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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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3D DART Resource Report Resource Website 1+ mentions |
3D DART (RRID:SCR_017588) | software resource, web application, service resource | DNA structure modelling server. Web server for generating custom 3D structural models of DNA with control over local and global conformation. | Generating, custom, 3D, structural, model, DNA, conformation | EU ; Netherlands Organization for Scientific Research |
PMID:19417072 | Free, Freely available | SCR_017588 | 3DNA-Driven DNA Analysis and Rebuilding Tool | 2026-08-01 12:06:07 | 1 | ||||||||
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Ngmlr Resource Report Resource Website 10+ mentions |
Ngmlr (RRID:SCR_017620) | NGMLR | image analysis software, alignment software, software application, software resource, data processing software | Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection. | Long, read, mapper, align, PacBio, Oxford Nanopore, read, reference, genome, structural, variantion, detection, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Science Foundation ; NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:ngmlr | https://bio.tools/ngmlr | SCR_017620 | coNvex Gap-cost alignMent for Long Reads | 2026-08-01 12:05:51 | 31 | ||||
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cytoNet Resource Report Resource Website |
cytoNet (RRID:SCR_017465) | image analysis software, service resource, software application, data processing software, production service resource, software resource, analysis service resource | Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory. | Cell, population, microscopy, image, network, analysis, quantify, structure, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Free, Freely available | SCR_017465 | 2026-08-01 12:06:14 | 0 | |||||||||
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IMOTIONS: SMI RED500 Eye Tracker Resource Report Resource Website 1+ mentions |
IMOTIONS: SMI RED500 Eye Tracker (RRID:SCR_017586) | instrument resource | Screen based eye tracker that combines high-speed capabilities at 500 Hz. | Eye, tracker, screen, high, speed, capability, 500Hz | Restricted | SCR_017586 | 2026-08-01 12:06:07 | 1 | |||||||||||
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Analysis, Visualization, and Informatics Lab-space (AnVIL) Resource Report Resource Website 10+ mentions |
Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) | AnVIL | project portal, data or information resource, data repository, storage service resource, portal, service resource | Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces. | Dataset, NHGRI, program, NIH, initiative, funded, human, genomic, data, access, sharing, FAIR, analysis, workflow |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIH | Restricted | https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL | SCR_017469 | Visualization, and Informatics Lab-space, AnVIL, Analysis Visualization and Informatics Lab-space, Analysis | 2026-08-01 12:06:14 | 24 | ||||||
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Hemodialysis Pilot Studies Consortium Resource Report Resource Website |
Hemodialysis Pilot Studies Consortium (RRID:SCR_017468) | HDPSC | portal, consortium, data or information resource, organization portal | Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium. | Novel, therapy, reduce, morbidity, patient, maintenance, hemodialysis, data, coordinating, center | has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | NIH ; NIDDK |
SCR_017468 | 2026-08-01 12:06:05 | 0 | |||||||||
|
PatchDock Resource Report Resource Website 50+ mentions |
PatchDock (RRID:SCR_017589) | data access protocol, software application, software resource, web service, simulation software | Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles. | Molecular, docking, structure, prediction, protein, molecule, shape, complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Israel Science Foundation ; Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University ; Israeli Ministry of Science ; National Cancer Institute ; NIH |
PMID:15980490 | Free, Freely available | biotools:patchdock | https://bio.tools/patchdock | SCR_017589 | 2026-08-01 12:06:15 | 85 | ||||||
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Rayyan QCRI Resource Report Resource Website 50+ mentions |
Rayyan QCRI (RRID:SCR_017584) | software resource, software application, mobile app, web application | Software tool for screening papers for systematic reviews. Web and mobile app to help to expedite initial screening of abstracts and titles using process of semi automation while incorporating high level of usability. | Screening, paper, systematic, review, abstract, title, process, semi, automation | DOI:10.1186/s13643-016-0384-4 | SCR_017584 | 2026-08-01 12:06:15 | 83 | |||||||||||
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LAN toolbox Resource Report Resource Website 1+ mentions |
LAN toolbox (RRID:SCR_017629) | LANtoolbox | time-series analysis software, software toolkit, data analysis software, 1d time-series analysis software, software application, software resource, data processing software | Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB. | Neuroscientist, data, EEG, experimental, analysis, code, script | is related to: MATLAB | Free, Available for download, Freely available | SCR_017629 | Laboratory of Analysis in Neurosciences Toolbox, EEG Toolbox | 2026-08-01 12:05:52 | 2 | ||||||||
|
Italian Twin Registry Resource Report Resource Website |
Italian Twin Registry (RRID:SCR_017476) | topical portal, data or information resource, portal | Portal with information about twins in Italy. | Twins, Italy, data, registry | Free, Freely available | SCR_017476 | National Register of Twins | 2026-08-01 12:06:14 | 0 | ||||||||||
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Macquarie University; Sydney; Australia Resource Report Resource Website 1+ mentions |
Macquarie University; Sydney; Australia (RRID:SCR_017596) | topical portal, data or information resource, portal | Public research university based in Sydney, Australia, in suburb of Macquarie Park. Founded in 1964 by New South Wales Government, it was third university to be established in metropolitan area of Sydney. | SCR_017596 | 2026-08-01 12:06:08 | 4 | |||||||||||||
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mBT: mBrainTrain Smarting PRO 32 Resource Report Resource Website |
mBT: mBrainTrain Smarting PRO 32 (RRID:SCR_017634) | instrument resource | 24 channel mobile electroencephalographic recording system. Supports synchronization with other sensors and simultaneous multi amplifier streaming via labstreaming layer. Wearable device that features motion sensors so body and head movements can be detected. | EEG, electroencephalographic, recording, system, motion, sensor, body, head, movement, detect | Restricted | SCR_017634 | 2026-08-01 12:06:08 | 0 | |||||||||||
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BioAssay Express Resource Report Resource Website |
BioAssay Express (RRID:SCR_017594) | software resource, data access protocol, service resource, web service | Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations. | Annotating, bioassay, protocol, semantic, web, term, ontology | is listed by: OMICtools | NCATS R44 TR000185 | DOI:10.7717/peerj-cs.61 | Free, Freely available | https://github.com/cdd/bioassay-template | SCR_017594 | 2026-08-01 12:06:15 | 0 | |||||||
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Data Information System - DAISY Resource Report Resource Website 1+ mentions |
Data Information System - DAISY (RRID:SCR_017472) | DAISY | software resource, web application | Open source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement. | Map, data, flow, GDPR | Free, Available for download, Freely available | https://github.com/elixir-luxembourg/daisy | SCR_017472 | DAta Information SYstem | 2026-08-01 12:05:50 | 2 | ||||||||
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Biotite Resource Report Resource Website 1+ mentions |
Biotite (RRID:SCR_017593) | data visualization software, software toolkit, data analysis software, service resource, software application, software resource, data processing software | Software Python package bundling popular tasks in computational molecular biology, from sequence analysis to structural bioinformatics. Comprehensive library for computational molecular biology. Package features sequence and structure data analysis and editing functionality, support for common sequence and structure file formats, visualization capabilities, interfaces to external software (MSA software, BLAST, DSSP). Operating system(s): Windows, OS X, Linux. | works with: Entrez | DOI:10.1186/s12859-018-2367-z | Free, Available for download, Freely available | SCR_017593 | 2026-08-01 12:06:08 | 4 | ||||||||||
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Mediation Analysis of Causality under Confounding Resource Report Resource Website |
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) | MACC | data processing software, data analysis software, software application, software resource | Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. | Casual, mediation, analysis, confounding, correlated, error, data, hierarchical, structure, parameter, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: CRAN |
NIBIB EB022911 | Free, Available for downloads, Freely available | SCR_017442 | Mediation Analysis of Causality under Confounding, macc | 2026-08-01 12:06:05 | 0 | |||||||
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NEURON Resource Report Resource Website 100+ mentions |
NEURON (RRID:SCR_017449) | software resource, software application, simulation software | Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software. | Computational, neurophysiology, model, neuron, network, building, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: Yale University; Connecticut; USA |
NIBIB EB022903 | Free, Available for download, Freely available | https://github.com/neuronsimulator/nrn | SCR_017449 | 2026-08-01 12:06:05 | 241 | ||||||||
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Transcriptomics Explorer Resource Report Resource Website 50+ mentions |
Transcriptomics Explorer (RRID:SCR_017567) | data visualization software, data analysis software, service resource, software application, software resource, data processing software | Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus. | Visualize, analyze, transcriptomic, data, cell, type, mouse, human, Allen, database, multiple, cortical, area, cortex, hippocampus | works with: Allen Brain Atlas | Free, Freely available | https://celltypes.brain-map.org/rnaseq/human/cortex, https://celltypes.brain-map.org/rnaseq/mouse/cortex-and-hippocampus, | SCR_017567 | 2026-08-01 12:06:15 | 78 | |||||||||
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Willoughby–Hoye Python Scripts A-D Resource Report Resource Website 1+ mentions Issue |
Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) | data processing software, data analysis software, software application, software resource | Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889. | Python, NMR, script, caluclating, chemical, shift, data | NIA R01 AG039468 | PMID:24556787 PMID:31591889 |
Free, Freely available | SCR_017562 | 2026-08-01 12:06:07 | 1 | |||||||||
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swMath Resource Report Resource Website 1+ mentions |
swMath (RRID:SCR_017607) | software repository, data or information resource, database, software resource | Repository of math software. Information service for mathematical software. Provides access to database of information on mathematical software and includes systematic linking of software packages with relevant mathematical publications. Database for references on mathematical software. | Repository, math, infromation, service, publication, database | Leibniz Association | Free, Freely available | r3d100014573 | https://doi.org/10.17616/R31NJNQL | SCR_017607 | 2026-08-01 12:06:15 | 2 |
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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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