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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NIH Blueprint NHP Atlas Resource Report Resource Website 10+ mentions |
NIH Blueprint NHP Atlas (RRID:SCR_010559) | NHP Atlas | atlas, data or information resource, database, expression atlas, reference atlas | Atlas of gene expression in the developing rhesus macaque brain. This atlas is a free online resource with a unique set of data and tools aimed to create a developmental neuroanatomical framework for exploring the cellular and molecular architecture of the developing postnatal primate brain with direct relevance for human brain development. The atlas includes: * Microarray ** Microdissection: Fine structure transcriptional profiling across postnatal development for fine nuclear subdivisions of the prefrontal cortex, primary visual cortex, hippocampus, amygdala and ventral striatum ** Macrodissection: Gross structure transcriptional profiling across postnatal development for the same structures * ISH: ** Cellular resolution in situ hybridization image data of five major brain regions during postnatal developmental periods for genes clinically important for a variety of human neurodevelopmental disorders, including prefrontal cortex, primary visual cortex, hippocampus, amygdala and ventral striatum. ** Serial analysis of selected genes across the entire adult brain, focusing on cellular marker genes, genes with cortical area specificity and gene families important to neural function. * ISH Anatomic Search: Detailed gene expression search on the ISH data based on expert annotation * Reference Data: Developmental stage-specific reference series, consisting of magnetic resonance imaging (MRI) and Nissl histology to provide a neuroanatomical context for the gene expression data. These data and tools are designed to provide a valuable public resource for researchers and educators to explore neurodevelopment in non-human primates, and a key evolutionary link between other Web-based gene expression atlases for adult and developing mouse and human brain. | molecular neuroanatomy resource, developing brain, development, brain, gene expression, postnatal, mrna transcript, in situ hybridization, prefrontal cortex, primary visual cortex, hippocampus, amygdala, ventral striatum, dna microarray, magnetic resonance imaging, nissl, histology, brain development, developmental stage, microdissection, macrodissection, microarray, cell density, neuroanatomy, non-human primate |
is related to: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) has parent organization: Allen Institute for Brain Science |
Neurodevelopmental disorder | NIH Blueprint for Neuroscience Research ; NIMH contract HHSN-271-2008-0047 |
Free | nlx_37895 | SCR_010559 | NIH Blueprint Non-Human Primate Atlas | 2026-08-29 11:23:44 | 27 | |||||
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Brain Observatory Resource Report Resource Website |
Brain Observatory (RRID:SCR_010641) | Brain Observatory | biospecimen repository, data or information resource, material storage repository, portal, service resource, storage service resource, topical portal, video resource | Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health. | human, brain, visual cortex, neuroimaging | has parent organization: University of California San Diego School of Medicine; California; USA | Human immunodeficiency virus, NeuroAIDS, AIDS, Amnesia | NIMH ; NSF ; The Dana Foundation ; NEI |
Public | nlx_69083 | http://thebrainobservatory.ucsd.edu/ | SCR_010641 | The Brain Observatory | 2026-08-29 11:23:34 | 0 | ||||
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Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | community building portal, data or information resource, portal, software application, software development environment, software development tool, software resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-08-29 11:24:28 | 27 | ||||
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Emergent Resource Report Resource Website 1+ mentions |
Emergent (RRID:SCR_008500) | Emergent | data or information resource, narrative resource, simulation software, software application, software resource, wiki | emergent is a comprehensive, full-featured neural network simulator that allows for the creation and analysis of complex, sophisticated models of the brain in the world. With an emphasis on qualitative analysis and teaching, it also supports the workflow of professional neural network researchers. Its high level drag-and-drop programming interface, built on top of a scripting language that has full introspective access to all aspects of networks and the software itself, allows one to write programs that seamlessly weave together the training of a network and evolution of its environment without ever typing out a line of code. Networks and all of their state variables are visually inspected in 3d, allowing for a quick visual regression of network dynamics and robot behavior. This same 3d world sports a highly accurate Newtonian physics simulation, allowing you to create rich robotics simulations (for example, a car). As a direct descendant of PDP (1986) and PDP (1999), emergent has been in development for decades. In the most recent versions available strive to distill it down to its essential elements. Those that take the time to learn the best practices will be rewarded with the ability to create and understand the most complicated neural models ever published. | neural, simulator, network, analysis, software, simulation, physics, newtonian |
is related to: PDP++ Software Home Page has parent organization: University of Colorado Boulder; Colorado; USA |
NIMH R01 MH069597-01; NIMH MH47566; DARPA/ONR N00014-05-1-0880; ONR N00014-03-1-0428 |
nif-0000-30515 | SCR_008500 | Emergent Neural Network Simulation System, PDP++ | 2026-08-29 11:23:06 | 4 | |||||||
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Brain's Inner Workings: Activities for Grades 9 through 12 Resource Report Resource Website 1+ mentions |
Brain's Inner Workings: Activities for Grades 9 through 12 (RRID:SCR_008842) | Brain's Inner Workings | data or information resource, narrative resource, training material, video resource | This comprehensive free collection of multimedia resources and inquiry-based activities tied to the National Science Education Standards help teachers and students learn about the structure, function and cognitive aspects of the human brain. The packet includes a teacher's manual, student manual, DVD of videos, and a CDROM of accompanying materials. | high school, brain, manual, student, teacher, brain structure, brain function, cognition, cerebral cortex, nerve cell, neurotransmitter, imaging, mri, mental disease, k-12 | has parent organization: NIMH Educational Resources | NIMH | nlx_146227 | SCR_008842 | The Brain's Inner Workings: Activities for Grades 9 through 12, Brains Inner Workings: Activities for Grades 9 through 12 | 2026-08-29 11:23:34 | 2 | |||||||
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Mango Resource Report Resource Website 100+ mentions |
Mango (RRID:SCR_009603) | Mango | data processing software, data visualization software, image analysis software, image processing software, software application, software resource | A viewer for medical research images that provides analysis tools and a user interface to navigate image volumes. There are three versions of Mango, each geared for a different platform: * Mango ? Desktop ? Mac OS X, Windows, and Linux * webMango ? Browser ? Safari, Firefox, Chrome, and Internet Explorer * iMango ? Mobile ? Apple iPad Key Features: * Built-in support for DICOM, NIFTI, Analyze, and NEMA-DES formats * Customizable: Create plugins, custom filters, color tables, file formats, and atlases * ROI Editing: Threshold and component-based tools for painting and tracing ROIs * Surface Rendering: Interactive surface models supporting cut planes and overlays * Image Registration: Semi-automatic image coregistration and manual transform editing * Image Stacking: Threshold and transparency-based image overlay stacking * Analysis: Histogram, cross-section, time-series analysis, image and ROI statistics * Processing: Kernel and rank filtering, arithmetic/logic image and ROI calculators | analyze, atlas application, console (text based), dicom, gifti, java, linux, macos, microsoft, magnetic resonance, nifti, os independent, platform, posix/unix-like, quantification, region of interest, registration, rendering, segmentation, spatial transformation, statistical operation, sunos/solaris, surface analysis, temporal transformation, visualization, volumetric analysis, web environment, win32 (ms windows), windows, windows vista, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA |
NIBIB P01-EB01955; NIBIB R01-EB015314-01a1; NIMH R01-MH074457 |
Free | nlx_155804 | http://www.nitrc.org/projects/mango | SCR_009603 | Multi-image Analysis GUI | 2026-08-29 11:23:38 | 491 | |||||
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GTRACT Resource Report Resource Website 1+ mentions |
GTRACT (RRID:SCR_009651) | GTRACT | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | A Diffusion Tensor fiber tracking software suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. NOTE: All new development is being managed in a github repository. Please visit, https://github.com/BRAINSia/BRAINSTools | c++, dicom, macos, microsoft, modeling, morphology, magnetic resonance, nifti, posix/unix-like, quantification, tensor metric, tractography, windows, dti, diffusion tensor fiber tracking, fiber tracking, nrrd, algorithm, connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: University of Iowa; Iowa; USA |
Aging | NARSAD ; NINDS R01NS050568-01A2S1; NINDS 5R01NS040068-04; NIMH 5R01MH063405-04; NIMH 5R01MH031593-23; NIMH 2R01MH040856-17A2; NIA 5K23AG020649-03; NIDCR 5R01DE014399-04 |
PMID:16631385 | BSD License | nlx_155992 | SCR_009651 | Guided Tensor Restore Anatomical Connectivity Tractography | 2026-08-29 11:23:37 | 2 | ||||
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JAX Neuroscience Mutagenesis Facility Resource Report Resource Website 1+ mentions |
JAX Neuroscience Mutagenesis Facility (RRID:SCR_007437) | NMU | biomaterial supply resource, material resource, organism supplier | Produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The impetus for the program resulted from the recognition that: * The value of genomic data would remain limited unless more information about the functionality of its individual components became available. * The task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e.N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. The resulting mutant mouse lines have been available to the scientific community for the last five years and over 700 NMF mice have been sent to interested investigators for research; these mutant mouse lines will remain available as frozen embryos (which can be re-derived on request) and can be ordered through the JAX customer service at 1-800-422-6423 (or 207-288-5845). The results of the work of the Neuroscience Mutagenesis Facility and that of two other neurogenesis centers, i.e. The Neurogenomics Project at Northwestern University, and the Neuromutagenesis Project of the Tennessee Mouse Genome Consortium, can also be seen at Neuromice.org, a common web site of these three research centers; in addition, information about all mutants produced by these groups has been recorded in MGI. | mouse model, mutant mouse line, mutant mouse, phenodeviant, phenodeviant mouse, heritability, phenotyping, genetic mapping |
is listed by: One Mind Biospecimen Bank Listing is related to: neuromice is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory is parent organization of: JAX Neuroscience Mutagenesis Facility Protocols is parent organization of: neuromice |
Neurobiological disease, Neurological disorder, Sensory disorder, Behavioral disorder, Aging | NIDA ; NIMH ; NINDS ; NEI ; NIA ; NIAAA ; NIDCD |
Public, Available to the scientific community | nif-0000-00784 | http://nmf.jax.org/ | SCR_007437 | JAX Neuromutagenesis Facility, JAX - Neuroscience Mutagenesis Facilty, Neuromutagenesis Facility, Neuroscience Mutagenesis Facility of the Jackson Laboratory | 2026-08-29 11:22:58 | 1 | ||||
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Sequenced Treatment Alternatives to Relieve Depression Study Resource Report Resource Website 10+ mentions |
Sequenced Treatment Alternatives to Relieve Depression Study (RRID:SCR_008051) | STAR*D | clinical trial, data or information resource, disease-related portal, portal, research forum portal, topical portal | A nationwide public health clinical trial conducted to determine the effectiveness of different treatments for people with major depression, in both primary and specialty care settings, who have not responded to initial treatment with an antidepressant. This is the largest and longest study ever done to evaluate depression treatment. The study is completed and no longer recruiting participants. Each of the four levels of the study tested a different medication or medication combination. The primary goal of each level was to determine if the treatment used during that level could adequately treat participants����?? major depressive disorder (MDD). Those who did not become symptom-free could proceed to the next level of treatment. The design of the STAR*D study reflects what is done in clinical practice because it allowed study participants to choose certain treatment strategies most acceptable to them and limited the randomization of each participant only to his/her range of acceptable treatment strategies. No prior studies have evaluated the different treatment strategies in broadly defined participant groups treated in diverse care settings. Over a seven-year period, the study enrolled 4,041 outpatients, ages 18-75 years, from 41 clinical sites around the country, which included both specialty care settings and primary medical care settings. Participants represented a broad range of ethnic and socioeconomic groups. All participants were diagnosed with MDD, were already seeking care at one of these sites, and were referred to the trial by their doctors. * STAR*D Study Medications: Citalopram (Celexa), Sertraline (Zoloft), Bupropion SR (Wellbutrin SR), Venlafaxine XR (Effexor XR), Buspirone (BuSpar), Mirtazapine (Remeron), Triiodothyronine (T3) (Cytomel), Nortriptyline (Pamelor, Aventyl), Tranylcypromine (Parnate), Lithium (Eskalith, Lithobid) *STAR*D Talk Therapy:Cognitive Therapy | depressive disorder, clinical trial, major depressive disorder, adult |
is used by: Limited Access Datasets From NIMH Clinical Trials is related to: NIMH Repository and Genomics Resources has parent organization: University of Pittsburgh; Pennsylvania; USA |
NIMH | PMID:17074942 PMID:15061154 |
nif-0000-10312 | http://www.star-d.org/ | SCR_008051 | Sequenced Treatment Alternatives to Relieve Depression (STAR*D) Study, NIMH Sequenced Treatment Alternatives to Relieve Depression (STAR*D) Study, NIMH Sequenced Treatment Alternatives to Relieve Depression Study | 2026-08-29 11:22:58 | 12 | |||||
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Hippocampal Slice Wave Animations Resource Report Resource Website |
Hippocampal Slice Wave Animations (RRID:SCR_008372) | animation software, data or information resource, data processing software, data visualization software, portal, resource, simulation software, software application, software resource, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest. | animation, hippocampal, hippocampus, mitochondrial, movie, neuroscience, rat, slice, wave | MRC of Canada MT10520; NIDA DA02575; NIDA DA02121; NIMH MH40165; NIDDK DK42086; NIDDK DK44840; NINDS NS-33502; NIGMS 5T32GM07151-22; NICHD HD07009 |
PMID:9614233 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25609 | SCR_008372 | GIF Animations | 2026-08-29 11:23:29 | 0 | |||||||
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Collaboratory of AIDS Researchers for Eradciation (CARE) Resource Report Resource Website |
Collaboratory of AIDS Researchers for Eradciation (CARE) (RRID:SCR_013681) | CARE | consortium, data or information resource, organization portal, portal | The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV. | AIDS, HIV, drug development, data-sharing enabler, |
is related to: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA is related to: Gladstone Institute of Neurological Disease is related to: UCSF School of Medicine; California; USA is related to: Case Western Reserve University; Ohio; USA is related to: Merck is related to: UC Davis School of Medicine; California; USA is related to: University of California at San Diego; California; USA is related to: University of Utah School of Medicine; Utah; USA is related to: University of Minnesota Twin Cities; Minnesota; USA |
NIAID ; NIMH |
SCR_013681 | 2026-08-29 11:24:41 | 0 | |||||||||
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Spatio-temporal transcriptome of the human brain Resource Report Resource Website |
Spatio-temporal transcriptome of the human brain (RRID:SCR_013743) | data or information resource, document, narrative resource | A research paper with supplementary materials reporting the generation and analysis of exon-level transcriptome and associated genotyping data. The experiment represented both males and females of multiple ethnicities and examines gene regulation and expression in different areas of the brain. A data set on the human brain transcriptome as well as insights into the transcriptional foundations of human neurodevelopment is provided. | spatio-temporal, transcriptome data, brain regions, human brain, gene expression, gene regulation |
is related to: Human Brain Transcriptome has parent organization: Yale University; Connecticut; USA |
Kavil Foundation ; NARSAD ; James S. McDonnell Foundation Scholar Award ; NIMH MH081896; NIMH MH089929; NINDS NS054273 |
PMID:22031440 | Public, Free | SCR_013743 | 2026-08-29 11:24:42 | 0 | ||||||||
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Northwestern University Schizophrenia Data and Software Tool (NUSDAST) Resource Report Resource Website |
Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) | NUSDAT | data or information resource, database, image collection | A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data. | database, neuroimaging, clinical, cognitive, genetic, schizophrenia, longitudinal |
uses: CAWorks is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Northwestern University; Illinois; USA |
Schizophrenia | NIMH 1R01 MH084803; NIMH 1U01 MH097435; NIMH P50 MH071616; NIMH R01 MH056584; NCRR P41 RR15241; NIGMS U24 GM104203; NIH Bio-Informatics Research Network Coordinating Center |
Available to the research community | SCR_014153 | Northwestern University Schizophrenia Data and Software Tool | 2026-08-29 11:24:42 | 0 | ||||||
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NeuroRD Resource Report Resource Website 10+ mentions |
NeuroRD (RRID:SCR_014769) | simulation software, software application, software resource | Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways. | simulation software, simulator, java, neuronal signaling pathway, neuron | HFSP ; NIMH K21-MH01141; NSF IBN 0077509; CRCNS program R01 AA16022; CRCNS program AA18066 |
Available for download | https://github.com/neurord/stochdiff/releases | SCR_014769 | 2026-08-29 11:24:52 | 13 | |||||||||
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Lyngby Resource Report Resource Website 1+ mentions |
Lyngby (RRID:SCR_007143) | Lyngby | data analysis software, data processing software, software application, software resource | Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files. | functional, statistical, fmri, pet, matlab, neuroimaging |
is listed by: Biositemaps has parent organization: THOR Center for Neuroinformatics |
Human Brain Project ; Danish Research Council ; European Union ; BIOMED2 ; MAPAWAMO ; NASA ; NSF ; DOE ; NIDA R01 DA09246; NIMH P20 MH57180 |
Free, Non-commercial | nif-0000-00324 | SCR_007143 | Lyngby Toolbox, Lyngby - A Toolbox for Functional Neuroimaging | 2026-08-29 11:23:02 | 2 | ||||||
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Cambridge Brain Activation Resource Report Resource Website 10+ mentions |
Cambridge Brain Activation (RRID:SCR_007109) | CamBA | data processing software, image analysis software, software application, software resource, software toolkit, workflow software | Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution. | analysis, brain, anova, resampling, statistical, wavelet, fmri, pipeline, affine warp, algorithm or reusable library, application, c, image-to-template, java, linux, macos, magnetic resonance, nifti-1, posix/unix-like, registration, regression, spatial transformation, spectral analysis, statistical operation, temporal transformation, time domain analysis, unix shell, warping, wavelet transformation, web environment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of Cambridge; Cambridge; United Kingdom |
GlaxoSmithKline ; Human Brain Project ; NIMH ; NIBIB |
GNU General Public License | nif-0000-00267 | http://www-bmu.psychiatry.cam.ac.uk/software/ | SCR_007109 | 2026-08-29 11:22:51 | 11 | ||||||
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fMRI Data Center Resource Report Resource Website 10+ mentions |
fMRI Data Center (RRID:SCR_007278) | fMRIDC | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community. | fmri, cognitive, cortex, mri, talairach, neuroimaging, cognitive neuroscience, brain, structure, function, magnetic resonance, intellect, image collection, data set |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: re3data.org has parent organization: University of California at Santa Barbara; California; USA |
NSF ; W. M. Keck Foundation ; NIMH ; Sun Microsystems Center of Excellence |
PMID:11545705 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00025 | http://www.fmridc.org/ | SCR_007278 | The fMRI Data Center | 2026-08-29 11:23:06 | 16 | ||||
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Center for Inherited Disease Research Resource Report Resource Website 100+ mentions |
Center for Inherited Disease Research (RRID:SCR_007339) | CIDR | analysis service resource, biomaterial analysis service, data computation service, material analysis service, production service resource, resource, service resource, training service resource | 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. | gene, genome, array, custom, dna, genome wide association study, genotyping, genotyping service, linkage scan, methylation profiling, hereditary disease, single gene disorder, snp, statistical genetics, whole genome, whole exome, exome sequencing, high throughput sequencing, single nucleotide polymorphism, sequencing, disease |
is listed by: NIDDK Information Network (dkNET) has parent organization: Johns Hopkins University; Maryland; USA |
Aging | NHGRI ; NCI ; NEI ; NIA ; NIAAA ; NIAMS ; NICHD ; NIDA ; NIDCD ; NIDCR ; NIDDK ; NIEHS ; NIMH ; NINDS ; NHGRI N01-HG-65403; US Department of Health and Human Services HHSN268200782096C; S Department of Health and Human Services HHSN268201100011I; S Department of Health and Human Services HHSN268201200008I; NHGRI U01HG004438; NHGRI U54HG006542 |
nif-0000-00223 | SCR_007339 | CIDR - Center for Inherited Disease Research | 2026-08-29 11:23:08 | 207 | ||||||
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Brain Architecture Management System Resource Report Resource Website 1+ mentions |
Brain Architecture Management System (RRID:SCR_007251) | BAMS | controlled vocabulary, data or information resource, data repository, database, ontology, service resource, storage service resource | Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions. | neurobiology, vertebrate, nervous, system, database, repository, neural, circuitry, analysis, data, nomenclature, taxonomy, axonal, connection, cell, |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is related to: Integrated Manually Extracted Annotation has parent organization: University of Southern California; Los Angeles; USA is parent organization of: BAMS Nested Regions is parent organization of: BAMS Connectivity is parent organization of: BAMS Cells is parent organization of: BAMS Neuroanatomical Ontology |
Human Brain Project ; NIBIB ; NIMH MH61223; NINDS NS16686; NINDS NS50792 |
Restricted | nif-0000-00018 | http://brancusi.usc.edu/bkms/ | SCR_007251 | Brain Architecture Management System, The Brain Architecture Management System | 2026-08-29 11:23:06 | 6 | |||||
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BICCN Resource Report Resource Website 100+ mentions |
BICCN (RRID:SCR_015820) | BICCN | consortium, data or information resource, organization portal, portal | Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains. | cell census, neuroscience, brain, brain initiative cell census network, whole mouse brain, |
uses: QuickNII uses: HistoloZee uses: CellLocator uses: Semi-Manual Alignment to Reference Templates uses: LoomPy uses: Cytosplore Viewer uses: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) uses: Blue Brain Cell Atlas uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Hippocampome.org uses: Neuron Phenotype Ontology uses: Brain Image Library uses: Distributed Archives for Neurophysiology Data Integration uses: NeuroMorpho.Org uses: Azimuth uses: Brain Observatory Storage Service and Database (BossDB) uses: Optimus Pipeline uses: scATAC Pipeline uses: Smart-seq2 Single Nucleus Multi Sample Pipeline uses: CEMBA MethylC Seq Pipeline uses: Brain Architecture Project uses: Single Cell Portal uses: MorphoHub uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Mouse Connectome Project uses: Allen Mouse Brain Reference Atlas uses: Allen Mouse Brain Common Coordinate Framework uses: Allen Human Reference Atlas, 3D, 2020 uses: NeMO Analytics uses: ANTS - Advanced Normalization ToolS uses: CloudReg uses: Brainome portal uses: CATlas uses: MetaNeighbor uses: Cell Annotation Platform uses: cellxgene uses: Neuroglancer uses: Vaa3D uses: QuickNII and VisuAlign uses: Hi5App uses: CloudVolume uses: neuroXiv uses: Brain Data Standards Ontology uses: Pittsburgh Supercomputing Center uses: Molecular Biosensor and Imaging Center uses: Generative Diffeomorphic Mapping uses: NIH NeuroBioBank uses: NeMOarchive lists: ccf_streamlines is related to: Mouse Connectome Project is related to: BarensLab Mini-Atlas is related to: Cumulus is related to: Pegasus is related to: Cirrocumulus is related to: Gene functional conservation across cell types and species is related to: BRAIN Initiative Cell Atlas Network is related to: ATAC Pipeline is related to: Slide-seq Pipeline is related to: Brain Knowledge Platform has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science provides: mBrainAligner provides: BICCN Cell Registry provides: Cell Type Knowledge Explorer provides: Epiviz has organization facet: BICCN Anatomy and Morphology Project has organization facet: Cell Type Knowledge Explorer has organization facet: mBrainAligner has organization facet: Terra has organization facet: Allen Brain Cell Atlas has organization facet: Multiome Pipeline has organization facet: Allen Software Development Kit has organization facet: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain has organization facet: Allen Brain Map BICCN Data Catalog has organization facet: snm3C Pipeline has organization facet: Paired-Tag Pipeline has organization facet: BuildIndices has organization facet: MapMyCells |
NIMH U19 MH114821; NIMH U19 MH114830; NIMH U19 MH114831 |
PMID:37390046 | Restricted | SCR_017266 | SCR_015820 | BICCN 2.0, BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Census Network (BICCN) | 2026-08-29 11:25:06 | 234 |
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