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.
Note: the newest versions of internet browsers will tend to open the manual in a new tab, instead of window. They also will block it, if the security is set on "high". Please allow temporary popups, or hit the "Ctrl" button when you click on the manual link.

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:
         Outputsleads to the option of construction of customized matrices of efferent projections reports.
         Inputsleads 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).

The author of BAMS would like to express his thanks to the following neuroscientists (in alphabetical order), who

Participated at the design of BAMS  Provided and/or collated data  Provided valuable input
  • Dr. Hong-Wei Dong
  • Dr. Luis Marenco (Yale)
  • Professor Larry Swanson
  • Professor Douglas Bowden (U. of Washington)
  • Dr. Gully A.P.C. Burns
  • Professor Patrick Hof (Mount Sinai School of Medicine)
  • Professor E.G. Jones (U.C. Davis)
  • Professor Jürgen K. Mai (U. of Duesseldorf)
  • Professor George Paxinos (U. of New South Wales, Sydney)
  • Professor David Van Essen (Washington University, San Louis)
  • Dr. Warren Young (Neurome)
  • Professor Michael A. Arbib
  • Professor Douglas Bowden (U. of Washington)
  • Dr. Arthur Toga (UCLA)
  • Professor Alan G. Watts
  • This work was supported by the NIH/NIMH Grant MH61223 (A Multimodal Multidimensional (4D) Map of the Mouse Brain), by NIH/NINDS Grant NS16686 and by the NINDS/NIMH/NIBIB Grant NS50792-01.

    If you would like to participate in the development of BAMS, and/or provide data to be stored in it, please contact the system administrator.