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  Purpose of BrainML

BrainML is a set of standards and practices for using XML to facilitate information exchange between user application software and neuroscience data repositories. It allows for common shared library routines to handle most of the data processing, but also supports use of structures specialized to the needs of particular neuroscience communities.

BrainML also enables the sharing of data structures. There is no reason for different groups to invent their own annotated representations for time series data, for example, if there are no technical differences in the information they wish to store. In practice, however, there are a variety of technical and social barriers to sharing formats, which BrainML is designed to reduce.

BrainML models are defined as collections of components. The components are published to a central location on the web (currently, this site) and may be easily viewed in order to determine their suitability for use in other applications. If a match is found, BrainML provides a mechanism for incorporating an existing component into the definition of a new model. This reduces the work needed to define a new data model, and provides the chance for software developed to handle data from one model to work with data from another to the extent that structures are shared.

To complement the BrainML modeling language, a set of protocols have been developed for BrainML document exchange between repositories and clients, for indexing of repositories, and for data query..

Neurodatabase.org is a repository of neurophysiology data based on BrainML models and protocols. The software running this server is 100% automatically customized to the data model -- none of its code is written specifically for the data representation it uses.

In the near future (fall, 2006), this software will be released open-source as a Neurodatabase Construction Kit for building neuroscience data servers that are BrainML-aware. This framework, written in Java, will include:

  • On the server side, a neurodatabase repository capable of accepting data submissions through a web interface, storing the contents in a relational database, and providing a web-based search-and-download interface for accessing the data.
  • On the client side, a graphical application for both searching for, retrieving, and viewing data from a repository.
  • On the client side, a graphical application for submitting data to a repository.

In addition the software will provide facilities for reading and writing data as XML documents conforming to BrainML models. Such documents may be submitted to repositories and/or read by other BrainML-aware software. In addition, tools for interconverting between this format and the file formats used by popular neurophysiology analysis and acquisition software are being developed in collaboration with the Bruxton Corporation.

Please click on the Architecture and About this Site links at left for more information.


Weill Medical College of Cornell University