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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
BAMS Neuroanatomical Ontology
 
Resource Report
Resource Website
1+ mentions
BAMS Neuroanatomical Ontology (RRID:SCR_004616) ontology, data or information resource, controlled vocabulary Ontology designed for neuroscience. Includes complete set of concepts that describe parts of rat nervous system, growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts. has parent organization: Brain Architecture Management System NIMH MH61223;
NINDS NS16668;
NINDS NS050792
PMID:18974794 Restricted nlx_61376 http://brancusi.usc.edu/bkms/bams-ontology.html SCR_004616 BAMS Ontology 2026-02-16 09:46:27 2
OpenNeuro
 
Resource Report
Resource Website
100+ mentions
OpenNeuro (RRID:SCR_005031) OpenNeuro, OpenfMRI image repository, data repository, database, storage service resource, service resource, data or information resource Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data. neuroinformatics, database, storing, dataset, neuroimaging, data, MRI, MEG, EEG, iEEG, ECoG, FASEB list uses: Brain Imaging Data Structure (BIDs)
uses: HED Tags
is used by: studyforrest.org
is used by: DataLad
is used by: NIF Data Federation
is used by: Integrated Datasets
is used by: NIH Heal Project
is used by: Baby Open Brains
is recommended by: National Library of Medicine
is recommended by: BRAIN Initiative
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: re3data.org
is listed by: DataCite
is listed by: FAIRsharing
is affiliated with: NEMAR
is related to: Integrated Manually Extracted Annotation
has parent organization: Stanford University; Stanford; California
has parent organization: Stanford Center for Reproducible Neuroscience
has parent organization: BRAIN Initiative
is provided by: OpenNeuro
NSF OCI1131441;
NIDA ;
Laura and John Arnold Foundation ;
Stanford ;
Squishymedia ;
BRAIN Initiative ;
NIMH
Free, Freely available DOI:10.25504/FAIRsharing.s1r9bw, r3d100010924, nlx_144048, DOI:10.17616/R33047, DOI:10.18112 http://www.nitrc.org/projects/openfmri
https://github.com/OpenNeuroDatasets
https://doi.org/10.17616/R33047
https://doi.org/10.17616/r33047
https://doi.org/10.18112/
https://dx.doi.org/10.18112/
https://fairsharing.org/10.25504/FAIRsharing.s1r9bw
https://doi.org/10.17616/R33047
http://openfmri.org SCR_005031 OpenfMRI, Open fMRI, OpenNeuro 2026-02-16 09:46:35 247
NeMOarchive
 
Resource Report
Resource Website
100+ mentions
NeMOarchive (RRID:SCR_016152) NeMO data repository, database, service resource, storage service resource, data or information resource Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility. omic, neuroscience, neurobiology, bcbc, biccn, nih, brain, genomic, region, abnormal, transcription, factor, binding, site, chromatin, regulatory, element, data is used by: BRAIN Initiative Cell Atlas Network
is used by: BICCN
is recommended by: BRAIN Initiative
is related to: NeMO Analytics
has parent organization: University of Maryland School of Medicine; Maryland; USA
NIMH MH114788;
BRAIN Initiative
Free, Freely available https://data.nemoarchive.org/ SCR_016152 NeMO Archive, Neuroscience Multi-omic Data Archive, The Neuroscience Multi-Omic Archive, Neuroscience Multi-Omic Archive 2026-02-16 09:48:59 113
Neuron Phenotype Ontology
 
Resource Report
Resource Website
1+ mentions
Neuron Phenotype Ontology (RRID:SCR_017403) NPO ontology, data or information resource, controlled vocabulary An ontology for describing the complex phenotypes of neurons. Cell, type, phenotype, neuron, ontology is used by: BICCN
is provided by: NIFSTD
NIMH U24 MH114827;
BRAIN Initiative
Free, Freely available SCR_017403 2026-02-16 09:49:14 2
gene Expression Analysis Resource
 
Resource Report
Resource Website
50+ mentions
gene Expression Analysis Resource (RRID:SCR_017467) gEAR analysis service resource, software resource, portal, production service resource, service resource, data or information resource Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. Visualization, analysis, multi, omic, data, upload, scRNA-seq, BRAIN Initiative is recommended by: BRAIN Initiative
has parent organization: University of Maryland School of Medicine; Maryland; USA
NIMH MH114788;
NIDCD R01 DC013817;
NIMH R24 MH114815;
Hearing Health Foundation (Hearing Restoration Project)
Restricted SCR_017467 gene Expression Analysis Resource 2026-02-16 09:49:15 76
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 research forum portal, clinical trial, topical portal, portal, data or information resource, disease-related 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 2026-02-16 09:47:06 12
Hippocampal Slice Wave Animations
 
Resource Report
Resource Website
Hippocampal Slice Wave Animations (RRID:SCR_008372) software application, data processing software, data visualization software, simulation software, resource, software resource, topical portal, animation software, portal, data or information resource 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 2026-02-16 09:47:10 0
Emergent
 
Resource Report
Resource Website
1+ mentions
Emergent (RRID:SCR_008500) Emergent software application, narrative resource, wiki, software resource, simulation software, data or information resource 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++ 2026-02-16 09:47:12 4
TReNA
 
Resource Report
Resource Website
TReNA (RRID:SCR_017458) software application, data processing software, network analysis software, data analysis software, software resource Methods for reconstructing transcriptional regulatory networks. Reconstructing, transcriptional, regulatory, network, BRAIN Initiative is recommended by: BRAIN Initiative NIMH MH114788 Free, Available for download, Freely available SCR_017458 2026-02-16 09:49:14 0
Brain Image Library
 
Resource Report
Resource Website
10+ mentions
Brain Image Library (RRID:SCR_017272) BIL service resource, data repository, data or information resource, storage service resource Repository for confocal microscopy brain imaging data. Data archives that have been established by BRAIN Initiative Data Sharing. National public resource enabling researchers to deposit, analyze, mine, share and interact with large brain image datasets. Operated as partnership between Biomedical Applications Group at Pittsburgh Supercomputing Center, Center for Biological Imaging at University of Pittsburgh and Molecular Biosensor and Imaging Center at Carnegie Mellon University. Provides persistent centralized repository for brain microscopy data. archive, dataset, confocal, microscopy, brain, image, data, brain microscopy data, is used by: BICCN
is used by: BRAIN Initiative Cell Atlas Network
is recommended by: National Library of Medicine
is recommended by: BRAIN Initiative
is listed by: DataCite
is listed by: re3data.org
is related to: BRAIN Initiative
is related to: Allen Institute for Brain Science
works with: CBI BrAinPI
is organization facet of: BRAIN Initiative Cell Atlas Network
BRAIN Initiative ;
NIMH R24 MH114793
PMID:38187527 Free, Available for download, Freely available DOI:10.17616/R31NJN9G, DOI:10.35077, r3d100013956 https://doi.org/10.17616/R31NJN9G
https://doi.org/10.17616/r31NJN9G
https://doi.org/10.35077/
https://dx.doi.org/10.35077/
https://doi.org/10.17616/R31NJN9G
SCR_017272 Brain Image Library 2026-02-16 09:49:12 16
Brain Observatory Storage Service and Database (BossDB)
 
Resource Report
Resource Website
10+ mentions
Brain Observatory Storage Service and Database (BossDB) (RRID:SCR_017273) BossDB, bossDB, BOSS DB 3d spatial image, data repository, database, storage service resource, image, service resource, data or information resource BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest. Johns Hopkins University Applied Physics Laboratory, JHU/APL, database, electron microscopy, xray, data, storage, archive, BRAIN Initiative, EM, XRM, XNH, ecosystem is used by: BICCN
is recommended by: National Library of Medicine
is recommended by: BRAIN Initiative
is related to: Scalable Analytics for Brain Exploration Research
is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research
has parent organization: BRAIN Initiative
has parent organization: Johns Hopkins University; Maryland; USA
BRAIN Initiative ;
NIMH R24 MH114785
DOI:10.1101/217745 Open https://github.com/jhuapl-boss/boss/ SCR_017273 Brain Observatory Storage Service, bossDB, Block and Object Storage Service, BOSSDB, Block and Object Storage Service Database, Brain Observatory Storage Service and Database, BossDB 2026-02-16 09:49:12 27
piNET
 
Resource Report
Resource Website
1+ mentions
piNET (RRID:SCR_018693) web service, data access protocol, analysis service resource, software resource, production service resource, service resource Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data is related to: LINCS Project NHLBI U54 HL127624;
NIEHS P30 ES006096;
NIMH R01 MH107487;
NCI T32 CA236764;
NCATS UL1 TR001425;
NIGMS U01 GM120953
DOI:10.1093/nar/gkaa436 Free, Freely available SCR_018693 2026-02-16 09:49:33 4
EpiModel
 
Resource Report
Resource Website
1+ mentions
EpiModel (RRID:SCR_018539) software application, data processing software, software toolkit, data analysis software, software resource Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools is listed by: Debian
is listed by: bio.tools
NICHD R01 HD068395;
NIMH R21 MH112449;
NICHD R21 HD075662;
NIDA P30 DA027828;
NIAID P30 AI050409;
NIAID P30 AI027757;
NICHD T32 HD007543
PMID:29731699 Free, Available for download, Freely available biotools:epimodel https://bio.tools/epimodel SCR_018539 2026-02-16 09:49:29 7
Scalable Analytics for Brain Exploration Research
 
Resource Report
Resource Website
1+ mentions
Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) SABER, saber software application, data processing software, software toolkit, software library, software resource, workflow software Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines. Running containerized workflow, large neuroimaging datasets, canonical neuroimaging workflow, neuroimaging pipeline deployment, neuroimaging pipeline optimization is related to: Brain Observatory Storage Service and Database (BossDB) NIMH R24 MH114799 DOI:10.1101/615161v1.full Free, Available for download, Freely available SCR_018812 2026-02-16 09:49:35 1
RAVE
 
Resource Report
Resource Website
1+ mentions
RAVE (RRID:SCR_019040) software application, data processing software, data visualization software, data analysis software, software resource Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG). Intracranial EEG data, data analysis, intracranial electroencephalogram data, electrocorticography data, depth electrodes, stereotactic EEG, iEEG data NIMH R24 MH117529 DOI:10.1016/j.neuroimage.2020.117341 Free, Available for download, Freely available SCR_019040 R Analysis and Visualization of intracranial EEG 2026-02-16 09:49:39 1
SnapATAC
 
Resource Report
Resource Website
10+ mentions
SnapATAC (RRID:SCR_020981) software application, data processing software, software toolkit, data analysis software, software resource Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories NCI K99 CA252020;
UCSD School of Medicine ;
NIMH U19 MH114831
PMID:33637727 Free, Available for download, Freely available https://github.com/r3fang/SnapATAC SCR_020981 Single Nucleus Analysis Pipeline for ATAC-seq 2026-02-16 09:49:55 22
TADS - Treatment for Adolescents with Depression Study
 
Resource Report
Resource Website
1+ mentions
TADS - Treatment for Adolescents with Depression Study (RRID:SCR_000037) TADS clinical trial, topical portal, portal, data or information resource, disease-related portal THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression. clinical trial, adolescent, major depressive disorder, depressive disorder, cognitive behavioral therapy, psychotherapy, drug, fluoxetine, nct00006286, young human is used by: Limited Access Datasets From NIMH Clinical Trials
has parent organization: Duke University School of Medicine; North Carolina; USA
has parent organization: ClinicalTrials.gov
Major Depressive Disorder, Depressive Disorder NIMH 1U01MH064107-01A1 THIS RESOURCE IS NO LONGER IN SERVICE nlx_146236 SCR_000037 Treatment for Adolescents with Depression Study (TADS), Treatment for Adolescents with Depression Study 2026-02-16 09:45:10 2
International Consortium for Brain Mapping
 
Resource Report
Resource Website
1+ mentions
International Consortium for Brain Mapping (RRID:SCR_000445) ICBM reference atlas, data or information resource, database, atlas Probabilistic reference system for human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. Project has expanded neuroinformatics tools for data sharing and created Conforming Site System that allows laboratories worldwide to contribute data to evolving atlas. Through implementation of ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality.ICBM atlas collection consists of ICBM Template, tool developed to provide reference that includes both set of coordinates and associated anatomical labels; the ICBM 452 T1 atlas, average of T1-weighted MRIs of normal young adult brains, ICBM probabilistic atlases, and Cytoarchitectonic Atlas. ICBM Subject Database is web-based database infrastructure that simplifies image dataset collection, organization and dissemination. Authorized users may view representations of data and form collections of datasets that can be downloaded or fed directly into Pipeline environment for distributed processing and analysis. Brain atlases, fmri, genetics, anatomy, architecture, atlas, brainstem, cerebellum, cortex, gray matter, histology, imaging, map, morphology, mri, neuroinformatics, pet, receptor, segmentation, subcortical, volume, warping, white matter, brain, early adult human, structural anatomy, functional anatomy, in vivo, post mortem, neuroanatomy, image collection is related to: MINC/Atlases
has parent organization: Laboratory of Neuro Imaging
NIMH PMID:9343592
PMID:11522763
Free, Freely available nif-0000-00103, SCR_001948, nif-0000-00041 https://resource.loni.usc.edu/ http://www.loni.ucla.edu/ICBM/Databases/, http://www.loni.usc.edu/ICBM/ SCR_000445 , ICBM Subject Database, ICBM - International Consortium for Brain Mapping, International Consortium for Brain Mapping (ICBM), ICBM Atlas 2026-02-16 09:45:15 6
Brain Basics
 
Resource Report
Resource Website
Brain Basics (RRID:SCR_005606) Brain Basics training material, narrative resource, data or information resource, video resource Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, and ongoing research that helps us better understand and treat disorders. Mental disorders are common. You may have a friend, colleague, or relative with a mental disorder, or perhaps you have experienced one yourself at some point. Such disorders include depression, anxiety disorders, bipolar disorder, attention deficit hyperactivity disorder (ADHD), and many others. Some people who develop a mental illness may recover completely; others may have repeated episodes of illness with relatively stable periods in between. Still others live with symptoms of mental illness every day. They can be moderate, or serious and cause severe disability. Through research, we know that mental disorders are brain disorders. Evidence shows that they can be related to changes in the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions of cells in the body, the results can affect many aspects of life. Scientists are continually learning more about how the brain grows and works in healthy people, and how normal brain development and function can go awry, leading to mental illnesses. Brain Basics will introduce you to some of this science, such as: * How the brain develops * How genes and the environment affect the brain * The basic structure of the brain * How different parts of the brain communicate and work with each other * How changes in the brain can lead to mental disorders, such as depression. brain, depression, anxiety disorder, bipolar disorder, attention deficit-hyperactivity disorder, depressive disorder, mental disease, gene, environment has parent organization: NIMH Educational Resources NIMH nlx_146226 SCR_005606 NIMH Brain Basics 2026-02-16 09:46:30 0
NIMH Resources for Research Training and Career Development
 
Resource Report
Resource Website
NIMH Resources for Research Training and Career Development (RRID:SCR_005624) NIMH Resources for Research Training and Career Development data or information resource, topical portal, training resource, portal A portal to the National Institute of Mental Health''s Research Training, Career Development, and Related Programs. Topics cover Resources for Applicants, Individual Fellowship Programs, Individual Career Development Programs, Institutional Training Programs, Additional Career Development/Training-Related Opportunities, and Training Programs to Increase Workforce Diversity. research, career development, fellowship, training, career has parent organization: National Institute of Mental Health NIMH nlx_146240 SCR_005624 NIMH Research Training Career Development and Related Programs, NIMH Resources for Research Training Career Development, Research Training Career Development and Related Programs 2026-02-16 09:46:30 0

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