Several efforts have been made to provide web-based databases to the
neuroscience community. Recent elaborations of the database concept are
providing tools for input of morphometric and time series data, links to
compartmental modeling, and scientific visualization all within coordinated
packages.
Models present in BioModels Database are annotated and linked to relevant
data resources, such as publications, databases of compounds and pathways,
controlled vocabularies. Models are available in SBML. All data is shared
between BioModels Database and DOQCS so that either set of interfaces and
tools may be used on the merged collection.
This database houses structural and protein distribution information derived
from confocal, multiphoton, and electron microscopy, including correlated
microscopy. Volume reconstructions are stored along with pointers to all of
the raw images and the processing details required to reconstruct the volume
from the raw data.
The main database contains details of hundreds (400+) of tracing studies in
their original descriptions. Further data are continuously added. There are
associated tools, and hooks to CARET and Catacomb software.
A repository of models of signaling pathways that includes GENESIS Kinetikit
files. Doqcs provides a navigation utility for exploring connections at the
level of molecules, between molecules and pathways, and between pathways.
Collaborations among several of the projects listed on this page are
ongoing. They grew out of a workshop presented at CNS*97, organized by
Rogene Eichler-West.
NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed
neurons. It contains contributions from over two-dozen labs and is being
continuously updated.
Neurons are characterized in terms of their morphological, physiological and
gene expression profiles. Synaptic connections are characterized in terms of
their physiological and anatomical profiles.
In addition to a hierarchical (XML) DBMS, the overall system provides tools
for visualization, analysis of structure-funtion relationships, and hypothesis
testing regarding neural computation. It provides specific hooks to the
Genesis, Nemosys and Neuron modeling packages. DBMS source available Spring
2004.
Morphologies of individual tangential cells from the blowfly lobula plate
are converted into a 3D mesh of cylinders of variable length and diameter.
Each of the, typically 2000, cylinders can then be treated as an
isopotential compartment in the compartmental modeling software package
NemoSys.
A database of behavioral and structural anatomy of Caenorhabditis elegans.
Includes images, 3-D reconstructions, viewers, search tools, literature
summaries and links to primary sources.
Additional Databases
Other web-enabled databases are less intrinsically tied to modeling
software, but neverthless provide much valuable neuroscience data to
modelers.
Mouse and primate brain atlases, and mouse connectivity data. Integrated
database and tools for image analysis and visualization of brain connectivity.
An Internet-accessible database of electrophysiological and other
information describing cortical neurons and their characteristic responses
to somatosensory and other stimuli.
Images depicting the spatial distribution of 2-deoxyglucose uptake evoked in
the glomerular layer of the rat olfactory bulb in response to a wide range of
defined odorant stimuli.
This page is maintained by Jim Perlewitz
(
perlewitz@earthlink.net
)
Please send reports of errors, updates, omissions, or suggestions.
Last updated Jan. 12, 2008.
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