The long-term goal of the proposed research is to create a fully functional online workbench for obtaining information about the biological circuits that make up the brain, and for modeling the functional organization of this circuitry in health and in a broad range of neurological diseases, including Alzheimer's, chronic pain, epilepsy, multiple sclerosis, Parkinson's, stroke, and narcolepsy. One strength of this approach in early stages of development is that it complements experimental systems neuroscience research in the lab on the fundamental structural and chemical organization of limbic system circuits that control the basic drives and emotions, along with learning and memory. The foundation of the neuroinformatics research proposed here is a functioning, relatively heavily used website begun in 2001 and called the Brain Architecture Knowledge Management System (Google: BAMS). It is currently the only online system that integrates neuroscience information at four levels of organization: gray matter Regions, neuronal Cell Types making up regions, white matter axonal Connections between regions and cell types, and expressed Molecules.

Public Health Relevance

All of the major neurological diseases are studied in animal models including rat. The goal of the proposed research is to create a widely used online website for accessing information about the structure and chemistry of brain circuits and systems involved in health and disease, and for modeling the basic wiring diagram of the brain and how it is affected in specific neurological diseases, treated in specific ways.

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
Research Project (R01)
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Special Emphasis Panel (ZRG1-NT-B (01))
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Liu, Yuan
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University of Southern California
Schools of Arts and Sciences
Los Angeles
United States
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Brown, Ramsay A; Swanson, Larry W (2015) Golgi: Interactive Online Brain Mapping. Front Neuroinform 9:26
Bota, Mihail; Talpalaru, Stefan; Hintiryan, Houri et al. (2014) BAMS2 workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections. J Comp Neurol 522:3160-76
Brown, Ramsay A; Swanson, Larry W (2013) Neural systems language: a formal modeling language for the systematic description, unambiguous communication, and automated digital curation of neural connectivity. J Comp Neurol 521:2889-906
Bota, Mihail; Dong, Hong-Wei; Swanson, Larry W (2012) Combining collation and annotation efforts toward completion of the rat and mouse connectomes in BAMS. Front Neuroinform 6:2
Bota, Mihail; Sporns, Olaf; Swanson, Larry W (2012) Neuroinformatics analysis of molecular expression patterns and neuron populations in gray matter regions: the rat BST as a rich exemplar. Brain Res 1450:174-93
Bota, Mihail; Swanson, Larry W (2010) Collating and Curating Neuroanatomical Nomenclatures: Principles and Use of the Brain Architecture Knowledge Management System (BAMS). Front Neuroinform 4:3
Swanson, Larry W; Bota, Mihail (2010) Foundational model of structural connectivity in the nervous system with a schema for wiring diagrams, connectome, and basic plan architecture. Proc Natl Acad Sci U S A 107:20610-7
Petersen, R C; Aisen, P S; Beckett, L A et al. (2010) Alzheimer's Disease Neuroimaging Initiative (ADNI): clinical characterization. Neurology 74:201-9
Simmons, Donna M; Swanson, Larry W (2008) High-resolution paraventricular nucleus serial section model constructed within a traditional rat brain atlas. Neurosci Lett 438:85-9
Bota, Mihail; Swanson, Larry W (2007) The neuron classification problem. Brain Res Rev 56:79-88

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