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Neuroscience at University of Florida: Databases and Tools

Resources and tools used in neuroscience research at University of Florida

Neuroscience Information Framework

  Neuroscience Information Framework provides a web-based search portal of neuroscience resources and tools including images, genes, clinical trials, datasets, multimedia, models, software, etc contained on databases that are not accessed through a typical search engine (hidden or invisible web). This is a great starting point for searching neuroscience-related data.

A video tutorial can be found here.

Connectome Workbench

 Connectome Workbench is a "visualization and discovery tool used to map data generated by the Human Connectome Project. This tool allows you to explore multiple types of data, including connectivity data, in a fully interactive way".

Autism Research Databases

 The National Database for Autism Research supports data sharing across a broad array of clinical, genomic, and brain imaging autism research data.

 The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature: databases and unpublished data

Gemma - Neurocarta

 Gemma "is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profile"

 Neurocarta "is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes"

Image Databases

 Allen Brain Atlas data portal from the Allen Institute for Brain Science contains a collection of public resources including gene expression, neuroanatomical data etc from human, mouse, and primate.These data can be analyzed and viewed using the portal tools (e.g. 3D viewer) as well as downloaded.

 The Human Connectome Project collects vdata using advanced brain imaging methods on a large population of healthy adults, and makes the data freely available.

The Brain Maps altas contains high-resolution annotated structural images (e.g. stained sections from brain) integrated with fuctional data. Includes datasets from Homo sapiens, Macaca mulatta, Mus musculus, Rattus novergicus, Felis catus, etc.

 The Alzheimer’s Disease Neuroimaging Initiative (ADNI) contains a collection of validated data such as MRI and PET images, cerebral spinal fluid, and blood biomarkers as predictors of the disease. You can login to the Image Data Archive to access ADNI data or apply for access to the ADNI biospecimens.

 The Brain Biodiversity Bank repository of images of and information about brain specimens contained in the collections associated with the National Museum of Health and Medicine, Michigan State University, and the University of Wisconsin.

The Cerebellar Development Transcriptome (CDT-DB) is a database (including DNA microarray and in situ hybridization) for mining cerebellar genes and gene expression.

  GENSAT is a collection of pictorial gene expression maps of the brain and spinal cord of the mouse.

  MindSeer is a visualization tool for multi-modality neuroimaging data.  It supports basic data management capabilities, visualization of 3D surfaces

 The Mouse Brain Library contains high-resolution images and datasets of brains from many genetically characterized strains of mice. 

 International Neuroimaging Data-sharing Initiative (INDI) - 1000 Functional Connectomes Project contains fMRI (R-fMRI) datasets collected from around the world as well as data processing tools.

 Neuromorpho is a curated public repository of digitally reconstructed neuronal arborizations.

Sense Lab Databases

The Sense Lab Project "contains six related databases that support experimental and theoretical research on the membrane properties" 

NEURONAL DATABASES

  Cellular Properties Database (CellPropDB) is a repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in glia, muscle, and gland cells, etc.

  NeuronDB database provides data on of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances.

 ModelDB provides access to computational neuroscience models.

OLFACTORY DATABASES

 Olfactory Receptors Databse (ORDB) contains data on vertebrates genes and proteins of olfactory and chemosensory recepors.

 Odor Database contains odorant molecules (attributes or identities) and the receptors they experimentally bind.

DISEASE DATABASE

 BrainPharma database contains data on drugs for the treatment of different neurological disorders.

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Joe Wu
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