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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mass Univariate ERP Toolbox Resource Report Resource Website 1+ mentions |
Mass Univariate ERP Toolbox (RRID:SCR_016108) | data analysis software, data processing software, data visualization software, software application, software resource | Software toolkit of Matlab functions for analyzing and visualizing large numbers of t-tests performed on event-related potential data. The toolbox supports within-subject and between-subject t-tests with false discovery rate controls and control of the family-wise error rate via permutation tests. | matlab, analysis, t test, statistic, erp, event related potential, visualization, neuroimaging, erf, magnetic, resonance, imaging | requires: MATLAB | NIA AG08313; NICHD HD22614 |
PMID:21895683 | Free, Available for download | https://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox | SCR_016108 | SciCrunch Registry | 2026-11-07 11:58:38 | 6 | |||||||
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iELVis Resource Report Resource Website 10+ mentions |
iELVis (RRID:SCR_016109) | data processing software, data visualization software, software application, software resource | Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization. | electrode, stimulus, visualization, brain, neuroimaging, intracranial, localization, anatomy, functional, BRAIN Initiative | is recommended by: BRAIN Initiative | Natural Sciences and Engineering Research Council of Canada RGPIN-2014-04465; Page and Otto Marx Jr. Foundation ; Swiss National Science Foundation P300P3_148388; Swiss National Science Foundation PBGEP3_139829 |
PMID:28192130 | Open source, Free, Available for download | https://github.com/iELVis/iELVis | SCR_016109 | SciCrunch Registry | iELVis (intracranial electrode visualization), Intracranial ELectrode VISualization | 2026-11-07 11:58:11 | 47 | ||||||
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HIRN Consortium on Human Islet Biomimetics Resource Report Resource Website |
HIRN Consortium on Human Islet Biomimetics (RRID:SCR_016199) | HIRN-CHIB, CHIB | consortium, data or information resource, organization portal, portal | Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is combining advances in beta cell biology and cell biology with tissue engineering technologies to develop microdevices that support functional human islets. | beta, cell, biology, tissue, bioengineering, nanoengineering, human, stem | is organization facet of: Human Islet Research Network (HIRN) | NIDDK ; NIDDK U01 DK104162; NIDDK UC4 DK104165; NIDDK UC4 DK104196; NIDDK UC4 DK104202; NIDDK UC4 DK104208; NIDDK UC4 DK116283 |
SCR_016199 | SciCrunch Registry | Consortium on Human Islet Biomimetics (HIRN-CHIB) | 2026-11-07 11:58:39 | 0 | ||||||||
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Mapping Population-based Structural Connectomes Resource Report Resource Website |
Mapping Population-based Structural Connectomes (RRID:SCR_016232) | data analysis software, data processing software, software application, software resource | 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 | CPRIT RR150054; NIMH MH086633; NIMH MH092335; NSF DMS-1407655; NSF DMS1127914; NSF SES-1357666 |
Free for non-commercial use, Available for download | SCR_016232 | SciCrunch Registry | 2026-11-07 11:58:39 | 0 | ||||||||||
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Garlic Resource Report Resource Website 10+ mentions |
Garlic (RRID:SCR_016118) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource | Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences. | visualization, editing, biomolecule, investigation, membrane, protein, analyze, sequence |
is listed by: Debian is listed by: OMICtools |
Open source, Free, Available for download | OMICS_21303 | https://sources.debian.org/src/garlic/ | SCR_016118 | SciCrunch Registry | 2026-11-07 11:58:38 | 38 | ||||||||
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REmAb Resource Report Resource Website |
REmAb (RRID:SCR_016239) | analysis service resource, biomaterial analysis service, material analysis service, production service resource, service resource | Service for monoclonal antibody protein sequencing. It derives the sequences directly from the protein using mass spectrometry and without the need to access the cell line. | mass, spectrometry, monoclonal, anitbody, protein, sequencing, cell, line | Commercially available, Free consultation | SCR_016239 | SciCrunch Registry | Antibody Sequencing Service | 2026-11-07 11:58:39 | 0 | ||||||||||
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YAMP Resource Report Resource Website 1+ mentions |
YAMP (RRID:SCR_016236) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability. | metagenomics, reproducibility, workflow, containerization, sequencing, gene, rna, annotating, portable, data, process | Free, Available for download | SCR_016236 | SciCrunch Registry | YAMP: Yet Another Metagenomic Pipeline, Yet Another Metagenomic Pipeline (YAMP), Yet Another Metagenomic Pipeline | 2026-11-07 11:58:23 | 8 | ||||||||||
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Gamgi Resource Report Resource Website |
Gamgi (RRID:SCR_016116) | GAMGI | data analysis software, data processing software, data visualization software, software application, software resource | Software application which provides a graphical interface to build, view and analyze atomic structures. It provides a graphical interface to study atomic structures, to prepare images for presentations, and teach the atomic structure of matter. | gui, graphical, interface, model, atom, atomic, structure |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Runs on Linux, Tutorial available | OMICS_21302 | https://sources.debian.org/src/gamgi/ | SCR_016116 | SciCrunch Registry | GAMGI: General Atomistic Modelling Graphic Interface, General Atomistic Modelling Graphic Interface | 2026-11-07 11:58:21 | 0 | ||||||
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International Initiative for Traumatic Brain Injury Research Resource Report Resource Website 1+ mentions |
International Initiative for Traumatic Brain Injury Research (RRID:SCR_016237) | InTBIR | access service resource, service resource | Project whose goal is to improve health care and lessen the global burden of TBI through the discovery of causal relationships between treatments and clinically meaningful outcomes. InTBIR seeks to encourage well-designed, hypothesis-driven studies that include the collection of high quality data followed by rigorous statistical analysis. | tbi, traumatic, brain, injury, neurology, neuroscience, neuroanatomy, medical, clinical, research, nih |
has parent organization: European Commission has parent organization: Canadian Institutes of Health Research |
SCR_016237 | SciCrunch Registry | International Initiative for Traumatic Brain Injury Research (InTBIR) | 2026-11-07 11:58:34 | 4 | |||||||||
|
LR Gapcloser Resource Report Resource Website 50+ mentions |
LR Gapcloser (RRID:SCR_016194) | alignment software, data processing software, image analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies. | long, short, read, alignment, assembly, gap, closer, sequence, gene | PMID:30576505 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017021 | SCR_016194 | SciCrunch Registry | LR_Gapcloser | 2026-11-07 11:58:12 | 71 | ||||||||
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Grass Stimulator Model S88 Resource Report Resource Website 1+ mentions |
Grass Stimulator Model S88 (RRID:SCR_016192) | resource | Hardware that is a electrical pulse generator. | hardware, instrument, equipment, electricity, pulse, stimulation, generator | Commercially available | SCR_016192 | SciCrunch Registry | Cyberonics VNS 103, S88 DUAL OUTPUT SQUARE PULSE, Pulse Stimulator, Grass Technologies Stimulator Pulse | 2026-11-07 11:58:33 | 4 | ||||||||||
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OpenEx Resource Report Resource Website 100+ mentions |
OpenEx (RRID:SCR_016230) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit that is designed for configuration and control of TDT hardware. It can also display and analyze neurophysiology data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tdt, analysis, neurophysiology, hardware, companion software, control, configuration, neuroimaging, eeg, stimulation | has parent organization: Tucker-Davis Technologies | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016230 | SciCrunch Registry | The OpenEx Software Suite, OpenEx suite | 2026-11-07 11:58:23 | 103 | |||||||||
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HIRN Consortium on Beta Cell Death and Survival Resource Report Resource Website |
HIRN Consortium on Beta Cell Death and Survival (RRID:SCR_016198) | HIRN-CBDS, CBDS | consortium, data or information resource, organization portal, portal | Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is using human tissues to discover highly specific biomarkers of beta cell injury in asymptomatic T1D and developing strategies to stop beta cell destruction early in the disease process. | kidney, tissue, biomarker, beta, cell, t1d, disease, research | is organization facet of: Human Islet Research Network (HIRN) | NIDDK ; NIDDK U01 DK104162; NIDDK UC4 DK104155; NIDDK UC4 DK104159; NIDDK UC4 DK104166; NIDDK UC4 DK104167; NIDDK UC4 DK104205; NIDDK UC4 DK104216; NIDDK UC4 DK108101; NIDDK UC4 DK108120; NIDDK UC4 DK108132; NIDDK UC4 DK116271; NIDDK UC4 DK116274; NIDDK UC4 DK116278 |
SCR_016198 | SciCrunch Registry | Consortium on Beta Cell Death and Survival (HIRN-CBDS) | 2026-11-07 11:58:33 | 0 | ||||||||
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NIX Resource Report Resource Website 10+ mentions |
NIX (RRID:SCR_016196) | data processing software, data storage software, software application, software resource | Software that defines a data model for annotated scientific datasets. It includes data together with metadata, and a corresponding file format based on HDF5 for storing and sharing such datasets. | data, model, metadata, scientific, integration, file, format, annotation, hdf5, dataset |
uses: Open metadata mark up language is used by: EEGbase has parent organization: German Neuroinformatics Node (G-Node) has parent organization: Ludwig-Maximilians-University; Munich; Germany |
BMBF 01GQ0801; BMBF 01GQ1302 |
DOI:10.3389/conf.fninf.2014.18.00027 | Public | https://fairsharing.org/bsg-s001169 | http://www.g-node.org/nix | SCR_016196 | SciCrunch Registry | Pandora, NIX Project | 2026-11-07 11:58:23 | 13 | |||||
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Brain Imaging Data Structure (BIDs) Resource Report Resource Website 100+ mentions |
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) | BIDS | data or information resource, narrative 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 |
European Regional Development Fund ; German federal state of Sachsen-Anhalt ; International Neuroinformatics Coordinating Facility ; Laura and John Arnold Foundation ; Medical Research Council United Kingdom ; NIAAA U01 AA021697; NIGMS P20 GM103472; NIMH Intramural Research Program ; NSF 1429999; Wellcome Trust |
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 | SciCrunch Registry | Brain Imaging Data Structure, BIDS, Brain Imaging Data Structure (BIDS), Brain Imaging Data Structure v1.4.0 | 2026-11-07 11:58:38 | 235 | |||||
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Gff2aplot Resource Report Resource Website |
Gff2aplot (RRID:SCR_016128) | data processing software, data visualization software, software application, software resource | Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis. | alignment, pair-wise, plot, genomic, sequence, visualize, together, annotate, analysis, parameter, dataset, |
is listed by: Debian is listed by: OMICtools |
PMID:14668236 | Free, Available for download | OMICS_19949 | https://sources.debian.org/src/gff2aplot/ | SCR_016128 | SciCrunch Registry | 2026-11-07 11:58:32 | 0 | |||||||
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Localite TMS Navigator Resource Report Resource Website 1+ mentions |
Localite TMS Navigator (RRID:SCR_016126) | resource | An instrument. Navigation system for transcranial magnetic stimulation (TMS). | hardware, instrument, equipment, tms, neuroimaging, neuroscience, neurology, transcranial, magnetic, stimulation | SCR_016126 | SciCrunch Registry | 2026-11-07 11:58:11 | 4 | ||||||||||||
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Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. | editing, database, management, plasmid maps, restriction, ligation, alignments, sequence, data, import, calculator, gel, image, display, PCR, cloning, genetic |
is listed by: Debian is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Free Software Foundation | Free, Available for download | OMICS_18307 | https://sources.debian.org/src/gentle/ | SCR_016127 | SciCrunch Registry | GENtle | 2026-11-07 11:58:21 | 6 | ||||||
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Singularity Hub Resource Report Resource Website 1+ mentions |
Singularity Hub (RRID:SCR_016248) | SHUB | application programming interface, data access protocol, data or information resource, database, software application, software development tool, software resource, web service | Database for singularity containers. It hosts container collections as well as articles about scientific advancements. | container, linux-container, singularity, singularity-container, builder, cloud-builder, google, storage | Stanford Research Computing and the School of Medicine | PMID:29186161 | Open source, Free, Available for download | SCR_016247 | SCR_016248 | SciCrunch Registry | singularity-registry, SingularityHub, shub, Singularity Registry | 2026-11-07 11:58:13 | 2 | ||||||
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MICtools Resource Report Resource Website 10+ mentions |
MICtools (RRID:SCR_016121) | data analysis software, data processing software, software application, software resource | Software which combines the TICe and MICe measures into a two-step procedure that allows to identify relationships of various degrees of complexity in large datasets. TICe is used to perform an efficient high throughput screening of all the possible pairwise relationships and a permutation based approach is used to assess their significance. | tice, mice, dataset, permutation, statistic | Open source | SCR_016121 | SciCrunch Registry | Maximal Information Coefficient (MIC) Tools, MIC Tools, Maximal Information Coefficient Tools | 2026-11-07 11:58:32 | 12 |
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