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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
iBEAT
 
Resource Report
Resource Website
10+ mentions
iBEAT (RRID:SCR_002470) iBEAT software application, software toolkit, image analysis software, image processing software, software resource, data processing software A toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. Linux operating system (64 bit) is required. A workstation or server with memory >8G is recommended for processing many images simutaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing. atlas application, atlas data, data resource, image display, information resource, magnetic resonance, registration, segmentation, spatial transformation, visualization, warping, mri, infant, brain is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA
PMID:23055044 THIS RESOURCE IS NO LONGER IN SERVICE nlx_155851 http://www.nitrc.org/projects/ibeat SCR_002470 Infant Brain Extraction and Analysis Toolbox, LIBRA, iBEAT: Infant Brain Extraction and Analysis Toolbox 2026-08-11 09:40:37 39
Non-Rigid Image Registration Evaluation Project
 
Resource Report
Resource Website
1+ mentions
Non-Rigid Image Registration Evaluation Project (RRID:SCR_002505) NIREP data or information resource, database, narrative resource, software resource, standard specification Project to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria. The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms. magnetic resonance, registration software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Iowa; Iowa; USA
NIBIB R33 EB004126 THIS RESOURCE IS NO LONGER IN SERVICE nlx_155904 http://www.nitrc.org/projects/nirep SCR_002505 Non-Rigid Image Registration Evaluation Project, Non-Rigid Image Registration Evaluation Project (NIREP) 2026-08-11 09:40:32 7
SCRalyze
 
Resource Report
Resource Website
10+ mentions
SCRalyze (RRID:SCR_002542) SCRalyze data analysis software, data processing software, software resource, software application A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: SourceForge
Free, Available for download, Freely available nlx_155950 http://www.nitrc.org/projects/scralyze SCR_002542 SCRalyze - A matlab environment for model-based psychophysiology 2026-08-11 09:40:33 17
Cancer Genomics Hub
 
Resource Report
Resource Website
100+ mentions
Cancer Genomics Hub (RRID:SCR_002657) CGHub service resource, data or information resource, storage service resource, database, data repository THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. CGHub gives scientific researchers the statistical power of large cancer genome datasets to attack the molecular complexity of cancer. genome, genome sequence, alignment, mutation has parent organization: University of California at Santa Cruz; California; USA Cancer PMID:25267794 THIS RESOURCE IS NO LONGER IN SERVICE. r3d100011174, nlx_156095 https://doi.org/10.17616/R3F919 SCR_002657 2026-08-11 09:40:41 179
RNA Abundance Database
 
Resource Report
Resource Website
1+ mentions
RNA Abundance Database (RRID:SCR_002771) RAD service resource, data or information resource, storage service resource, database, resource, data repository THIS RESOURCE IS NO LONGER IN SERVICE, Documented on March 24, 2014. A resource for gene expression studies, storing highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR. Data were available for querying and downloading based on the MGED ontology, publications or genes. Both public and private studies (the latter viewable only by users having appropriate logins and permissions) were available from this website. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format. RAD is part of a more general Genomics Unified Schema (http://gusdb.org), which includes a richly annotated gene index (http://allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. NOTE: Due to changes in technology and funding, the RAD website is no longer available. RAD as a schema is still very much active and incorporated in the GUS (Genomics Unified Schema) database system used by CBIL (EuPathDB, Beta Cell Genomics) and others. The schema for RAD can be viewed along with the other GUS namespaces through our Schema Browser. gene expression, gene, affymetrix, biomaterial, genomics, microarray, mpss, ontology, rna, rt-pcr, sage, functional genomics, transcript abundance is listed by: OMICtools
is related to: MIAME
is related to: MGED Ontology
is related to: MicroArray and Gene Expression Markup Language
has parent organization: University of Pennsylvania; Philadelphia; USA
NIH ;
NHGRI RO1-HG-01539;
NIDDK U01DK56947;
NHGRI K25-HG-02296;
NHGRI K25-HG-00052
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00133, OMICS_00869, r3d100000017 https://doi.org/10.17616/R3QP4Q SCR_002771 RNA Abundance Database 2026-08-11 09:40:43 4
New Science of Addiction: Genetics and the Brain
 
Resource Report
Resource Website
1+ mentions
New Science of Addiction: Genetics and the Brain (RRID:SCR_002770) New Science of Addiction portal, topical portal, data or information resource, narrative resource, training material, disease-related portal A physiologic and molecular look at drug addiction involving many factors including: basic neurobiology, a scientific examination of drug action in the brain, the role of genetics in addiction, and ethical considerations. Designed to be used by students, teachers and members of the public, the materials meet selected US education standards for science and health. Drug addiction is a chronic disease characterized by changes in the brain which result in a compulsive desire to use a drug. A combination of many factors including genetics, environment and behavior influence a person's addiction risk, making it an incredibly complicated disease. The new science of addiction considers all of these factors - from biology to family - to unravel the complexities of the addicted brain. * Natural Reward Pathways Exist in the Brain: The reward pathway is responsible for driving our feelings of motivation, reward and behavior. * Drugs Alter the Brain's Reward Pathway: Drugs work over time to change the reward pathway and affect the entire brain, resulting in addiction. * Genetics Is An Important Factor In Addiction: Genetic susceptibility to addiction is the result of the interaction of many genes. * Timing and Circumstances Influence Addiction: If you use drugs when you are an adolescent, you are more likely to develop lifetime addiction. An individual's social environment also influences addiction risk. * Challenges and Issues in Addiction: Addiction impacts society with many ethical, legal and social issues. drug abuse, drug delivery, drug, drug of abuse, environmental risk factor, genetic factor, genetics, addiction, gene, treatment, brain, brain circuit, pathway, human, lesson plan, neuron, reward pathway, spanish, teacher, chronic disease has parent organization: University of Utah Genetic Science Learning Center - Learn Genetics Substance-Related Disorder NIDA 1 R25 DA 15461 Free nif-0000-00430 SCR_002770 2026-08-11 09:40:38 3
National Gnotobiotic Rodent Resource Center
 
Resource Report
Resource Website
10+ mentions
National Gnotobiotic Rodent Resource Center (RRID:SCR_002768) biomaterial supply resource, organism supplier, material resource Material resource that provides germ-free and selectively colonized rodents to requesting investigators. Germ-free rodents are axenic, with no detectible bacteria, yeast, molds, parasites or viruses (except retroviruses). embryo, axenic, bacteria, germ, mold, mouse, parasite, rat, retrovirus, rodent, specie, strain, virus, yeast has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA NIH Office of the Director P40 OD010995 Free nif-0000-24375 SCR_002768 NGRRC 2026-08-11 09:40:43 12
Macaque.org
 
Resource Report
Resource Website
1+ mentions
Macaque.org (RRID:SCR_002767) Macaque.org portal, topical portal, research forum portal, data or information resource, disease-related portal, organization portal, laboratory portal THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on June 8, 2020.Macaque genomic and proteomic resources and how they are providing important new dimensions to research using macaque models of infectious disease. The research encompasses a number of viruses that pose global threats to human health, including influenza, HIV, and SARS-associated coronavirus. By combining macaque infection models with gene expression and protein abundance profiling, they are uncovering exciting new insights into the multitude of molecular and cellular events that occur in response to virus infection. A better understanding of these events may provide the basis for innovative antiviral therapies and improvements to vaccine development strategies. genomic, hiv, infection, proteomic, virus, simian immunodeficiency virus, influenza virus, animal model has parent organization: University of Washington; Seattle; USA Viral infection, Infectious disease NCRR ;
NIAID ;
NHLBI ;
NIDA
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-24370 SCR_002767 Macaque.org 2026-08-11 09:40:38 3
PySurfer
 
Resource Report
Resource Website
10+ mentions
PySurfer (RRID:SCR_002524) PySurfer software application, software toolkit, software resource, software library, data processing software, data visualization software Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. eeg, meg, electrocorticography, magnetic resonance, mri, python, neuroimaging is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is related to: FreeSurfer
Free, Available for download, Freely available nlx_155930 http://www.nitrc.org/projects/pysurfer, https://sources.debian.org/src/python3-surfer/ SCR_002524 2026-08-11 09:40:38 29
ShotGun
 
Resource Report
Resource Website
10+ mentions
ShotGun (RRID:SCR_002529) data analysis software, software application, software resource, simulation software, data processing software, sequence analysis software Software for short read simulating in order to facilitate sequencing-based study designs. sequence based study design, short read stimulation, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA
PMID:23357921 Free, Available for download, Freely available biotools:abcd, OMICS_00255 https://bio.tools/abcd SCR_002529 ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs 2026-08-11 09:40:36 35
CRE Driver Network
 
Resource Report
Resource Website
1+ mentions
CRE Driver Network (RRID:SCR_002720) CRE Driver Network biomaterial supply resource, organism supplier, material resource Project to provide Neuroscience Community with mouse strains that are suitable for tissue and cell-type-specific perturbation of gene function in nervous system. NIH Neuroscience Blueprint has established three centers in the USA for generation of genetically modified mice expressing CRE recombinases in nervous system on the C57BJ/6 genetic background. Mouse lines are generated at Cold Spring Harbor Lab, at Scripps Research Institute, and at Baylor College of Medicine. cre-recombinase, expression, neuroscience, mutant mouse strain, knock out mouse, phenotype, expression profile, image collection, microarray, electrophysiology, atlas, morphology, cell, annotation is related to: JAX Cre Repository
is related to: Recombinase (cre) Activity
has parent organization: NIH Blueprint for Neuroscience Research
is parent organization of: Mouse Neuronal Expression Database
NIH Blueprint for Neuroscience Research ;
NIH
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-23753 SCR_002720 Mouse Models for Neuroscience Research, CRE-driver Network, CRE-Driver Network, NIH Neuroscience Blueprint CRE Driver Network 2026-08-11 09:40:36 9
Simbody(tm): SimTK Multibody Dynamics Toolset
 
Resource Report
Resource Website
1+ mentions
Simbody(tm): SimTK Multibody Dynamics Toolset (RRID:SCR_002684) software application, simulation software, software resource This project is a SimTK Core toolset providing general multibody dynamics capability, i.e., the capability to solve Newton's 2nd law F=ma in any set of coordinates. The techniques of rigid body mechanics are used to provide results in Order(n) time for any set of n coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait. Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results. Binaries of this software are bundled with other SimTK Core modules. articulated body, coarse-grained molecule modeling, constrained motion, internal coordinates, mechanical simulation, mechanics, molecular dynamics, multibody dynamics, rigid body, simtk core, skeletal mechanics, torsion coordinates is used by: CPODES numerical integrator
is related to: Simtk.org
PMID:25866705 Free, Available for download, Freely available nif-0000-23309 SCR_002684 Simbody 2026-08-11 09:40:37 1
Slice:Drop
 
Resource Report
Resource Website
1+ mentions
Slice:Drop (RRID:SCR_002557) Slice:Drop service resource, analysis service resource, source code, software resource, production service resource A viewer for medical imaging data that supports a variety of scientific file formats out-of-the-box (see https://github.com/xtk/X/wiki/X:Fileformats for a complete list). We think that the best way to render your files is without any necessary conversions. Just drop'em on a website and they are ready to render. Just drag'n'drop some medical imaging files on this website or try one of the four examples in the right corner. Then, play with the panels on the left and click, drag and rotate the 3d content. Slice:Drop uses WebGL and HTML5 Canvas to render the data in 2D and 3D. We use our own open-source toolkit to perform the rendering, called XTK ( http://goxtk.com ). ascii, clinical neuroinformatics, computed tomography, dicom, javascript, mgh/mgz, magnetic resonance, nifti, nrrd, medical imaging, 3d, visualization, rendering is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) Free, Available for download, Freely available nlx_155964 http://www.nitrc.org/projects/slicedrop SCR_002557 2026-08-11 09:40:39 5
Gibbs Motif Sampler
 
Resource Report
Resource Website
1+ mentions
Gibbs Motif Sampler (RRID:SCR_002550) Gibbs Motif Sampler service resource, analysis service resource, software resource, data analysis service, production service resource Software to identify motifs, conserved regions, in DNA or protein sequences. dna, protein, motif, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
Free, Available for download, Freely available biotools:gibbs_motif_sampler, OMICS_00496 https://bio.tools/gibbs_motif_sampler SCR_002550 The Gibbs Motif Sampler 2026-08-11 09:40:39 2
Sleuth
 
Resource Report
Resource Website
100+ mentions
Sleuth (RRID:SCR_002555) data analysis software, software application, web application, software resource, data processing software, data visualization software Software application that searches the BrainMap Database for papers of interest, reads their corresponding meta-data, and plots their results as coordinates on a standard glass brain in Talairach space. brain map database, data visualization, neuroscience literature, talairach space, search software, meta-data analysis uses: MNI brain and the Talairach atlas
uses: MNI brain and the Talairach atlas
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: brainmap.org
Public, Account required, Available for download nlx_155963 http://www.nitrc.org/projects/brainmap SCR_002555 Sleuth Version 2.4 2026-08-11 09:40:36 224
NCBI database of Genotypes and Phenotypes (dbGap)
 
Resource Report
Resource Website
500+ mentions
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) dbGaP service resource, data or information resource, storage service resource, database, data repository Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools is used by: International Genomics of Alzheimers Project
is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium
is used by: NIH Heal Project
is used by: Genomic Data Commons Data Portal (GDC Data Portal)
is recommended by: National Library of Medicine
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: OMICtools
is listed by: re3data.org
is listed by: NIDDK Information Network (dkNET)
is listed by: bio.tools
is listed by: Debian
is related to: NIDDK Central Repository
is related to: eMERGE Network: electronic Medical Records and Genomics
is related to: Framingham Heart Study
is related to: PhenoExplorer
is related to: Chronic Renal Insufficiency Cohort Study
is related to: DbGaP Cleaner
is related to: Psychiatric Genomics Consortium
is related to: ISCA Consortium
is related to: Allen Institute for Brain Science
has parent organization: NCBI
is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging
NLM PMID:24297256
PMID:17898773
Restricted nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap, https://bio.tools/dbgap, https://doi.org/10.17616/R3GS4K SCR_002709 database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes 2026-08-11 09:40:42 736
Volocity 3D Image Analysis Software
 
Resource Report
Resource Website
1000+ mentions
Volocity 3D Image Analysis Software (RRID:SCR_002668) Volocity Imaging software software application, image analysis software, software resource, data processing software, commercial organization THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. 3D image analysis software to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems. It is fully integrated for a seamless user experience. 3d, confocal microscopy, visualization, analyze THIS RESOURCE IS NO LONGER IN SERVICE. SciRes_000112 SCR_002668 2026-08-11 09:40:41 4003
Aging Genes and Interventions Database
 
Resource Report
Resource Website
1+ mentions
Aging Genes and Interventions Database (RRID:SCR_002701) AGEID service resource, data or information resource, storage service resource, database, data repository THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link. allele, strain, gene function, phenotype, mutant, homolog, mutation, degeneration, gene, intervention, life-span is used by: Aging Portal
is used by: NIF Data Federation
has parent organization: University of Washington; Seattle; USA
Aging, Age-related neurological disease, Neurological disease Ellison Medical Foundation PMID:12044961 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-23326 http://sageke.sciencemag.org/highlights/gidb/ SCR_002701 Aging Genes DB, Aging Genes Database, Genes/Interventions Database 2026-08-11 09:40:42 2
BioStar
 
Resource Report
Resource Website
50+ mentions
BioStar (RRID:SCR_002580) Biostar portal, discussion, data or information resource, forum, narrative resource, community building portal A question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply. bioinformatics, computational genomics, biological data analysis, data analysis, forum, question, answer is listed by: OMICtools
is related to: NeuroStars
NIH ;
Luma Education ;
NHGRI 5R25HG006243-02
PMID:22046109 Free, Freely available OMICS_01706, nlx_155982 SCR_002580 biostars.org 2026-08-11 09:40:36 88
WFU Biological Parametric Mapping Toolbox
 
Resource Report
Resource Website
1+ mentions
WFU Biological Parametric Mapping Toolbox (RRID:SCR_002613) WFU_BPM, WFU BPM software application, software toolkit, image analysis software, software resource, data processing software Software toolbox that performs SPM analysis with voxel-wise imaging covariates. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in Matlab with a user-friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely used T-field, has been implemented in the correlation analysis for more accurate results. Requirements: * SPM2 or SPM5 * MATLAB version 6.5 or higher analyze, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, statistical operation, win32 (ms windows), windows is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: SPM
has parent organization: Wake Forest School of Medicine; North Carolina; USA
Human Brain Project ;
NIBIB 1R01EB004673
PMID:17070709 Free, Available for download, Freely available nlx_156016 http://www.nitrc.org/projects/wfu_bpm SCR_002613 BPM - Integrated Tool for Biological Parametric Mapping, WFU Biological Parametric Mapping, BPM toolbox, BPM 2026-08-11 09:40:34 4

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