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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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University of California at Los Angeles, School of Medicine: Neuro Imaging Lab of Thompson Resource Report Resource Website |
University of California at Los Angeles, School of Medicine: Neuro Imaging Lab of Thompson (RRID:SCR_001924) | curriculum material, data or information resource, narrative resource, slide, training material, video resource | The UCLA laboratory of neuroimaging is working in several areas to enhance knowledge of anatomy, including brain mapping in large human populations, HIV, Schizophrenia, methamphetamine, tumor growth and 4d brain mapping, genetics and detection of abnormalities. | engineer, genetics, abnormality, alzheimer's, anatomy, atlas, brain, computational, cortical, dementia, disease, growth, histologic, hiv, human, image, knowledge, mapping, mathematical, mathematician, medical doctor, methamphetamine, model, mri, neuroscientist, pet, polymorphism, population, schizophrenia, spect, structure, tumor, neuroimaging | has parent organization: University of California at Los Angeles; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10496 | SCR_001924 | SciCrunch Registry | UCLA, Thompson Lab | 2026-10-31 12:18:28 | 0 | ||||||||
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Antarctic Glaciological Data Center Resource Report Resource Website |
Antarctic Glaciological Data Center (RRID:SCR_002219) | AGDC | data or information resource, data repository, data set, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Archives and distributes Antarctic glaciological and cryospheric system data collected by the U.S. Antarctic Program. The Data Catalog contains data sets collected by individual investigators and products assembled from many different PI data sets, published literature, and other sources. The catalog provides useful compilations of important geophysical parameters, such as accumulation rate or ice velocity. The NSF OPP Guidelines and Award Conditions for Scientific Data state that PIs should submit data collected as a result of their OPP grant to a designated data center as soon as possible, but no later than two years after the data are collected. | antarctic, glaciology, atmosphere, glacier, ice sheet, land surface, paleoclimate, ice core, sea ice, smow, land ice, spectral, engineering |
is listed by: CINERGI has parent organization: National Snow and Ice Data Center |
NSF OPP ANT 0944763 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_154741, r3d100011579 | https://doi.org/10.17616/R3KH07 | SCR_002219 | SciCrunch Registry | Antarctic Glaciological Data Center at the National Snow and Ice Data Center, Antarctic Glaciological Data Center at NSIDC | 2026-10-31 12:18:28 | 0 | |||||
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Ontology for Genetic Interval Resource Report Resource Website |
Ontology for Genetic Interval (RRID:SCR_003423) | OGI | controlled vocabulary, data or information resource, ontology | An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure. | owl, genomic, genetic, dna, rna, allele, marker, chromosome, rna molecule |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157517 | https://bioportal.bioontology.org/ontologies/OGI | SCR_003423 | SciCrunch Registry | 2026-10-31 12:18:31 | 0 | |||||||
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MorphBank Resource Report Resource Website 10+ mentions |
MorphBank (RRID:SCR_003147) | Morphbank | data or information resource, data repository, database, image repository, service resource, storage service resource | An NSF supported image repository of over 374,000 high-resolution photographs of approximately 4,000 species for research and education, used largely but not exclusively in the area of biodiversity research. Images can be annotated by users and browsed by specimen, view, taxonomy, location, collection, or annotation. | anatomy, phylogenetics, taxonomy, biodiversity, image, photographic, biological specimen, biology, herbaria, botany, entomology, morphology, phylogeny, evolution |
is listed by: re3data.org has parent organization: Florida State University; Florida; USA |
NSF DBI-0446224 | Free, Freely available | nlx_156841, r3d100010566 | https://doi.org/10.17616/R30P5K | SCR_003147 | SciCrunch Registry | Morphbank : Biological Imaging | 2026-10-31 12:18:23 | 28 | |||||
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ImaGene Resource Report Resource Website 100+ mentions |
ImaGene (RRID:SCR_002178) | data analysis software, data processing software, software application, software resource | Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microarray analysis, machine vision, convolutional neural network, quantify natural selection, genomic data, population genomic data, evolutionary population, genetics model, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Imperial College London ; Politecnico di Milano |
PMID:31757205 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ImaGene, OMICS_00841 | https://github.com/mfumagalli/ImaGene, https://bio.tools/ImaGene | http://www.biodiscovery.com/software/imagene/ | SCR_002178 | SciCrunch Registry | 2026-10-31 12:18:21 | 405 | |||||
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PeerLibrary Resource Report Resource Website |
PeerLibrary (RRID:SCR_003812) | PeerLibrary | data or information resource, database, discussion, narrative resource, service resource | Open source project providing a collaborative layer of knowledge over academic publications by allowing users to share real-time highlights and annotations. Participate in open discussion that drives ideas and academia forward. It provides a supportive space to learn about research and ask questions of peers and experts. Follow authors and other users to understand their perspectives, make connections, and discover new ideas. | annotation, scholarship, publication | Creative Commons Zero License, V1 or newer, The community can contribute to this resource | nlx_158113 | SCR_003812 | SciCrunch Registry | Peer Library | 2026-10-31 12:18:23 | 0 | ||||||||
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MindSeer Resource Report Resource Website |
MindSeer (RRID:SCR_003019) | MindSeer | data processing software, data visualization software, software application, software resource | A cross-platform application for 3D brain visualization for multi-modality neuroimaging data written in Java/Java3D, that runs in both standalone and client-server mode. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets. MindSeer has 2 different modes: # Client/Server is designed to allow users to visualize data that is stored centrally and enhance collaboration. # Standalone mode is available to view local data and is built for more performance than Client/Server Both modes have the same interface and support the same features. It has a modular architecture and is designed to be extensible. Requirements: # Java 5.0 or above. # Java Web Start. # Java3D (installed automatically by Web Start). | 3d surface, visualization, multimodal, volume, neuroimaging, 3-d volume, surface, java, java3d, brain, brain structure, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of Washington; Seattle; USA |
Human Brain Project ; NIDCD DC02310 |
PMID:17937818 | GNU General Public License, With some, GNU Lesser General Public License, Components (MatFile and NIFTI jar files). | nif-0000-00525 | http://www.nitrc.org/projects/mindseer | SCR_003019 | SciCrunch Registry | 2026-10-31 12:18:31 | 0 | |||||
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Pristionchus.org Resource Report Resource Website 10+ mentions |
Pristionchus.org (RRID:SCR_003414) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | This data resource is a genetic, molecular, and genomic toolkit that establishes one particular species, Pristionchus pacificus, as a major satellite system for evolutionary developmental biology. Users may download Pristionchus Sequences and use the Pristionchus pacificus genome browser where they may find gene or gene prediction data. Users can also use the BLAST feature, which allows users to search the assembly for position information of bacs, reads and contigs using the mapping tool. The center of the site's research is the evolutionary analysis of vulva formation. The general aim of the Department is to develop the nematode vulva as a suitable case study into the evolutionary alterations of developmental processes. By studying and comparing two distantly related species of the same phylum, such as P. pacificus and C. elegans, macroevolutionary alterations of developmental processes and mechanisms can be identified. The final goal of the Department is to achieve a comprehensive description of macro- and microevolutionary changes of developmental mechanisms at the molecular level in a phylogenetic and ecological context. | pristionchus, pristionchus pacificus, database, data analysis service, genetic toolkit, molecular toolkit, genomic toolkit | has parent organization: Max Planck Institute for Developmental Biology; Tubingen; Germany | PMID:17062617 | Free, Freely available | nif-0000-03339 | SCR_003414 | SciCrunch Registry | www.pristionchus.org | 2026-10-31 12:18:23 | 38 | |||||||
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TumorSim Resource Report Resource Website 1+ mentions |
TumorSim (RRID:SCR_002604) | simulation software, software application, software resource | Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images. | clinical neuroinformatics, magnetic resonance, mri, brain, segmentation, simulation, tumor, ground truth |
uses: BrainWeb - Simulated Brain Database is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
Cancer | NIBIB R01 EB000219 | PMID:19119055 | Free, Available for download, Freely available | nlx_156007 | SCR_002604 | SciCrunch Registry | 2026-10-31 12:18:30 | 1 | ||||||
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SNPMeta Resource Report Resource Website 1+ mentions |
SNPMeta (RRID:SCR_002005) | SNPMeta | analysis service resource, data analysis service, production service resource, service resource, software resource | A Python and BioPython-based tool to generate metadata for single nucleotide polymorphisms (SNPs) for easy filtering, or submission to SNP databases. Information reported includes gene name, whether the SNP is coding or noncoding, and whether the SNP is synonymous or nonsynonymous. SNPMeta outputs in either a dbSNP submission report format, or a tab-delimited format. There is a also Web-based version available that only annotates with default settings, and only annotates a maximum of 20 SNPs at one time. The script may be downloaded for full functionality. | single nucleotide polymorphism, coding, noncoding, , synonymous, nonsynonymous, python, biopython, metadata, annotation |
is listed by: OMICtools has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:24237904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01923 | SCR_002005 | SciCrunch Registry | 2026-10-31 12:18:24 | 1 | |||||||
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SEER Datasets and Software Resource Report Resource Website 10+ mentions |
SEER Datasets and Software (RRID:SCR_003293) | data or information resource, disease-related portal, portal, software resource, topical portal | Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data. | NCI, cancer, statistics, epidemiology, analysis |
lists: SEER*Stat lists: NCI SEER Cancer Stage Variable Documentation is related to: Surveillance Epidemiology and End Results has parent organization: National Cancer Institute |
cancer | NCI | Free, Freely available | nif-0000-31490 | SCR_003293 | SciCrunch Registry | The Surveillance Epidemiology and End Results (SEER) Program, SEER Datasets Software, SEER Datasets & Software, The Surveillance Epidemiology and End Results (SEER) Program of the National Cancer Institute | 2026-10-31 12:18:26 | 28 | ||||||
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QualitySNPng Resource Report Resource Website 1+ mentions |
QualitySNPng (RRID:SCR_002479) | data processing software, data visualization software, software application, software resource, standalone software | Software for the detection and visualization of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy. | single nucleotide polymorphism, haplotype strategy, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23632165 | Free, Available for download, Freely available | biotools:qualitysnpng, OMICS_00070 | https://bio.tools/qualitysnpng | SCR_002479 | SciCrunch Registry | 2026-10-31 12:18:25 | 7 | |||||||
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PBSIM Resource Report Resource Website 10+ mentions |
PBSIM (RRID:SCR_002512) | simulation software, software application, software resource | Software that simulates PacBio reads by using either a model-based or sampling-based simulation. | pacbio simulation, model-based simulation, sampling-based simulation |
is listed by: OMICtools is listed by: Debian |
PMID:23129296 DOI:10.1093/bioinformatics/bts649 |
Free, Available for download, Freely available | OMICS_00253 | https://sources.debian.org/src/pbsim/ | SCR_002512 | SciCrunch Registry | PacBio reads simulator | 2026-10-31 12:18:22 | 11 | ||||||
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Biologic Stylus Resource Report Resource Website |
Biologic Stylus (RRID:SCR_002991) | Biologic Stylus | simulation software, software application, software resource, source code | Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python | bioinformatics, simulation | has parent organization: SourceForge | Free, Available for download, Freely available | nif-0000-30198 | SCR_002991 | SciCrunch Registry | biologicstylus | 2026-10-31 12:18:26 | 0 | |||||||
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MAQC Resource Report Resource Website 10+ mentions |
MAQC (RRID:SCR_002351) | MAQC | data or information resource, knowledge environment, narrative resource, standard specification | Project to improve the microarray and next-generation sequencing technologies and foster their proper applications in discovery, development and review of FDA regulated products by developing standards and quality measures. Microarrays and next-generation sequencing represent core technologies in pharmacogenomics and toxicogenomics; however, before these technologies can successfully and reliably be used in clinical practice and regulatory decision-making, standards and quality measures need to be developed. Everyone is invited to participate in the MAQC project. | microarray, next-generation sequencing, pharmacogenomics, toxicogenomics, quality control |
is listed by: OMICtools has parent organization: National Center for Toxicological Research |
OMICS_01784 | SCR_002351 | SciCrunch Registry | MicroArray Quality Control | 2026-10-31 12:18:25 | 21 | ||||||||
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SpineSegmentation module for 3DSlicer Resource Report Resource Website 1+ mentions |
SpineSegmentation module for 3DSlicer (RRID:SCR_002593) | Spine Segmentation Module in Slicer3 | data processing software, image analysis software, segmentation software, software application, software resource | 3D Slicer module for automated segmentation of the spine. This is an implementation of a novel model-based segmentation algorithm. This work was presented at the NA-MIC Week in Salt Lake City, Jan 2010. | magnetic resonance, spine |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: National Alliance for Medical Image Computing |
Free, Freely available | nlx_155997 | http://www.nitrc.org/projects/sylvainproject | SCR_002593 | SciCrunch Registry | Spine Segmentation module for 3D Slicer | 2026-10-31 12:18:22 | 3 | ||||||
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BTMORPH Resource Report Resource Website 1+ mentions |
BTMORPH (RRID:SCR_003566) | software library, software resource, software toolkit | Small Python library containing a data structure and tools to represent and analyze neuronal morphologies stored in the de facto standard SWC format. | PMID:9821633 | Acknowledgement requested | nlx_157700 | SCR_003566 | SciCrunch Registry | 2026-10-31 12:18:27 | 4 | ||||||||||
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GitHub Resource Report Resource Website 1000+ mentions |
GitHub (RRID:SCR_002630) | GitHub | commercial organization, mobile app, service resource, software application, software repository, software resource | A web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go. | source code, database, java, php, python, objective-c, c++, c, c#, perl, issue, computer science, FASEB list |
is used by: Observational Medical Outcomes Partnership is used by: NIH Heal Project lists: Digital Asset Management System lists: IBMA toolbox lists: NeuroSynth lists: MIAPA lists: FACS lists: RSEM lists: flowPeaks lists: BRAINSCut lists: Mspire-Simulator is listed by: FORCE11 is listed by: re3data.org is related to: Karma is related to: ImpactStory hosts: SciUnit hosts: FlashX hosts: BioBlend Library hosts: Vision Egg hosts: Cufflinks hosts: MetAMOS hosts: ProtVista hosts: Big Data Bag hosts: FUSIM hosts: GDC hosts: ProtTest hosts: State Space Models hosts: OpenWorm hosts: Zero Mode Waveguide Imaging and Analysis package tools hosts: Taxonomer hosts: Eelbrain hosts: N2A hosts: Pilon hosts: MicroDraw hosts: BrainBox hosts: Stanford CoreNLP hosts: AnaMorph hosts: wMICA hosts: SEER hosts: phytools hosts: PhenVar hosts: JuncBASE hosts: HISAT2 hosts: NeuroManager |
Free, Available for download, Freely available | nlx_156051 | http://www.force11.org/node/4710 | SCR_002630 | SciCrunch Registry | 2026-10-31 12:18:26 | 3749 | |||||||
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neuromice Resource Report Resource Website |
neuromice (RRID:SCR_002993) | neuromice | biomaterial supply resource, material resource, organism supplier | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 08, 2013. A consortium of three facilities whose purpose is to establish, characterize, and distribute novel mutant mouse models with neural and/or behavioral phenotypes, and distribute them to the worldwide research community. Interested scientists are able to obtain information about mouse lines at all three sites in a single unified database. GOALS * Increase genomic and genetic tools for functional gene identification * Provide mice with mutations that alter the nervous system or behavior * Build collaborations between geneticists and neuroscientists The consortium is made up of three mutagenesis and phenotypic screening facilities, focused on identifying alterations in nervous system function and behavior, and established by NIH. They are the Neurogenomics Project at Northwestern University, the Neuroscience Mutagenesis Facility at The Jackson Laboratory, and the Neuromutagenesis Project of the Tennessee Mouse Genome Consortium. The NIH Neurogenomics Project at Northwestern University is directed by Dr. Joseph S. Takahashi, who also acts as the Director of the Neuromice.org consortium. Chemical mutagenesis is used to induce mutations throughout the genome and combined with phenotypic screens to detect mice with mutations. In order to maximize the genomic coverage and recover both dominant and recessive mutations, a dominant G1 screen and a recessive G3 screen are utilized. Phenotypic screens focus on five primary domains: learning and memory, behavioral responses to stress, responses to psychostimulants, circadian rhythmicity, and vision. The Neuroscience Mutagenesis Facility at the Jackson Laboratory is directed by Dr. Wayne N. Frankel. The Neuroscience Mutagenesis Facility is using a three-generation backcross breeding scheme to produce homozygous mutants and will thus recover dominant, semidominant, and recessive mutations. In addition, some mutagenesis will be done in ES cells followed by two generations of breeding. Phenotypic screens focus on identifying mutations affecting: motor function, seizure threshold, hearing, vision, and neurodevelopment. The Neuromutagenesis Project of the Tennessee Mouse Genome Consortium (TMGC) involves researchers throughout the state of Tennessee, under the direction of Dr. Daniel Goldowitz, Ph.D., at the University of Tennessee Health Science Center, Memphis. TMGC also includes researchers at Oak Ridge National Laboratory, Vanderbilt University, Meharry Medical College, University of Tennessee-Knoxville, St. Jude Children's Research Hospital, and the University of Memphis. The Project is using regional mutagenesis, covering regions on chromosomes 10, 14, 15, 19, and X, thus including approximately 15 of the genome in the screened region. Phenotypic screens include: motor and sensory function, learning and memory, neurohistology, aging, alcohol response, abused drug response, visual function, and social behavior. Neuromice.org has stopped taking orders online but mutants are orderable please contact the originating center for availability and pricing details. Live targeted mutant Fragile X model mice are now available for distribution. | eye, fragile x syndrome, gene expression phenotype, geneticist, anxiety, ataxia, behavior, b-wave, cocaine, mus, musculoskeletal movement, mutant mouse strain, mutated variant site, mutation, nervous system, nervous system behavior, nervous system function, neuromuscular function, neuroscientist, phenotype, scotopic threshold response, substance-related disorder, tremor, visual perception, mutant, mouse model, neural phenotype, behavioral phenotype, neuron, mutagenesis, learning, memory, stress, psychostimulant, circadian rhythm, vision, motor function, seizure threshold, hearing, neurodevelopment, chromosome, motor function, sensory function, neurohistology, alcohol abuse, drug abuse, visual function, social behavior |
is listed by: One Mind Biospecimen Bank Listing is related to: JAX Neuroscience Mutagenesis Facility has parent organization: Northwestern University; Illinois; USA has parent organization: JAX Neuroscience Mutagenesis Facility |
Aging | NIH Blueprint for Neuroscience Research | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00046 | http://www.neuromice.org | SCR_002993 | SciCrunch Registry | neuromice.org | 2026-10-31 12:18:28 | 0 | ||||
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RAVEN Resource Report Resource Website 100+ mentions |
RAVEN (RRID:SCR_001937) | RAVEN | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor binding site, phylogenetic footprint, regulatory sequence variation, genetic variation, in silico, regulatory sequence, FASEB list |
uses: Embassy-domsearch is listed by: OMICtools has parent organization: University of British Columbia; British Columbia; Canada |
PMID:18208319 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01932 | SCR_001937 | SciCrunch Registry | Regulatory analysis of Variation in Enhancers, RAVEN - Regulatory analysis of Variation in ENhancers | 2026-10-31 12:18:24 | 127 |
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