COMPUTATIONAL
NEUROSCIENCE

Web Databases


Neuroinformatics Packages

Several efforts have been made to provide web-based databases to the neuroscience community. Some provide tools for input of morphometric and time series data, links to compartmental modeling, and scientific visualization.


NIF Navigator

BioModels Database

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.

Brain Architecture Management System

Database of Rat brain regions, cells, molecules and connectivity (Mihail Bota).

BrainMaps.org

Mouse and primate brain atlases, and mouse connectivity data. Integrated database and tools for image analysis and visualization of brain connectivity.

Brainnetome

Chinese effort to map the human connectome.

Cell Centered Database (CCDB)

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.

Cerebellar Development Transcriptome Database (CDT-DB)

The CDT-DB provides spatio-temporal gene expression profile data on the postnatal development of the mouse cerebellum.

Cerebellum Database

Experimental and modeling literature related to information transfer and computation in the cerebellar cortex.

Channelpedia

Channelpedia is a knowledge base system centered on genetically expressed ion channel models. It is web-based, freely accessible and currently contains 187 annotated ion channels with 50 Hodgkin-Huxley models.

CoCoMac - Cortical Connectivity in Macaque

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 (begun by Rolf Kötter).

CONNECT - Consortium Of Neuroimagers for the Non-invasive Exploration of Brain Connectivity and Tracts

Mapping of human brain microstructure and connectivity with diffusion MRI.

Cortical Neurophysiology Database

An Internet-accessible database of electrophysiological and other information describing cortical neurons and their characteristic responses to somatosensory and other stimuli.

CRCNS - Collaborative Research in Computational Neuroscience - Data sharing

The data include physiological recordings from sensory and memory systems, eg: single electrode recordings from macaque visual cortex, locust auditory receptor cells, multi-unit recordings from the rat hippocampusa. More to be added.

Cricket Cercal System Database

Contains over 100 anatomical reconstructions of sensory neurons and interneurons from the cricket cercal sensory system. Each neuron has been aligned to a common coordinate system, preserving anatomical relationships.

DOQCS - Database of Quantitative Cellular Signaling

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.

Duke Southampton Archive of Neuronal Morphology

FlyBrain

An online atlas and database of the Drosophila nervous system.

GENESIS Database and Modeler's Workspace

ChannelDB

An implementation of a database of ionic conductance models stored in simulator-independent NeuroML format.

Reciprocal Development Agreements

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.

Glomerular Response Archive

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.

Histology World: Nervous System Histology

IUPHAR Database of Receptors and Ion Channels

Incorporating detailed pharmacological, functional and pathophysiological information on G Protein-Coupled Receptors, Voltage-Gated Ion Channels, Ligand-Gated Ion Channels and Nuclear Hormone Receptors.

L-Neuron Database

Virtual Neuromorphology Electronic Database

Ligand Gated Ion Channel Database

Mouse Connectome Project

The Mouse Connectome Project aims to create a three-dimensional digital connectome atlas of the C57Black/6J mouse brain. The site will offer a catalog of neural tracer injection cases, which will be updated continuously to eventually cover the entire brain.

Neurodatabase.org BrainML Data Server

This site hosts a public neurophysiology database at Weill Medical College, Cornell. Initial data is predominately from cortical areas.

NeuroElectro

The goal of the NeuroElectro Project is to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database.

NeuroMorpho.Org

NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. It contains over 11,000 3D neuronal reconstructions reflecting more than 120 cell types from over 140 labs and is being continuously updated. Reconstructions can be saved in GENESIS, NEURON and NeuroML formats.

NeuronBank

NeuronBank will organize information about identified neuron location, physiology, morphology, and connectivity in nudibranch molluscs.

Open Connectome Project

Data sharing across conectome methodologies from EM to MRI.

SenseLab Project

A set of interoperable databases and database tools for collecting and analyzing information initially on the olfactory pathway.

Cellular Properties Database

archives synaptic receptors, ion channels, and neurotransmitters by neuron type, now across 18 brain regions.

MicroCurcuit Database

models of circuits within different brain regions.

Model Database

now contains over 700 models of neurons and circuits, that can be searched by model type, and that can be run as published or modified by the user.

Neuron Database

archives cell properties within dendritic and axonal compartments.

Odor Database

now contains over 200 odor molecules known to interact with odorant receptors.

Odor Map Database

archives 2DG and fMRI spatial activity patterns elicited by odorants in the glomerular layer of rats and mice.

Olfactory Receptor Database

now contains over 14,000 genes and proteins.

TanBase

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 a compartmental modeling package. Images only.

USC Brain Project

Brain Operation Database (BODB)

NeuroScholar 1.00

A web-based connectivity database that is multi-user and textual.

Virtual Atlas of the Honeybee Brain

Wormatlas

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.

Zebrafish Database



This page is maintained by Jim Perlewitz ( perlewitz@earthlink.net )
Please send reports of errors, updates, omissions, or suggestions.
Last updated Jun. 16, 2014.

Valid XHTML 1.1 Transitional Valid CSS! Registered with NIF