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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Tissue Mapper Resource Report Resource Website 1+ mentions |
Tissue Mapper (RRID:SCR_017321) | 3d visualization software, data processing software, data visualization software, image analysis software, image reconstruction software, segmentation software, software application, software resource | Software for comprehensive annotation and delineation of tissue structures by MBF Bioscience. Creates 3D model from image data and annotates regions of interest from customizable ontology list. Map images acquired with brightfield, confocal, two-photon, widefield fluorescence, or light sheet microscopes. | MBF Bioscience, annotation, delineation, mapping, 3D model, image, data, tissue, structure | is used by: SPARC Portal | Restricted | SCR_017321 | Tissue MapperTM, Tissue Mapper | 2026-09-12 12:58:51 | 4 | |||||||||
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Relacs Resource Report Resource Website 1+ mentions |
Relacs (RRID:SCR_017280) | data acquisition software, data analysis software, data processing software, software application, software resource | Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings. | data, acquisition, analysis, electrophysiology, neuronal, response, control, stimulation | Free, Available for download, Freely available | SCR_017280 | Control, and Stimulation, Relaxed Electrophysiological Data Acquisition | 2026-09-12 12:58:51 | 2 | ||||||||||
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Vesselucida 360 Resource Report Resource Website 1+ mentions |
Vesselucida 360 (RRID:SCR_017320) | VL360 | 3d visualization software, data analysis software, data processing software, data visualization software, image analysis software, segmentation software, software application, software resource | Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience. | MBF Bioscience, vasculature, reconstruction, image, analysis, 3D, vessel, data, automatic, quantify, anastomoses, microvascular |
is used by: SPARC Portal works with: Vesselucida Explorer |
Restrcited | https://learn.mbfbioscience.com/vle.html | SCR_017320 | Vesselucida 360, Vesselucida | 2026-09-12 12:58:51 | 2 | |||||||
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BioWheel Resource Report Resource Website |
BioWheel (RRID:SCR_017441) | data processing software, data visualization software, software application, software resource | Software tool for interactive graphs of high dimensional data. Interactive cloud based software tool by DIBSVIS. | Interactive, graph, high, dimensional, data, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Restricted | SCR_017441 | , bio wheel, biowheel | 2026-09-12 12:58:53 | 0 | ||||||||
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NOVOPlasty Resource Report Resource Website 100+ mentions |
NOVOPlasty (RRID:SCR_017335) | alignment software, data processing software, image analysis software, software application, software resource | Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data. | de novo, assembler, heteroplasmy, variance, caller, short, circular, genome, organelle, whole, data | is listed by: OMICtools | Belgian Kids Fund ; Hôpital Universitaire des Enfants Reine Fabiola ; Interuniversity Institute of Bioinformatics in Brussels |
PMID:28204566 | Free, Available for download, Freely available | SCR_017335 | 2026-09-12 12:58:51 | 202 | ||||||||
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Silver Lab Microscopy Software Resource Report Resource Website 1+ mentions |
Silver Lab Microscopy Software (RRID:SCR_017456) | data acquisition software, data processing software, data visualization software, software application, software resource | Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system. | Imaging, visualising, electrophysiological, data, acousto, optic, lens, microscope, Silver Lab, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University College London; London; United Kingdom |
NINDS NS099689 | Free, Available for download, Freely available | http://silverlab.org/software-resources/ | SCR_017456 | 2026-09-12 12:58:53 | 2 | ||||||||
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Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | data or information resource, data processing software, software application, software resource | Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed. | Single, cell, RNA-seq, data, gene, list, build, index, organize |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | https://genat.uk/post/scfind/, http://bioconductor.org/packages/scfind/, https://github.com/hemberg-lab/scfind | SCR_017339 | 2026-09-12 12:58:51 | 1 | |||||||||
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MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | data analysis software, data processing software, software application, software resource | Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab. | post, process, magnetic, resonance, spectroscopy, data, analysis |
has parent organization: University of Minnesota Twin Cities; Minnesota; USA works with: MATLAB |
Restricted | SCR_017292 | Magnetic Resonance signal processing and analysis | 2026-09-12 12:58:51 | 19 | |||||||||
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Kinetic Models of Biological Systems (KiMoSys) Resource Report Resource Website 1+ mentions |
Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) | data access protocol, data repository, service resource, software resource, storage service resource, web service | Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community. | Quantitative, kinetic, model, biological, system, data, storage, search, exchange, experiment |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
EU ; Portuguese national funding agency for science ; research and technology. |
Restricted | r3d100011562 | https://doi.org/10.17616/R3864V | https://fairsharing.org/FAIRsharing.6erywc | SCR_017423 | , Kinetic Models of Biological Systems (KiMoSys), KInetic MOdels of biological SYStems, KiMoSys | 2026-09-12 12:58:52 | 1 | |||||
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Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | data analysis software, data processing software, data visualization software, software application, software resource | Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data. | Interactive, graphic, gene, expression, analysis, visualisation, RNAseq, data |
uses: LIMMA uses: edgeR uses: DESeq2 |
NHMRC ; Victorian State Government Operational Infrastructure Support and Australian Government ; Viertel Fellowship |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-09-12 12:58:52 | 23 | ||||||||
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HomoplasyFinder Resource Report Resource Website 1+ mentions |
HomoplasyFinder (RRID:SCR_017300) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R. | homoplasy, phylogeny, sequence, alignment, identify, data, annotate | Science Foundation Ireland | PMID:30663960 | Free, Available for download, Freely available | https://github.com/JosephCrispell/homoplasyFinder | SCR_017300 | 2026-09-12 12:58:51 | 6 | ||||||||
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The Decoding Toolbox Resource Report Resource Website 10+ mentions |
The Decoding Toolbox (RRID:SCR_017424) | TDT | data analysis software, data processing software, software application, software resource | Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data. | Multivariate, analysis, structural, MRI, data, functional, imaging, brain | German Ministry of Education and Research ; German Research Foundation |
PMID:25610393 | Free, Available for download, Freely available | SCR_017424 | 2026-09-12 12:58:52 | 16 | ||||||||
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Inorganic Crystal Structure Database (ICSD) Resource Report Resource Website 10+ mentions |
Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) | ICSD | data or information resource, data repository, database, service resource, storage service resource | Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research. | Inorganic, crystal, structure, data, atomic, coordinate, quality, FIZ Karlsruhe — Leibniz Institute for Information Infrastructure |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Restricted | r3d100010085 | http://www2.fiz-karlsruhe.de/icsd_home.html, https://doi.org/10.17616/R3GW2V | SCR_017429 | Inorganic Crystal Structure Database, Inorganic Crystal Structure Database (ICSD), ICSD | 2026-09-12 12:58:52 | 11 | ||||||
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SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data. | raw, data, PacBio, Sequel, analysis, sequence, DNA, read, length, plot | NSF Plant Genome Research Program IOS-1744001 | DOI:10.1101/611814 | Free, Freely available, Available for download | SCR_017279 | 2026-09-12 12:58:51 | 2 | |||||||||
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QtiPlot Resource Report Resource Website 10+ mentions |
QtiPlot (RRID:SCR_017311) | data analysis software, data processing software, software application, software resource | Software tool for data analysis and scientific visualization by IONDEV SRL. | data, analysis, visualization, IONDEV SRL | Restricted | SCR_017311 | 2026-09-12 12:58:51 | 30 | |||||||||||
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Human Neocortical Neurosolver Resource Report Resource Website 10+ mentions |
Human Neocortical Neurosolver (RRID:SCR_017437) | HNN | data analysis software, data processing software, simulation software, software application, software resource | Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data. | Neural, modeling, human, imaging, data, EEG, MEG, electrical, neocortical, cell, circuit, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Debian is listed by: bio.tools has parent organization: Brown University; Rhode Island; USA has parent organization: Yale University; Connecticut; USA has parent organization: Massachusetts General Hospital |
NIBIB R01 EB022889; NIDCD R01 DC012947 |
DOI:10.1101/740597 | Free, Available for download, Freely available | SCR_017678, biotools:HNN | https://github.com/jonescompneurolab/hnn, https://github.com/jonescompneurolab/hnn/tree/0.0.5, https://github.com/jonescompneurolab/hnn/tree/0.1.2, https://zenodo.org/record/2394296#.Xg4rCEdKiM9, https://bio.tools/HNN | SCR_017437 | 2026-09-12 12:58:52 | 13 | |||||
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4D Genome Resource Report Resource Website 10+ mentions |
4D Genome (RRID:SCR_017489) | data or information resource, data repository, database, service resource, storage service resource | Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community. | Repository, chromatic, interaction, data, genomic, region, gene, name, detection, technology, curated | has parent organization: University of Pennsylvania; Philadelphia; USA | Free, Available for download, Freely available | r3d100012282 | https://doi.org/10.17616/R3SH37 | SCR_017489 | 2026-09-12 12:58:53 | 11 | ||||||||
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National Twin Registry of Sri Lanka Resource Report Resource Website |
National Twin Registry of Sri Lanka (RRID:SCR_017481) | NTR | data or information resource, data repository, database, service resource, storage service resource | Independent academic and research institution to establish registration for twins in Sri Lanka , to facilitate study of twins. Center for twin, sibling, family and genetic studies for South Asian Region. | Registration, twin, data, repository, genetics, South Asian Region | Wellcome Trust UK | https://www.ird.lk/ | SCR_017481 | Sri Lankan Twin Registry | 2026-09-12 12:58:53 | 0 | ||||||||
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Virginia Commonwealth University Mid-Atlantic Twin Registry MATR Core Facility Resource Report Resource Website |
Virginia Commonwealth University Mid-Atlantic Twin Registry MATR Core Facility (RRID:SCR_017484) | access service resource, core facility, data or information resource, service resource | Core scientists collaborate with research teams from a variety of disciplines and institutions. MATR services include recruitment, data and sample collection, dataset curation and access, protocol development, cost estimates, grant development support, and IRB submissions. Twins and their families who are willing to consider taking part in twin-based, health-related research can participate. For twins of any age, ethnicity, and zygosity (identical or fraternal), as well as higher order multiples such as triplets, quadruplets and quintuplets. Most of twins registered in MATR are from Virginia, North Carolina, and South Carolina, but twins from all over the country and all around the world are welcome to register. MATR repository containing DNA samples provided by twins and allows to study twin data collected by studies along with their DNA. | ABRF, twin, data, repository, DNA, sample, Virginia Commonwealth University, |
is listed by: ABRF CoreMarketplace has parent organization: Virginia Commonwealth University; Virginia; USA |
Open | ABRF_5679 | https://https://coremarketplace.org/?FacilityID=5679&citation=1, https://matr.vcu.edu/ | SCR_017484 | , Mid-Atlantic Twin Registry (MATR), VCU Mid-Atlantic Twin Registry, Virginia Commonwealth University VCU Mid-Atlantic Twin Registry (MATR) | 2026-09-12 12:58:53 | 0 | |||||||
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Accessible Resource for Integrated Epigenomics Studies Resource Report Resource Website 50+ mentions |
Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) | data access protocol, data or information resource, portal, software resource, topical portal, web service | Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time. | Epigenomic, human, tissue, DNA, methylation, data, peripheral, blood | BBSRC ; Medical Research Council ; University of Bristol ; Wellcome Trust |
PMID:25991711 | Free, Freely available | http://www.bristol.ac.uk/alspac/ | SCR_017492 | ARIES | 2026-09-12 12:58:53 | 50 |
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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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