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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Incorporated Research Institutions for Seismology Resource Report Resource Website 500+ mentions |
Incorporated Research Institutions for Seismology (RRID:SCR_002201) | IRIS | organization portal, portal, institution, consortium, data or information resource | Passive and active source waveform data, event (earthquake) catalog, channel response data is available. This comprehensive data store of raw geophysical time-series data is collected from a large variety of sensors, courtesy of a vast array of US and International scientific networks, including seismometers (permanent and temporary), tilt and strain meters, infrasound, temperature, atmospheric pressure and gravimeters, to support basic research aimed at imaging the Earth's interior. IRIS also provides data and software for educational purposes. This consortium of over 100 US universities is dedicated to the operation of science facilities for the acquisition, management, and distribution of seismological data. IRIS programs contribute to scholarly research, education, earthquake hazard mitigation, and verification of the Comprehensive Nuclear-Test-Ban Treaty. Data is stored at the IRIS Data Management Center in Seattle, Washington. They currently manage a large archive from over tens of thousands of seismic stations and ship hundreds of terabytes of data yearly. | seismology, geophysics, earth science, earthquake, seismic, time series, metadata, channel response, waveform |
is listed by: CINERGI is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing is parent organization of: IRIS DMC Web Services |
NSF | Free, Freely available | nlx_154710, DOI:10.25504/FAIRsharing.x9rqf7, grid.300201.0, Wikidata: Q16074398, ISNI: 0000 0004 6078 0424, DOI:10.17616/R3X607, DOI:10.7914, DOI:10.17611 | https://ror.org/05xkn9s74, https://doi.org/10.17616/R3X607, https://doi.org/10.17616/r3X607, https://doi.org/10.7914/, https://doi.org/10.17611/, https://dx.doi.org/10.7914/, https://dx.doi.org/10.17611, https://fairsharing.org/10.25504/FAIRsharing.x9rqf7 | SCR_002201 | IRIS Consortium, Incorporated Research Institutions for Seismology | 2026-08-03 09:31:35 | 540 | |||||
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U.S. Antarctic Program Data Coordination Center Resource Report Resource Website 1+ mentions |
U.S. Antarctic Program Data Coordination Center (RRID:SCR_002221) | USAP-DCC | data repository, data or information resource, database, storage service resource, service resource | Assists scientists in finding Antarctic scientific data of interest and submitting data for long-term preservation in accordance with their obligations under the National Science Foundation (NSF) Office of Polar Programs (OPP) Data Policy. | antarctica, southern ocean, polar |
is listed by: CINERGI has parent organization: Marine Geoscience Data System |
NSF | Free, Freely available | r3d100010660, nlx_154744 | https://doi.org/10.17616/R31898 | http://www.usap-data.org/ | SCR_002221 | 2026-08-03 09:31:49 | 5 | |||||
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EarthChem Resource Report Resource Website 10+ mentions |
EarthChem (RRID:SCR_002207) | EarthChem | data repository, data or information resource, database, storage service resource, service resource | Accepts and makes available geochemical, geochronlogical, and petrological data (analytical and synthesis) through this community-driven effort to facilitate the preservation, discovery, access and visualization of data generated. * PetDB holds geochemical data from sub-oceanic igneous and metamorphic rocks generated at mid-ocean ridges including back-arc basins, young seamounts, and old oceanic crust. Data are compiled primarily from the published literature. * SedDB integrates marine and terrestrial sediment geochemical data compiled primarily from the published literature. * Deep Lithosphere Data Set contains geochemical and petrological data from lower crust and upper mantle xenoliths. (more info) * VentDB contains hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. * NAVDAT - The Western North American Volcanic and Intrusive Rock Database * Geochron is an application that helps with the onerous task of data management for geochronological and thermochronological studies. * EarthChemPortal is the one-stop-shop for geochemical data that gives users the ability to search federated databases PetDB, NAVDAT, and GEOROC simultaneously, integrated into a common output format. (more info) * The EarthChem Library is a repository for geochemical datasets (analytical data, experimental data, synthesis databases) and other digital resources relevant to the field of geochemistry, contributed by the geochemistry community. * SESAR - System for Earth SAmple Registration | geochemical, geochronological, petrological |
is listed by: CINERGI has parent organization: Columbia University; New York; USA is parent organization of: VentDB is parent organization of: PetDB is parent organization of: SedDB is parent organization of: System for Earth Sample Registration |
NSF | Free, Available for download, Freely available | nlx_154721, r3d100011538 | https://doi.org/10.17616/R3V644 | SCR_002207 | IEDA: EarthChem | 2026-08-03 09:31:48 | 24 | |||||
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MetPetDB Resource Report Resource Website 1+ mentions |
MetPetDB (RRID:SCR_002208) | MetPetDB | data repository, data or information resource, database, storage service resource, service resource | Database / data repository for metamorphic petrology that is being designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative. | metamorphic, petrology, geology, geochemistry |
is listed by: CINERGI has parent organization: Rensselaer Polytechnic Institute; New York; USA |
NSF EAR 0949318 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154722, r3d100012514 | SCR_002208 | 2026-08-03 09:31:42 | 1 | |||||||
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Community Surface Dynamics Modeling System Resource Report Resource Website |
Community Surface Dynamics Modeling System (RRID:SCR_002196) | CSDMS | data repository, data or information resource, storage service resource, computational hosting, service resource, software resource, data set | Model repository and data related to earth-surface dynamics modeling. The CSDMS Modeling Tool (CMT) allows you to run and couple CSDMS model components on the CSDMS supercomputer in a user-friendly software environment. Components in the CMT are based on models, originally submitted to the CSDMS model repository, and now adapted to communicate with other models. The CMT tool is the environment in which you can link these components together to run new simulations. The CMT software runs on your own computer; but it communicates with the CSDMS HPCC, to perform the simulations. Thus, the CMT also offers you a relatively easy way of using the CSDMS supercomputer for model experiments. CSDMS deals with the Earth's surface - the ever-changing, dynamic interface between lithosphere, hydrosphere, cryosphere, and atmosphere. They are a diverse community of experts promoting the modeling of earth surface processes by developing, supporting, and disseminating integrated software modules that predict the movement of fluids, and the flux (production, erosion, transport, and deposition) of sediment and solutes in landscapes and their sedimentary basins. CSDMS: * Produces protocols for community-generated, continuously evolving, open software * Distributes software tools and models * Provides cyber-infrastructure to promote the quantitative modeling of earth surface processes * Addresses the challenging problems of surface-dynamic systems: self-organization, localization, thresholds, strong linkages, scale invariance, and interwoven biology & geochemistry * Enables the rapid development and application of linked dynamic models tailored to specific landscape basin evolution (LBE) problems at specific temporal and spatial scales * Partners with related computational and scientific programs to eliminate duplication of effort and to provide an intellectually stimulating environment * Supports a strong linkage between what is predicted by CSDMS codes and what is observed, both in nature and in physical experiments * Supports the imperatives in Earth Science research | model, earth, surface, surface dynamics |
is listed by: CINERGI has parent organization: University of Colorado Boulder; Colorado; USA |
NSF | PMID:17406970 | Free, Freely available | r3d100012544, nlx_154705 | https://doi.org/10.17616/R3051W | SCR_002196 | 2026-08-03 09:31:48 | 0 | |||||
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Neotoma Paleoecology Database Resource Report Resource Website 10+ mentions |
Neotoma Paleoecology Database (RRID:SCR_002190) | Neotoma | data repository, production service resource, data analysis service, service resource, database, storage service resource, analysis service resource, data or information resource | Paleoecology database for plio-pleistocene to holocene fossil data with a centralized structure for interdisciplinary, multiproxy analyses and common tool development; discipline-specific data can also be easily accessed. Data currently include North American Pollen (NAPD) and fossil mammals (FAUNMAP). Other proxies (plant macrofossils, beetles, ostracodes, diatoms, etc.) and geographic areas (Europe, Latin America, etc.) will be added in the near future. Data are derived from sites from the last 5 million years. | data sharing, paleoecology, plio-pleistocene, holocene, fossil |
is listed by: CINERGI has parent organization: Pennsylvania State University |
NSF | Free, Available for download, Freely available | nlx_154700, r3d100011761 | SCR_002190 | NeotomaDB, Neotoma DB | 2026-08-03 09:31:47 | 31 | ||||||
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Sal-Site Resource Report Resource Website 50+ mentions |
Sal-Site (RRID:SCR_002850) | Sal-Site | image collection, portal, production service resource, data analysis service, organism-related portal, service resource, database, topical portal, analysis service resource, data or information resource | Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network. | gene, genomic, expressed sequence tag, blast, model organism, genome, salamander, animal model, genetic map, genetic marker, gene expression, limb regeneration, microarray, quantitative-pcr, rna-seq, nanostring, husbandry, embryo, limb, mutant, strain, neural, olfaction, phentotype, regeneration, renal, retina, sequence, vision, human, chicken, xenopus tropicalis, FASEB list | has parent organization: University of Kentucky; Kentucky; USA | NSF OB0242833; NSF DBI0443496; NCRR R24 RR016344; NIH Office of the Director R24 OD010435 |
PMID:16359543 | Free, Freely available | nif-0000-25309 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | SCR_002850 | Ambystoma Resources for Model Amphibians Database | 2026-08-03 09:32:09 | 92 | ||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | data repository, production service resource, data analysis service, service resource, database, image repository, atlas, storage service resource, analysis service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb, https://doi.org/10.17616/R3JC76 | SCR_002759 | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2026-08-03 09:32:00 | 13 | ||||
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HDBIG Resource Report Resource Website |
HDBIG (RRID:SCR_014120) | software toolkit, software application, data processing software, image analysis software, software resource | A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association. | image analysis software, genomics, imaging, joint analysis, toolkit, sparse association, sparse regression |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University; Indiana; USA |
NLM R01 LM011360; NSF IIS-1117335 |
http://www.iu.edu/~hdbig/ | SCR_014120 | High Dimensional Brain Imaging Genomics Toolkit | 2026-08-03 09:35:22 | 0 | ||||||||
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Wisconsin Cortical Thickness Analysis (CTA) Toolbox Resource Report Resource Website |
Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) | software toolkit, software application, data processing software, data analysis software, software resource | A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR). | matlab, software toolkit, cortical thickness signal, data analysis software |
uses: FreeSurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Wisconsin Partnership Program ; NIA R01AG040396; NIA R01AG021155; NSF RI 1116584; NSF CAREER 1252725; UW ADRC NIA P50 AG033514; UW ICTR NCRR 1UL1RR025011; NIA P30 AG010129; NIA K01 AG030514 |
http://pages.cs.wisc.edu/~wonhwa/code/CTA_toolbox.html, http://pages.cs.wisc.edu/~wonhwa/project/ctdiscrim.html | SCR_014180 | 2026-08-03 09:35:37 | 0 | |||||||||
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Group Sparse Canonical Correlation Analysis Resource Report Resource Website |
Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) | GSCCA | software resource, data processing software, software application, data analysis software | Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data. | group analysis, correlation analysis | has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) | NSF ; NIH |
Available for download | SCR_014977 | 2026-08-03 09:35:58 | 0 | ||||||||
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HISAT2 Resource Report Resource Website 10000+ mentions |
HISAT2 (RRID:SCR_015530) | sequence analysis software, software application, data processing software, source code, data analysis software, software resource | Graph-based alignment of next generation sequencing reads to a population of genomes. | alignment program, mapping reads, population genomics, human genome, bio.tools |
is used by: Fcirc is listed by: Debian is listed by: bio.tools is related to: TopHat has parent organization: Johns Hopkins University; Maryland; USA is required by: SL-quant is hosted by: GitHub |
NLM R01-LM06845; NIGMS R01-GM083873; NSF CCF-0347992 |
PMID:25751142 DOI:10.1038/s41587-019-0201-4 |
Available for download | OMICS_07225, biotools:hisat2 | https://github.com/infphilo/hisat2, https://bio.tools/hisat2, https://sources.debian.org/src/hisat2/ | SCR_015530 | HISAT | 2026-08-03 09:36:11 | 17595 | |||||
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | software application, data processing software, image analysis software, software resource, data visualization software | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NLM R01 LM011360; NIA U01 AG024904; NIA RC2 AG036535; NIA R01 AG19771; NIA P30 AG10133; NSF IIS-1117335; NIBIB R01 EB022574 |
PMID:27171688 | Free, Available for download | SCR_015846 | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-08-03 09:36:14 | 5 | ||||||
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Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | software toolkit, software application, data processing software, data analysis software, software resource, data visualization software | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/, https://github.com/avogadro, https://bio.tools/avogadro, https://sources.debian.org/src/axe-demultiplexer/ | SCR_015983 | 2026-08-03 09:36:16 | 1965 | ||||||
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Brain Imaging Data Structure (BIDs) Resource Report Resource Website 100+ mentions |
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) | BIDS | narrative resource, data or information resource, portal, standard specification | Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data. | Data storing structure, neuroimaging, standardized template, data sharing, MRI data, MEG data, EEG data, iEEG data, FASEB list |
is used by: OpenNeuro is used by: SPARC Portal is used by: SPARC Data Standard is listed by: FAIRsharing is related to: BIDS-Matlab is related to: NiPoppy works with: MNE-BIDS |
International Neuroinformatics Coordinating Facility ; Laura and John Arnold Foundation ; NIGMS P20 GM103472; Wellcome Trust ; NIAAA U01 AA021697; NIMH Intramural Research Program ; German federal state of Sachsen-Anhalt ; European Regional Development Fund ; Medical Research Council United Kingdom ; NSF 1429999 |
PMID:27326542 PMID:29917016 PMID:31239435 PMID:31239438 PMID:37744469 |
Free, Freely available | https://bids-specification.readthedocs.io/en/stable/, https://doi.org/10.25504/FAIRsharing.rd1j6t | SCR_016124 | Brain Imaging Data Structure, BIDS, Brain Imaging Data Structure (BIDS), Brain Imaging Data Structure v1.4.0 | 2026-08-03 09:36:18 | 212 | |||||
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Linear Fascicle Evaluation Resource Report Resource Website 1+ mentions |
Linear Fascicle Evaluation (RRID:SCR_016153) | software resource, data processing software, software application, data analysis software | Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes. | connectome, encode, framework, neuroanatomy, tract, dissection, array, tensor, edge, node | requires: MATLAB | NSF IIS-1636893; NSF BCS-1734853; NCATS ULT TR001108; Indiana University Areas of Emergent Research initiative Learning: Brains ; Machines ; Children |
Free, Available for download, Demo available | SCR_016153 | 2026-08-03 09:36:17 | 1 | |||||||||
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HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | sequence analysis software, software toolkit, software application, data processing software, data analysis software, software resource | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NSF DBI-0096033; NSF DEB-9996118; NIH R01 AI47745; NIH U01 AI43638; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214; NIGMS R01 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/, https://veg.github.io/hyphy-site/, https://github.com/veg/hyphy, https://bio.tools/HyPhy, | SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-08-03 09:36:37 | 1497 | |||||
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Mapping Population-based Structural Connectomes Resource Report Resource Website |
Mapping Population-based Structural Connectomes (RRID:SCR_016232) | software resource, data processing software, software application, data analysis software | Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis. | dwi, t1, tractography, algorithm, white matter, bundle, gray matter, shape, analysis, network, workflow | NIMH MH086633; NIMH MH092335; NSF SES-1357666; NSF DMS-1407655; CPRIT RR150054; NSF DMS1127914 |
Free for non-commercial use, Available for download | SCR_016232 | 2026-08-03 09:36:40 | 0 | ||||||||||
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | software toolkit, software application, data processing software, data analysis software, software resource, data visualization software | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | model, modelling, python, neuroelectrophysiology, object, neuroimaging, analysis, neurophysiology, electrophysiology, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF CBET-1351692; NSF IOS-1550994; Human Frontiers Science Program RGY0088 |
Free, Available for download, Freely available | SCR_016209 | Nelpy (Neuroelectrophysiology) | 2026-08-03 09:36:19 | 3 | ||||||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | service resource, data repository, storage service resource | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | 2026-08-03 09:36:18 | 35 |
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