BAMS | About

About

BAMS is a neuroinformatics environment for handling data from different species. The information that can be stored, processed or retrieved from BAMS is collated from the literature, or consists of experimental data inserted by neuroscientists.

He highly encourage users to read the online manual. This manual explains in details each function of BAMS, and includes examples of queries.
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BAMS was designed and implemented by Dr. Mihail Bota under the supervision of Dr. Larry W. Swanson at the University of Southern California, NIBS Neuroscience Program.

The status of BAMS is "in development". Several modules of the system are fully functional and can be used by the members of the neuroscience community. The current features of BAMS include:

1. Hierarchical representations of brain structures from different neuroanatomical atlases and mammalian species. BAMS contains to date the following nomenclatures:
Species: Rat: Swanson 1992, complete, hierarchically organized; Swanson 1998, complete, hierarchically organized; Swanson 2004, complete, hierarchically organized; Paxinos & Watson 1997, complete
Species: Human: Bowden 2002, complete, hierarchically organized; Mai et al. 1997, complete, partial hierarchy; Nomina Anatomica 1895, hierarchically organized
Species: Macaca fascicularis: Bowden 2002, complete, hierarchically organized
Species: Macaque (general): Felleman & Van Essen, hierarchically organized
Species: Cat: Berman and Jones 1982, complete, partial hierarchy
Species: Mouse: Paxinos and Franklin 2001, complete, partial hierarchy; Hof et al. 2000, strain C57BL/6, complete; Dong, 2007 (ABA), strain C57BL/6, complete, hierarchically organized
2. Inference of relations between regions (cell groups) from different neuroanatomical atlases and species. Relations between brain regions are hierarchical dependencies, identity of terms and qualitative spatial relations between pairs of nuclei from different atlases.
3. Inference of projection matrices involving regions of interest from unrelated information. A projection is an axonal connection from a region A to a region B, as defined in a given atlas.
4. Fully functional user interface for insertion, processing and organizing of experimental neuroanatomical data (restricted to Swanson lab).
5. Customized matrices of projections for sets of brain regions of interest.
6. Reconstructions of connectivity matrices as reported in associated papers.
7. Reconstruction of cell type profiles for structures of interest.
The basic functionality of BAMS Menu (left frame) is provided below:

Brain Parts           leads to the search options by names of brain parts (partial match), abbreviation, full text, nomenclature, and species

References           leads to the option of search for information by reference (author, source, year).

Molecules           leads to the option of search for chemicals (cell bodies).

Cells           leads to the option of search for cell types and classes.

Evaluate           contains modalities of evaluation and processing data inserted in BAMS.

     Reports      leads to the options of construction of customized matrices of connectivity reports:

          Outputs leads to the option of construction of customized matrices of efferent projections reports.

          Inputs leads to the option of construction of customized matrices of afferent projections reports.

     Networks      leads to the engine for constructing potential networks of regions from the connectivity data inserted in BAMS (works for any nomenclature, as long as is associated with projections reports).