[Comp-neuro] Linking Brain Models and Data: An Invitation from James Bonaiuto and Michael A. Arbib

James Bonaiuto j.bonaiuto at ucl.ac.uk
Tue Jul 15 11:27:31 CEST 2014


The USC Brain Project has just released a new version of their
neuroinformatics tool, the Brain Operation DataBase (BODB) v4.0.

BODB is a tool for modelers and experimentalists to document computational
models of the brain and their linkages to summaries of experimental data.
Models can be compared in terms of these relations, and experimental data
summaries can be visualized in a variety of ways. Groups of users can build
collaboratory workspaces which allow them to share groups of models and
data and work together to develop new models.

This latest version of BODB includes many new features:

- Improved search functionality: users can now search federated databases
such as CoCoMac (macaque neural connectivity) and Brede (human brain
imaging) directly as well as use boolean combinations of search terms

- Users can now maintain a list of their favorite entries outside any
workspace

- Model and BOP diagrams: users can generate clickable and zoomable graphs
showing the relationships between brain operating principles (BOPs) and
between models and summaries of empirical data (SEDs)

- ERP SED visualization: users can view the locations of ERP components on
a standard electrode placement system

- Improved workspaces: workspaces now include an activity stream,
discussion board, and bookmarks. Workspaces administrators can send
invitations to other users to join the workspace.

- ModelDB import: users can search ModelDB for models and import them to
BODB for documentation of their linkage to SEDs

- New Documentation System: the new system is far more extensive, is linked
from pages on BODB, and users can now search the documentation

- Web API: it is now possible to return BODB entries in JSON aand XML
format through a simple URL protocol

An overview of our general methodology for the neuroinformatics of brain
modeling can be found at http://www.ncbi.nlm.nih.gov/pubmed/24234915. It is
just one paper from a special issue of Neuroinformatics (Volume 12, Number
1, January 2014) on “Action, Language and Neuroinformatics” (Michael Arbib,
Guest Editor). The Manual for BODB can be found at
http://bodb.usc.edu/media/BODB_Manual.pdf.

We invite you to register for a free account on BODB and add your own
models and experimental data: http://bodb.usc.edu

------------------------------------------------------
James Bonaiuto, PhD
Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
UCL Institute of Neurology
33 Queen Square, London WC1N3BG, United Kingdom
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