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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | International Initiative for Traumatic Brain Injury Research (InTBIR) | 2026-09-12 12:58:37 | 4 | |||||||||
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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 | LR_Gapcloser | 2026-09-12 12:58:36 | 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 | Cyberonics VNS 103, S88 DUAL OUTPUT SQUARE PULSE, Pulse Stimulator, Grass Technologies Stimulator Pulse | 2026-09-12 12:58:36 | 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 | The OpenEx Software Suite, OpenEx suite | 2026-09-12 12:58:36 | 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 | Consortium on Beta Cell Death and Survival (HIRN-CBDS) | 2026-09-12 12:58:36 | 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 | Pandora, NIX Project | 2026-09-12 12:58:36 | 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 | Brain Imaging Data Structure, BIDS, Brain Imaging Data Structure (BIDS), Brain Imaging Data Structure v1.4.0 | 2026-09-12 12:58:35 | 235 | |||||
|
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 | 2026-09-12 12:58:35 | 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 | 2026-09-12 12:58:35 | 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 | GENtle | 2026-09-12 12:58:35 | 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 | singularity-registry, SingularityHub, shub, Singularity Registry | 2026-09-12 12:58:37 | 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 | Maximal Information Coefficient (MIC) Tools, MIC Tools, Maximal Information Coefficient Tools | 2026-09-12 12:58:35 | 12 | ||||||||||
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | 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 | Human Frontiers Science Program RGY0088; NSF CBET-1351692; NSF IOS-1550994 |
Free, Available for download, Freely available | SCR_016209 | Nelpy (Neuroelectrophysiology) | 2026-09-12 12:58:36 | 3 | ||||||||
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UTHSCSA ImageTool Resource Report Resource Website 100+ mentions |
UTHSCSA ImageTool (RRID:SCR_016208) | IT | data processing software, image analysis software, image processing software, software application, software resource | Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images. | image, analysis, processing, data, acquisition, compression, modification | has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA | Free, Available for download, Runs on Windows | http://en.bio-soft.net/draw/ImageTool.html | SCR_016208 | UTHSCSA Image Tool, UTHSCSA ImageTool (IT) | 2026-09-12 12:58:36 | 120 | |||||||
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InterLex Resource Report Resource Website 1+ mentions |
InterLex (RRID:SCR_016178) | controlled vocabulary, data or information resource, narrative resource, ontology, wiki | The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it. InterLex is being constructed to help improve the way that biomedical scientists communicate about their data, so that information systems like NIF and dkNET can find data more easily and provide more powerful means of integrating that data across distributed resources. One of the big roadblocks to data integration in the biomedical sciences is the inconsistent use of terminology in databases and other resources such as the literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources. For example, if three databases have information about what genes are expressed in cortex, but they all use different definitions of cerebral cortex, then it is hard to compare them. InterLex allows for the association of data values (i.e. the value of a field or text within a field) to terminologies enabling the crowdsourcing of data-terminology mappings. InterLex was built on the foundation of NeuroLex (see Larson and Martone 2013 Neurolex: An online framework for neuroscience knowledge. Frontiers in Neuroinformatics, 7:18) and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies. NIFSTD currently has about 60,000 concepts (includes both classes and synonyms) that span gross anatomy, cells, subcellular structures, diseases, functions and techniques. InterLex models terms using primitives of the Web Ontology Language (OWL) and can export directly to a variety of standard ontology formats. A primary goal of interlex is to provide a stable layer on top of the many other existing terminologies, lexicons, and ontologies (i.e. provide a way to federate ontologies for data applications) and to provide a set of inter-lexical and inter-data-lexical mappings. In the future, InterLex will support user specific namespaces so that users can customize the exact definitions or ontologies they source from, as well as the relationships on those terms. Importantly, however, InterLex enforces a simple rule which is that terms which represent the same concept under the same superclass will maintain the same identifier fragment (i.e. 'ilx_1234567'). However, each user will be able to 'fork' a term into their own namespace (e.g. http://uri.interlex.org/user/ilx_1234567). This enables the various perspectives on a term or concept to have equal space so that the full diversity of views on a term can be seen and expressed. Sign-up for updates to get notified about updates to InterLex and when new features are available. | terminology, lexicon, vocabulary |
is used by: SPARC Portal is related to: NeuroLex is related to: NIFSTD has parent organization: SciCrunch |
https://scicrunch.org/scicrunch/interlex/dashboard | SCR_016178 | 2026-09-12 12:58:36 | 6 | ||||||||||
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CATNAP Resource Report Resource Website 10+ mentions |
CATNAP (RRID:SCR_016170) | data analysis software, data processing software, software application, software resource | Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, analysis, | PMID:26044712 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016170 | CATNAP - Compile Analyze and Tally Neutralizing Antibody Panels | 2026-09-12 12:58:36 | 49 | |||||||||
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L1000 Fireworks Display Resource Report Resource Website 10+ mentions |
L1000 Fireworks Display (RRID:SCR_016175) | L1000FWD | data processing software, data visualization software, software application, software resource, web application | Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase. | drug, small molecule, gene, expression, signature, moa, clinical, phase | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | PMID:29420694 | Freely available, Free, Available for download | SCR_016175 | L1000FWD: Large-scale Visualization of Drug-Induced Transcriptomic Signatures | 2026-09-12 12:58:36 | 16 | |||||||
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ObservableHQ Resource Report Resource Website 1+ mentions |
ObservableHQ (RRID:SCR_016173) | application programming interface, data access protocol, software resource, web application | Web application for a code and text writing environment. It uses javascript and can be used to produce executable papers. | code, text, environment, writing, paper, research, journal, execute, programming, javascript | Open source, Freely available, Account required, Account required for full access | SCR_016173 | 2026-09-12 12:58:36 | 7 | |||||||||||
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Necklace Resource Report Resource Website 1+ mentions |
Necklace (RRID:SCR_016103) | alignment software, data processing software, image analysis software, software application, software resource | Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations. | RNA, Transcriptome, Non-model species, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:28836999 | Free, Available for download | biotools:necklace | https://bio.tools/necklace | SCR_016103 | Lace software | 2026-09-12 12:58:35 | 3 | ||||||
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Wave_clus Resource Report Resource Website 50+ mentions |
Wave_clus (RRID:SCR_016101) | algorithm resource, data analysis software, data processing software, software application, software resource | Algorithm for spike detection and sorting that uses wavelets and super-paramagnetic clustering. It generates an unsupervised solution, but this can be modified according to the experimenters’ preference for semi-automatic sorting. | spike, detection, wave, wavelet, magnetic, para-magnetic, solution, sorting, Automatic | requires: MATLAB | Free for non-commercial use, Available for download, Tutorial available | SCR_016101 | WaveClus, WaveClus spike-sorting algorithm | 2026-09-12 12:58:35 | 67 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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