BODB

From USCBPWiki

Advances in neuroscientific research have led to a flood of information that can only be structured and navigated with the aid of databases and the technology of the World Wide Web. As one contribution to channeling this flood we are developing BODB, in which the aim is to facilitate the interchange between those developing new brain models and new experiments. The current ideas are that the system (1) houses capsules of neuroscientific literature information that will facilitate comparison and integration of original articles; (2) provides a standard form and its repository for entering BOPs, Brain Operating Principles – the gist of the brain mechanisms that abstract away from their heterogeneities, as a way to organize experiments, models and technological spin-off of brain mechanisms; (3) provides a standard form and its repository for entering Model summaries; (4) supplies a sharing point for the data in (1,2,3) among users to enhance the knowledge development; (5) provides a repository of experimental data with a standard structure, and the experimental-data and cross-experiment data analysis tools (currently our focus is on brain imaging data); and (6) provides a means to connect the related documents together and a practical entry-searching tool to enhance the accessibility of information.

Introduction

We describe the basic features of an online integrated environment for neuroscientists, the Brain Operation DataBase (BODB – pronounced “Beau DB”; http://neuroinformatics.usc.edu/BODB)

Conceptual Overview

Advances in neuroscientific research have led to a flood of information that can only be structured and navigated with the aid of databases and the technology of the World Wide Web. As one contribution to channeling this flood,1 we are developing BODB to facilitate the interchange between those developing new brain models and those developing new experiments. The current ideas are that the system

1. houses capsules of neuroscientific literature information that will facilitate comparison and integration of original articles;
2. provides a standard form and repository for entering BOPs;
3. provides a standard form and repository for entering Model summaries;
4. supplies a sharing point for the data in (1,2,3) among users to enhance knowledge development;
5. provides a repository of experimental data with a standard structure, and the experimental-data and cross-experiment data analysis tools (currently our focus is on brain imaging data); and
6. provides a means to connect related documents together with practical search tools to enhance the accessibility of information.

These features are intended for use by both brain modelers and brain experimenters. The experimental data and analysis tools will be used by the brain modeler in extracting knowledge and developing new models, and by the experimenter in designing further experimental protocols. Furthermore, the BOP and Model entries will supply knowledge for the modeler to construct new models, and provide the experimenter suggestions to contrive new experiments. Consequently, the implementation and integration of these features would enhance a theory-experiment cycle (Arbib, 2001).

User Registration and Login

Once registering, users can login to the site from the main page.

Structure of the BODB Site

A description of the layout of the BODB website and an overview of its functionality.

Insert

The insert page provides links for adding new Literature, Brain Operating Principle (BOP), Model, and Summary of Experimental Data (SED) entries.

Literature

Literature (Journal Article, Book, Chapter, Conference, Thesis, and Unpublished) information

Brain Operating Principles (BOPs)

Brain Operating Principle (e.g. Winner-Take-All)

Models

Structured description of a model with links to related entities. (e.g. Didday Model based on the Winner-Take-All Principle)

Summaries of Experimental Data (SEDs)

A summary of experimental data (e.g. brain imaging).

Search

The search page allows the user to search all entries, Literature, Brain Operating Principle (BOP), Model, Summary of Experimental Data (SED), Summary of Simulation Results (SSR), and Brain Region entries.

Talairach Applet

The Talairach Applet allows users to visualize brain imaging SEDs in two-dimensional or three-dimensional mode.

Workspace

The Workspace provides users an area to manage their Model, BOP, and SED drafts, selected Models for benchmarking, and selected coordinates.

Tags

Each BODB entry can be associated with a list of tags, or keywords, that can be used to group and search for related entries.

Report Generation

Reports for Model and BOP entries can be generated in either RTF or PDF format by clicking on the appropriate button at the bottom of the Model view or BOP view page. The report will contain all of the information on the view page, including any expanded subsections. Information in collapsed subsections will not be included.

User Profile

The User Profile page allows the user to manage their account information and preferences.

Messaging

BODB's internal messaging system allows users to send and receive messages with other users.

Administration

The Administration section allows BODB administrators to manage users, user groups, and their permissions, as well as brain regions and nomenclatures.