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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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REmAb Resource Report Resource Website |
REmAb (RRID:SCR_016239) | material analysis service, production service resource, analysis service resource, service resource, biomaterial analysis service | 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 | Antibody Sequencing Service | 2026-08-08 12:00:29 | 0 | ||||||||||
|
YAMP Resource Report Resource Website 1+ mentions |
YAMP (RRID:SCR_016236) | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 | YAMP: Yet Another Metagenomic Pipeline, Yet Another Metagenomic Pipeline (YAMP), Yet Another Metagenomic Pipeline | 2026-08-08 12:00:51 | 8 | ||||||||||
|
Gamgi Resource Report Resource Website |
Gamgi (RRID:SCR_016116) | GAMGI | software resource, software application, data analysis software, data visualization software, data processing software | 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 | GAMGI: General Atomistic Modelling Graphic Interface, General Atomistic Modelling Graphic Interface | 2026-08-08 12:00:49 | 0 | ||||||
|
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) | 2026-08-08 12:00:51 | 4 | |||||||||
|
LR Gapcloser Resource Report Resource Website 50+ mentions |
LR Gapcloser (RRID:SCR_016194) | image analysis software, software resource, software application, alignment software, data processing software | 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 | 2026-08-08 12:00:50 | 71 | ||||||||
|
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 | 2026-08-08 12:00:29 | 4 | ||||||||||
|
OpenEx Resource Report Resource Website 100+ mentions |
OpenEx (RRID:SCR_016230) | software toolkit, software resource, software application, data analysis software, data visualization software, data processing software | 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 | 2026-08-08 12:00:29 | 103 | |||||||||
|
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 | data or information resource, portal, organization portal, consortium | 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 DK104205; NIDDK UC4 DK104155; NIDDK UC4 DK104167; NIDDK UC4 DK104166; NIDDK UC4 DK104159; NIDDK UC4 DK104216; NIDDK UC4 DK108132; NIDDK UC4 DK108101; NIDDK UC4 DK108120; NIDDK UC4 DK116274; NIDDK UC4 DK116278; NIDDK UC4 DK116271 |
SCR_016198 | Consortium on Beta Cell Death and Survival (HIRN-CBDS) | 2026-08-08 12:00:50 | 0 | ||||||||
|
NIX Resource Report Resource Website 10+ mentions |
NIX (RRID:SCR_016196) | data storage software, software resource, software application, data processing software | 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 | 2026-08-08 12:00:29 | 13 | |||||
|
Dotter Resource Report Resource Website 50+ mentions |
Dotter (RRID:SCR_016080) | sequence analysis software, image analysis software, software resource, software application, data analysis software, alignment software, data visualization software, data processing software | Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences. | sequence, alignment, graphical, dot-matrix, program, comparison, two, detail |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Grant 098051; NHGRI U54 HG00455 |
PMID:26801397 | Free, Available for download | SCR_016080 | Seqtools Dotter | 2026-08-08 12:00:47 | 84 | |||||||
|
Brain Imaging Data Structure (BIDs) Resource Report Resource Website 100+ mentions |
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) | BIDS | data or information resource, portal, narrative resource, 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 | 2026-08-08 12:00:49 | 235 | |||||
|
Falcon Resource Report Resource Website 100+ mentions |
Falcon (RRID:SCR_016089) | image analysis software, software resource, software application, alignment software, data processing software | Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes. | fast, aligner, sequencing, diploid, genome, assembly, non-inbred, rearranged, heterozygous, single-molecule |
is listed by: Debian is listed by: OMICtools is related to: Howard Hughes Medical Institute |
National Science Foundation DBI-1350041; National Science Foundation IOS-1237880; National Science Foundation MCB 0929402; National Science Foundation MCB 1122246; Gordon and Betty Moore Foundation GBMF 3034; NHGRI R01 HG006677 |
PMID:27749838 | Free, Available for download, Freely available | OMICS_13514 | https://sources.debian.org/src/falcon/ | SCR_016089 | 2026-08-08 12:00:28 | 293 | ||||||
|
Gff2aplot Resource Report Resource Website |
Gff2aplot (RRID:SCR_016128) | software resource, software application, data visualization software, data processing software | 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 | 2026-08-08 12:00:49 | 0 | |||||||
|
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 | 2026-08-08 12:00:28 | 4 | ||||||||||||
|
Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:48 | 6 | ||||||
|
Singularity Hub Resource Report Resource Website 1+ mentions |
Singularity Hub (RRID:SCR_016248) | SHUB | data or information resource, web service, software resource, data access protocol, software application, software development tool, application programming interface, database | 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 | 2026-08-08 12:00:51 | 2 | ||||||
|
Exonerate Resource Report Resource Website 100+ mentions |
Exonerate (RRID:SCR_016088) | software toolkit, image analysis software, software resource, software application, alignment software, data processing software | Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, pairwise, comparison, dynamic, programming, heuristic, bio.tools |
is used by: ExonerateTransferAnnotation is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:15713233 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:exonerate | https://bio.tools/exonerate | SCR_016088 | 2026-08-08 12:00:48 | 376 | |||||||
|
MICtools Resource Report Resource Website 10+ mentions |
MICtools (RRID:SCR_016121) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:48 | 12 | ||||||||||
|
DOMALIGN Resource Report Resource Website |
DOMALIGN (RRID:SCR_016085) | image analysis software, software resource, software application, alignment software, data processing software | Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. | protein, domain, alignment, embassy, dhf, daf, fragment, redundancy, psi-blast | is listed by: Debian | Free, Available for download | https://sources.debian.org/src/embassy-domalign/ | SCR_016085 | Embassy-domalign | 2026-08-08 12:00:47 | 0 | ||||||||
|
nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | software toolkit, software resource, software application, data analysis software, data visualization software, data processing 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) | 2026-08-08 12:00:29 | 3 |
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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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