatics initiative. He earned his PhD from the Division of Biological Sciences, Department of Pharmacology, University of Chicago. He is a fellow of the American Association for the Advancement of Science, the American College of Medical Informatics, and the American College of Neuropsychopharmacology. He has been awarded several distinctions, including the Public Health Service Special Recognition Award, two NIH Director s Awards, the Presidents Award from the International Neural Network Society, and the President Award from the International Neural Network Society. He has 72 publications in referred journals, 20 invited chapters in books and edited 13 books. Shankar Subramaniam is a Professor of Bioengineering, Chemistry and Biochemistry and Biology and Director of the Bioinformatics Graduate Program at the University of California at San Diego. He also has adjunct Professorships at the Salk Institute for Biological Studies and the San Diego Supercomputer Center. He has previously served as Director of the Bioinformatics and Computational Biology Program at the National Center for Supercomputing Applications and the Co Director of the W.M. Keck Center for Comparative and Functional Genomics at UIUC. He is a fellow of the American Institute for Medical and Biological Engineering and is a recipient of Smithsonian Foundation and Association of Laboratory Automation Awards.

Preface. Contributors. PART I: COMPUTER SCIENCE MEETS NEUROSCIENCE. Chapter 1. Database Needs of Neuroscience: Schema and Design (Floyd E. Bloom and Warren G. Young). Chapter 2. Neuroanatomical Nomenclature and Ontology (Douglas M. Bowden and Mark Dubach). Chapter 3. Neuroinformatics for Neurophysiology: The Role, Design, and Use of Databases (Daniel Gardner, Michael Abato, Kevin H. Knuth, and Adrian Robert). Chapter 4. Persistent Collections (Reagan W. Moore). Chapter 5. Entity Attribute Value Database Approaches for Heterogeneous, Evolving Neuroscience Data (Perry L. Miller, Luis Marenco, Gordon M. Shepherd, and Prakash M. Nadkarni). Chapter 6. Data Grids (Ian Foster). Chapter 7. Building Grid Based Resources for Neurosciences (Maryann E. Martone, Steven T. Peltier, and Mark H. Ellisman). Chapter 8. Visualization in Life Sciences (Donna J. Cox). Chapter 9. Biology Workbenches(Andreia Maer, Brian Saunders, Roger Unwin, and Shankar Subramaniam). PART II: SYSTEM APPROACHES. Chapter 10. Genome to Disease (Iiris Hovatta and Carrolee Barlow). Chapter 11. Stimulus Dependent Regulation of Gene Expression in the Nervous System (Colleen A. McClung and Eric J. Nestler). Chapter 12. Cell Signaling Networks in Long Term Potentiation (Elizabeth A. Grace, Emmanuel M. Landau, Ravi Iyengar, and Robert D. Blitzer). Chapter 13. Genetic Analyses of Functional Connectivity in the Nervous System (Amit Etkin, Gleb Shumyatsky, Christopher J. Pittenger, and Eric R. Kandel). Chapter 14. GeneWays: A System for Extracting, Analyzing, Visualizing, and Integrating Molecular Pathway Data (Andrey Rzhetsky, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu, Pablo Ariel Duboue, Wubin Weng, John W. Wilbur, Vasileios Hatzivassiloglou, and Carol Friedman). Chapter 15. Cellular Morphology at the Cellular Level (Christopher J. Beaver, Robert C. Cannon, and Dennis A. Turner). Chapter 16. cellular Models (Raimond L. Winslow). Chapter 17. Electrophysiological Models (Mark E. Nelson). Chapter 18. Models of Neuronal Outgrowth (Duncan E. Donohue and Giorgio A. Ascoli). PART III: DATABASE APPLICATIONS. Chapter 19. The Neocortical Microcircuit Database (NMDB) (Henry Markram, Xiaozhong Luo, Gilad Silberberg, Maria Toledo Rodriguez, and Anirudh Gupta). Chapter 20. SenseLab: A Decade of Experience with Multilevel, Multidisciplinary Neuroscience Databases (Luis Marenco, Chiquito J. Crasto, Nian Liu, Michele Migliore, Jian Liu, Thomas M. Morse, Michael L. Hines, Prakash M. Nadkarni, Perry L. Miller, and Gordon M. Shepherd). Chapter 21. Three Dimensional Visualization and Analysis of Wiring Patterns in the Brain: Experiments, Tools, Models,and Databases (Jan G. Bjaalie and Trygve B. Leergaard). Chapter 22. Surface Based Atlases and a Database of Cortical Structure and Function (David C. Van Essen, John Harwell, Donna Hanlon, and James Dickson). Chapter 23. Brain Atlases of Normal Human Subjects (John Mazziotta). Chapter 24. Overcoming Challenges to Sharing Neuroimagery (Kenneth Smith). Chapter 25. Probabilistic Brain Atlases of Normal and Diseased Populations (Arthur W. Toga, Paul M. Thompson, Katherine L. Narr, and Elizabeth R. Sowell). Chapter 26. Maximizing Information Content in Shared and Archived Neuroimaging Studies of Human Cognition (John Darrell Van Horn and Michael S. Gazzaniga). Index.