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http://brainml.org/goto.do?page=.home

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.
The repository function of this site includes the following features:
* BrainML models are published in searchable, browsable form.
* Registered users may submit new models or new versions of existing models to accommodate data of interest. * BrainML model schema and vocabulary files are made available at fixed URLs to allow software applications to reference them.
* Users can check models and/or instance documents for correct format before submitting them using an online validation service.
To complement the BrainML modeling language, a set of protocols have been developed for BrainML document exchange between repositories and clients, for indexing of repositories, and for data query.

Proper citation: BrainML (RRID:SCR_007087) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu/modeldb/

Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.

Proper citation: ModelDB (RRID:SCR_007271) Copy   

•   Source: SciCrunch Registry

http://trans.nih.gov/CEHP/

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 Factors

Proper citation: Cognitive and Emotional Health Project: The Healthy Brain (RRID:SCR_007390) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu/ordb/

Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors.

Proper citation: Olfactory Receptor DataBase (RRID:SCR_007830) Copy   

•   Source: SciCrunch Registry

http://cng.gmu.edu/brava

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).

Proper citation: BraVa (RRID:SCR_001407) Copy   

•   Source: SciCrunch Registry

https://bams1.org/cells/list.php, https://bams1.org/cells/search_bams_ref.php, https://bams1.org/cells/search_by_brain_region.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.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.

Proper citation: BAMS Cells (RRID:SCR_003531) Copy   

•   Source: SciCrunch Registry

https://www.phenxtoolkit.org/

Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols.

Proper citation: Phenotypes and eXposures Toolkit (RRID:SCR_006532) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=nuro

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools.

Proper citation: Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSDemonWarp

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 ).

Proper citation: BRAINSDemonWarp (RRID:SCR_009524) Copy   

•   Source: SciCrunch Registry

http://trans.nih.gov/bmap/index.htm

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 Committee

Proper citation: BMAP - Brain Molecular Anatomy Project (RRID:SCR_008852) Copy   

•   Source: SciCrunch Registry

http://narc.wustl.edu/narc/default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Neurologic AIDS Research Consortium (NARC) is supported by the National Institutes of Health to design and carry out clinical trials to improve the therapy for HIV induced neurologic disease, and neurologic conditions associated with the AIDS virus. This consortium was established in 1993 when the NARC grant submitted by David B. Clifford, M.D. of Washington University School of Medicine was funded by the National Institute of Neurologic Disorders and Stroke (NINDS) to establish the consortium. Since that time the grant has supported studies of the natural history of neurologic performance in advanced AIDS, treatment of HIV associated peripheral neuropathy, progressive multifocal leukoencephalopathy, and cytomegalovirus.

Proper citation: Neurologic AIDS Research Consortium (RRID:SCR_005019) Copy   

•   Source: SciCrunch Registry

http://krasnow1.gmu.edu/cn3/hippocampus3d/

Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites.

Proper citation: Hippocampus 3D Model (RRID:SCR_005083) Copy   

•   Source: SciCrunch Registry

http://www.musicianbrain.com/#index

The human brain has the remarkable ability to adapt in response to changes in the environment over the course of a lifetime. This is the mechanism for learning, growth, and normal development. Similar changes or adaptations can also occur in response to focal brain injuries, e.g., partially-adapted neighboring brain regions or functionally-related brain systems can either substitute for some of the lost function or develop alternative strategies to overcome a disability. Through ongoing research, the Music and Neuroimaging Laboratory''s mission is to: * Reveal the perceptual and cognitive aspects of music processing including the perception and memory for pitch, rhythmic, harmonic, and melodic stimuli. * Investigate the use of music and musical stimuli as an interventional tool for educational and therapeutic purposes. * Reveal the behavioral and neural correlates of learning, skill acquisition, and brain adaptation in response to changes in the environment or brain injury in the developing and adult brain. * Reveal the determinants and facilitators for recovery from brain injury. Project topics include: Aphasia Therapy, Singing and Speaking, Tone Deafness / Congenital Amusia, Motor Recovery Studies, Music and Emotions, Music and Autism, Children and Music Making, Brain Stimulation, Adult Musician Studies, Absolute Pitch Studies, Acute Stroke Studies

Proper citation: Music and Neuroimaging Laboratory (RRID:SCR_005447) Copy   

•   Source: SciCrunch Registry

http://www.gensat.org/

Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community.

Proper citation: Gene Expression Nervous System Atlas (RRID:SCR_002721) Copy   

•   Source: SciCrunch Registry

http://rsb.info.nih.gov/nih-image/index.html

Public image processing and analysis program for Macintosh.

Proper citation: NIH Image (RRID:SCR_003073) Copy   

•   Source: SciCrunch Registry

http://trans.nih.gov/bmap/resources/resources.htm

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.com

Proper citation: BMAP cDNA Resources (RRID:SCR_002973) Copy   

•   Source: SciCrunch Registry

http://datasharing.net

The U.S. National Institutes of Health Final NIH Statement on Sharing Research Data (NIH-OD-03-032) is now in effect. It specifies that all high-direct-cost NIH grant applications include plans for sharing of research data. To support and encourage collegial, enabling, and rewarding data sharing for neuroscience and beyond, the Laboratory of Neuroinformatics at Weill Medical College of Cornell University has established this site. A source of, and portal to, tools and proposals supporting the informed exchange of neuroscience data.

Proper citation: Datasharing.net (RRID:SCR_003312) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/ir/

Data repository for neuroimaging data in DlCOM and NIFTI formats. It allows users to search for and freely download publicly available data sets relating to normal subjects and those with diagnoses such as: schizophrenia, ADHD, autism, and Parkinson's disease.XNAT-based image registry that supports both NIfTI and DICOM images to promote re-use and integration of NIH funded data.

Proper citation: NITRC-IR (RRID:SCR_004162) Copy   

•   Source: SciCrunch Registry

https://nda.nih.gov/

The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI).

Proper citation: NIMH Data Archive (RRID:SCR_004434) Copy   

•   Source: SciCrunch Registry

http://caintegrator-info.nci.nih.gov/rembrandt

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Repository of molecular brain neoplasia data (RRID:SCR_004704) Copy   

•   Source: SciCrunch Registry