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Cite this (3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood, RRID:SCR_009437)
URL: http://www.nitrc.org/projects/dti_rat_atlas/
Resource Type: Resource, atlas, reference atlas, data or information resource
3D DTI anatomical rat brain atlases have been created by the UNC- Chapel Hill Department of Psychiatry and the CAMID research collaboration. There are three age groups, postnatal day 5, postnatal day 14, and postnatal day 72. The subjects were Sprague-Dawley rats that were controls in a study on cocaine abuse and development. The P5 and P14 templates were made from scans of twenty rats each (ten female, ten male); the P72, from six females. The individual cases have been resampled to isotropic resolution, manually skull-stripped, and deformably registered via an unbiased atlas building method to create a template for each age group. Each template was then manually segmented using itk-SNAP software. Each atlas is made up of 3 files, a template image, a segmentation, and a label file.Cite this (Archive of Data on Disability to Enable Policy ADDEP, RRID:SCR_016315)
URL: https://www.icpsr.umich.edu/icpsrweb/content/addep/index.html
Resource Type: Resource, service resource, data repository, storage service resource
ADDEP provides access to data including a wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of the Americans with Disabilities Act and other disability policies.Cite this (BAMS Cells, RRID:SCR_003531)
URL: http://brancusi.usc.edu/bkms/
Resource Type: Resource, data or information resource, database
BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein.Cite this (BAMS Nested Regions, RRID:SCR_000238)
URL: http://brancusi.usc.edu/bkms/
Resource Type: Resource, data or information resource, database
BAMS is an online resource for information about neural circuitry. The BAMS Nested Regions view focuses on the major brain regions and their relationshipsCite this (BAMS Neuroanatomical Ontology, RRID:SCR_004616)
URL: http://brancusi.usc.edu/bkms/bams-ontology.html
Resource Type: Resource, ontology, data or information resource, controlled vocabulary
BAMS Neuroanatomical Ontology is a lightweght ontology designed specifically for neuroscience. It contains a complete set of concepts that describe the structure of the rat CNS and a growing set of concepts that describe different neuron populations in the rat CNS.Cite this (BMAP - Brain Molecular Anatomy Project, RRID:SCR_008852)
URL: http://trans.nih.gov/bmap/index.htm
Resource Type: Resource, topical portal, portal, funding resource, data or information resource
The Brain Molecular Anatomy Project is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major scientific goals: # Gene discovery: to catalog of all the genes expressed in the nervous system, under both normal and abnormal conditions. # Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage, and physiological state, and thus gain insight into gene function. In pursuit of these goals, BMAP has launched several initiatives to provide resources and funding opportunities for the scientific community. These include several Requests for Applications and Requests for Proposals, descriptions of which can be found in this Web site. BMAP is also in the process of establishing physical and electronic resources for the community, including repositories of cDNA clones for nervous system genes, and databases of gene expression information for the nervous system. Most of the BMAP initiatives so far have focused on the mouse as a model species because of the ease of experimental and genetic manipulation of this organism, and because many models of human disease are available in the mouse. However, research in humans, other mammalian species, non-mammalian vertebrates, and invertebrates is also being funded through BMAP. For the convenience of interested investigators, we have established this Web site as a central information resource, focusing on major NIH-sponsored funding opportunities, initiatives, genomic resources available to the research community, courses and scientific meetings related to BMAP initiatives, and selected reports and publications. When appropriate, we will also post initiatives not directly sponsored by BMAP, but which are deemed relevant to its goals. Posting decisions are made by the Trans-NIH BMAP CommitteeCite this ( BMAP cDNA Resources , RRID:SCR_002973)
URL: http://trans.nih.gov/bmap/resources/resources.htm
Resource Type: Resource, topical portal, resource, production service resource, material service resource, service resource, portal, biomaterial manufacture, data or information resource
As part of BMAP gene discovery efforts, mouse brain cDNA libraries and Expressed Sequence Tags (ESTs) have been generated. Through this project a BMAP mouse brain UniGene set consisting of over 24,000 non-redundant members of unique clusters has been developed from EST sequencing of more than 50,000 cDNA clones from 10 regions of adult mouse brain, spinal cord, and retina (http://brainEST.eng.uiowa.edu/). In 2001, NIMH along with NICHD, NIDDK, and NIDA, awarded a contract to the University of Iowa ( M.B. Soares, PI) to isolate full-length cDNA clones corresponding to genes expressed in the developing mouse nervous system and determine their full-coding sequences. The BMAP mouse brain EST sequences can be accessed at NCBI's dbEST database (http://www.ncbi.nlm.nih.gov/dbEST/). Arrayed sets of BMAP mouse brain UniGenes and cDNA libraries, and individual BMAP cDNA clones can be purchased from Open Biosystems, Huntsville, AL (http://www.openbiosystems.comCite this (Brain Architecture Management System, RRID:SCR_007251)
URL: http://brancusi.usc.edu/bkms/
Resource Type: Resource, data repository, ontology, database, service resource, storage service resource, controlled vocabulary, data or information resource
Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. BAMS is also an online knowledge management system designed to handle neurobiological information at different levels of organization of the vertebrate nervous system (NS).Cite this (Brain atlas of the common marmoset, RRID:SCR_005135)
URL: http://udn.nichd.nih.gov/brainatlas_home.html
Resource Type: Resource, atlas, data or information resource
The first brain atlas for the common marmoset to be made available since a printed atlas by Stephan, Baron and Schwerdtfeger published in 1980. It is a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. For the present atlas, an adult female was perfused through the heart with PBS followed by 10% formalin. The brain was then sent to Neuroscience Associates of Knoxville, TN, who prepared the brain for histological analysis. The brain was cut in the coronal (frontal) plane at 40 microns, every sixth section stained for Nissl granules with thionine and every seventh section stained for myelinated fibers with the Weil technique. The mounted sections were photographed at the NIH (Medical Arts and Photography Branch). The equipment used was a Nikon Multiphot optical bench with Zeiss Luminar 100 mm lens, and scanned with a Better Light 6100 scan back driven by Better Light Viewfinder 5.3 software. The final images were saved as arrays of 6000x8000 pixels in Adobe Photoshop 6.0. A scale in mm provided with these images permitted construction of the final Nissl atlas files with a horizontal and vertical scale. Some additional re-touching (brightness and contrast) was done with Adobe Photoshop Elements 2.0. The schematic (labeled) atlas plates were created from the Nissl images. The nomenclature came almost exclusively from brainmaps.org, where a rhesus monkey brain with structures labeled can be found. The labels for the MRI images were placed by M. R. Zametkin, under supervision from Dr. Newman.Cite this (Brain Gene Expression Map, RRID:SCR_001517)
URL: http://www.stjudebgem.org/web/mainPage/mainPage.php
Resource Type: Resource, atlas, database, data or information resource, expression atlas
This database contains gene expression patterns assembled from mouse nervous tissues at 4 time points throughout brain development including embryonic (e) day 11.5, e15.5, postnatal (p) day 7 and adult p42. Using a high throughput in situ hybridization approach we are assembling expression patterns from selected genes and presenting them in a searchable database. The database includes darkfield images obtained using radioactive probes, reference cresyl violet stained sections, the complete nucleotide sequence of the probes used to generate the data and all the information required to allow users to repeat and extend the analyses. The database is directly linked to Pubmed, LocusLink, Unigene and Gene Ontology Consortium housed at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine. These data are provided freely to promote communication and cooperation among research groups throughout the world.Cite this (BrainML, RRID:SCR_007087)
URL: http://brainml.org/goto.do?page=.home
Resource Type: Resource, database, standard specification, narrative resource, service resource, storage service resource, data repository, data or information resource
Set of standards and practices for using XML to facilitate information exchange between user application software and neuroscience data repositories. It allows for common shared library routines to handle most of the data processing, but also supports use of structures specialized to the needs of particular neuroscience communities. This site also serves as a repository for BrainML models. (A BrainML model is an XML Schema and optional vocabulary files describing a data model for electronic representation of neuroscience data, including data types, formats, and controlled vocabulary. ) It focuses on layered definitions built over a common core in order to support community-driven extension. One such extension is provided by the new NIH-supported neuroinformatics initiative of the Society for Neuroscience, which supports the development of expert-derived terminology sets for several areas of neuroscience. Under a cooperative agreement, these term lists will be made available Open Source on this site.Cite this (Brain Research Institute Biobank Resources, RRID:SCR_008756)
URL: http://www.bri.ucla.edu/research/resources
Resource Type: Resource, biomaterial supply resource, image collection, tissue bank, brain bank, material resource, data or information resource
Brain bank resources which include postmortem human frozen brain tissue and matched cerebrospinal fluid (CSF) and blood available for scientists to search for etiopathogeneses of human disease. The National Neurological Research Specimen Bank and the Multiple Sclerosis Human Neurospecimen Bank maintains a collection of quick frozen and formalin fixed postmortem human brain tissue and frozen cerebrospinal fluid from patients with neurological diseases, including Alzheimer's Disease, amyotrophic lateral sclerosis, depressive disorder/suicide, and epilepsy, among others. Diagnoses are documented by clinical medical records and gross/microscopic neuropathology. The Neuropathology Laboratory at the UCLA Medical Center maintains a bank of frozen, formalin and paraformaldehyde-fixed and paraffin-embedded postmortem human brain tissues and frozen cerebrospinal fluid (CSF) from patients who die with Alzheimer's disease and other dementing and degenerative illnesses, as well as control materials removed in a similar fashion from patients who are neurologically normal.Cite this (Brain RNA-Seq, RRID:SCR_013736)
URL: http://web.stanford.edu/group/barres_lab/brain_rnaseq.html
Resource Type: Resource, data or information resource, database
A database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of the cerebral cortex.Cite this (BRAINSDemonWarp, RRID:SCR_009524)
URL: https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSDemonWarp
Resource Type: Resource, software resource, image analysis software, registration software, data processing software, software application
A command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ).Cite this (BraVa, RRID:SCR_001407)
Resource Type: Resource, data or information resource, database
A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs).Cite this (Cell Properties Database, RRID:SCR_007285)
URL: http://senselab.med.yale.edu/cellpropdb
Resource Type: Resource, data or information resource, database
A repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells. The database is presently focused on neurons but will eventually include other cell types, such as glia, muscle, and gland cells. This resource is intended to: * Serve as a repository for data on gene products expressed in different brain regions * Support research on cellular properties in the nervous system * Provide a gateway for entering data into the cannonical neuron forms in NeuronDB * Identify receptors across neuron types to aid in drug development * Serve as a first step toward a functional genomics of nerve cells * Serve as a teaching aidCite this ( Center for Inherited Disease Research , RRID:SCR_007339)
URL: http://www.cidr.jhmi.edu/
Resource Type: Resource, resource, production service resource, analysis service resource, training service resource, material analysis service, service resource, biomaterial analysis service, data computation service
Next generation sequencing and genotyping services provided to investigators working to discover genes that contribute to disease. On-site statistical geneticists provide insight into analysis issues as they relate to study design, data production and quality control. In addition, CIDR has a consulting agreement with the University of Washington Genetics Coordinating Center (GCC) to provide statistical and analytical support, most predominantly in the areas of GWAS data cleaning and methods development. Completed studies encompass over 175 phenotypes across 530 projects and 620,000 samples. The impact is evidenced by over 380 peer-reviewed papers published in 100 journals. Three pathways exist to access the CIDR genotyping facility: * NIH CIDR Program: The CIDR contract is funded by 14 NIH Institutes and provides genotyping and statistical genetic services to investigators approved for access through competitive peer review. An application is required for projects supported by the NIH CIDR Program. * The HTS Facility: The High Throughput Sequencing Facility, part of the Johns Hopkins Genetic Resources Core Facility, provides next generation sequencing services to internal JHU investigators and external scientists on a fee-for-service basis. * The JHU SNP Center: The SNP Center, part of the Johns Hopkins Genetic Resources Core Facility, provides genotyping to internal JHU investigators and external scientists on a fee-for-service basis. Data computation service is included to cover the statistical genetics services provided for investigators seeking to identify genes that contribute to human disease. Human Genotyping Services include SNP Genome Wide Association Studies, SNP Linkage Scans, Custom SNP Studies, Cancer Panel, MHC Panels, and Methylation Profiling. Mouse Genotyping Services include SNP Scans and Custom SNP Studies.Cite this (Cerebrovascular Disease Knowledge Portal, RRID:SCR_015628)
URL: http://cerebrovascularportal.org
Resource Type: Resource, disease-related portal, topical portal, portal, data or information resource
Portal for accelerating genetic discoveries in cerebrovascular disease. It enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of its data.Cite this (Cognitive and Emotional Health Project: The Healthy Brain, RRID:SCR_007390)
URL: http://trans.nih.gov/CEHP/
Resource Type: Resource, topical portal, database, portal, data or information resource
Trans-NIH project to assess the state of longitudinal and epidemiological research on demographic, social and biologic determinants of cognitive and emotional health in aging adults and the pathways by which cognitive and emotional health may reciprocally influence each other. A database of large scale longitudinal study relevant to healthy aging in 4 domains was created based on responses of investigators conducting these studies and is available for query. The four domains are: * Cognitive Health * Emotional Health * Demographic and Social Factors * Biomedical and Physiologic FactorsCite this (Computational Neuroanatomy Group, RRID:SCR_007150)
URL: http://krasnow1.gmu.edu/cn3/index3.html
Resource Type: Resource, software resource, topical portal, portal, data or information resource
Multidisciplinary research team devoted to the study of basic neuroscience with a specific interest in the description and generation of dendritic morphology, and in its effect on neuronal electrophysiology. In the long term, they seek to create large-scale, anatomically plausible neural networks to model entire portions of a mammalian brain (such as a hippocampal slice, or a cortical column). Achievements by the CNG include the development of software for the quantitative analysis of dendritic morphology, the implementation of computational models to simulate neuronal structure, and the synthesis of anatomically accurate, large scale neuronal assemblies in virtual reality. Based on biologically plausible rules and biophysical determinants, they have designed stochastic models that can generate realistic virtual neurons. Quantitative morphological analysis indicates that virtual neurons are statistically compatible with the real data that the model parameters are measured from. Virtual neurons can be generated within an appropriate anatomical context if a system level description of the surrounding tissue is included in the model. In order to simulate anatomically realistic neural networks, axons must be grown as well as dendrites. They have developed a navigation strategy for virtual axons in a voxel substrate.Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
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