Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
NEURON Resource Report Resource Website 100+ mentions |
NEURON (RRID:SCR_017449) | simulation software, software application, software resource | 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 | SciCrunch Registry | 2026-10-10 12:40:05 | 244 | ||||||||
|
GraphClust2 Resource Report Resource Website 1+ mentions |
GraphClust2 (RRID:SCR_017286) | data analysis software, data processing software, software application, software resource, web application | Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function. | scalable, clustering, RNA, sequence, secondary, structure, function, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
German Federal Ministry of Education and Research ; German Research Foundation Collaborative Research Centre 992 Medical Epigenetics |
PMID:31808801 PMID:22689765 |
Free, Available for download, Freely available | biotools:GraphClust2 | https://bio.tools/GraphClust2 | SCR_017286 | SciCrunch Registry | GraphClust, GraphClust-2 | 2026-10-10 12:40:47 | 4 | |||||
|
redbiom Resource Report Resource Website 1+ mentions |
redbiom (RRID:SCR_017285) | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data. | microbiome, feature, identify, characterize, analysis, metadata, sample, data | PMID:31239397 | Free, Available for download, Freely available | SCR_017285 | SciCrunch Registry | 2026-10-10 12:40:01 | 5 | ||||||||||
|
Seizure-Waves Resource Report Resource Website |
Seizure-Waves (RRID:SCR_017455) | data analysis software, data processing software, software application, software resource | Analysis and modeling code for waves of seizure activity. | Analysis, modeling, wave, seizure, brain, activity, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1451384 | Free, Freely available | SCR_017455 | SciCrunch Registry | SeizureWaves, Seizure Waves, Seizure-Waves | 2026-10-10 12:40:03 | 0 | ||||||||
|
PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | data analysis software, data processing software, software application, software resource | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | SciCrunch Registry | 2026-10-10 12:40:06 | 15 | ||||||||
|
Excel Statistics Resource Report Resource Website 10+ mentions |
Excel Statistics (RRID:SCR_017294) | data analytics software, software application, software resource, software toolkit | Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu . | statistical, analysis, BellCurve, Excell | Restricted | SCR_017294 | SciCrunch Registry | 2026-10-10 12:40:05 | 29 | |||||||||||
|
SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | data acquisition software, data processing software, software application, software resource | Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. | automated, data, acquisition, tilt, image, capture, display, storage, microscope | NCRR RR00592; NIGMS P01 GM61306 |
PMID:16182563 | Restricted | SCR_017293 | SciCrunch Registry | 2026-10-10 12:40:47 | 228 | |||||||||
|
TWOSEX-MSChart Resource Report Resource Website 10+ mentions |
TWOSEX-MSChart (RRID:SCR_017298) | data analysis software, data processing software, software application, software resource | Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan. | life, table, analysis, development, cohort, population, animal, species, sex | Restricted | SCR_017298 | SciCrunch Registry | 2026-10-10 12:40:47 | 14 | |||||||||||
|
Proovread Resource Report Resource Website 10+ mentions |
Proovread (RRID:SCR_017331) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for PacBio hybrid error correction through iterative short read consensus. | PacBio, hybrid, error, correction, short, read, consensus, DNA, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BWA is related to: BLASR is related to: SHRiMP |
European Research Council | PMID:25015988 | Free, Available for download, Freely available | biotools:proovread | https://bio.tools/proovread | SCR_017331 | SciCrunch Registry | 2026-10-10 12:40:01 | 14 | ||||||
|
SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | analysis service resource, controlled vocabulary, data analysis service, data or information resource, ontology, production service resource, service resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | CERCA Program/Generalitat de Catalunya ; European Union ; German Federal Ministry of Education and Research ; NINDS NS36251; Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard |
PMID:31171447 | Free, Freely available | SCR_017330 | SciCrunch Registry | Synaptic Gene Ontologies | 2026-10-10 12:40:04 | 187 | |||||||
|
Protomo Resource Report Resource Website 1+ mentions |
Protomo (RRID:SCR_017296) | data processing software, image processing software, software application, software resource | Software tool for electron tomography and 3D image processing. Software package used in electron tomography for marker free alignment and 3D reconstruction of tilt series. Tomography software package distributed for linux operating system and developed by Hanspeter Winkler. | electron, tomography, 3D, image, processing | NIGMS GM30598; NIGMS GM64346 |
PMID:16973379 | Restricted | SCR_017296 | SciCrunch Registry | 2026-10-10 12:40:01 | 5 | |||||||||
|
TOMO3D Resource Report Resource Website 1+ mentions |
TOMO3D (RRID:SCR_017295) | data processing software, image analysis software, image reconstruction software, software application, software resource | Software tool for fast tomographic reconstruction on multicore computers. Used for electron tomography studies with increasing resolution needs. | tomographic, reconstruction, multicore, computer, electron, resoulion | ERDF | PMID:25528570 | Restricted | SCR_017295 | SciCrunch Registry | 2026-10-10 12:40:04 | 6 | |||||||||
|
Phangorn Resource Report Resource Website 10+ mentions |
Phangorn (RRID:SCR_017302) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks. | phylogenetic, tree, network, reconstruction, analysis, estimation, Maximum, Likelihood, Parsimony, distance, method, Hadamard conjugation |
is listed by: Debian is listed by: OMICtools is related to: CRAN |
Muséum National D Histoire Naturelle | DOI:10.1093/bioinformatics/btq706 | Free, Available for download, Freely available | OMICS_12497 | https://github.com/KlausVigo/phangorn, https://sources.debian.org/src/r-cran-phangorn/ | SCR_017302 | SciCrunch Registry | Phangorn R package | 2026-10-10 12:40:01 | 28 | |||||
|
STRENDA Resource Report Resource Website 1+ mentions |
STRENDA (RRID:SCR_017422) | STRENDA | data or information resource, data repository, database, service resource, storage service resource | Storage and search platform supported by Beilstein-Institut that incorporates STRENDA Guidelines. For authors who prepare manuscript containing functional enzymology data, STRENDA DB provides means to ensure that data sets are complete and valid before submitting them to journal. | Storage, Beilstein Institut, functional, enzymology, data, complition, validation, dataset, guideline, standard, reporting |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: re3data.org is listed by: FigShare |
Restricted | DOI:10.22011, DOI:10.17616/R3536N, DOI:10.25504/FAIRsharing.ekj9zx, r3d100012329 | http://www.strenda-db.org/, https://doi.org/10.17616/R3536N, https://doi.org/10.17616/r3536n, https://doi.org/10.22011/, https://dx.doi.org/10.22011/, https://fairsharing.org/10.25504/FAIRsharing.ekj9zx, https://doi.org/10.17616/R3536N | SCR_017422 | SciCrunch Registry | , Standards for Reporting Enzymology Data, Beilstein-Institut, STRENDA | 2026-10-10 12:40:05 | 3 | ||||||
|
Image Data Resource (IDR) Resource Report Resource Website 1+ mentions |
Image Data Resource (IDR) (RRID:SCR_017421) | IDR | data repository, service resource, storage service resource | Public repository of reference image datasets from published scientific studies. Platform for publishing, mining and integrating bioimaging data, following FAIR principles and Euro-BioImaging/ELIXIR imaging strategy using OMERO and Bio-Formats open source software built by Open Microscopy Environment. Deployed on OpenStack cloud running on EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super resolution microscopy, and digital pathology. | Repository, reference, image, published, annotated, dataset, FAIR |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Free, Available for download, Freely available | r3d100012435 | https://doi.org/10.17616/R3XR0R | SCR_017421 | SciCrunch Registry | Image Data Resource, IDR, Image Data Resource (IDR) | 2026-10-10 12:40:07 | 1 | ||||||
|
Suiplus: SSA-II sperm analysis system Resource Report Resource Website 1+ mentions |
Suiplus: SSA-II sperm analysis system (RRID:SCR_017387) | instrument resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 1, 2023. System developed under guidance of experts in reproduction and andrology from Andrological Branch of Chinese Medical Association and Research Institute of National Health Planning Commission. Designed according to standard of 5th edition of World Health Organization laboratory manual for examination and processing of human semen. | Reproduction, andrology, Chinese, medical, association, examination, processing, human, semen, Beijing Suijia Software Co., Ltd. | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017387 | SciCrunch Registry | 2026-10-10 12:40:07 | 1 | |||||||||||
|
SICAS Medical Image Repository Resource Report Resource Website 1+ mentions |
SICAS Medical Image Repository (RRID:SCR_017420) | data repository, service resource, storage service resource | Medical image repository to store medical research data. | Medical, image, repository, store, data |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Free, Freely available | r3d100011560 | https://doi.org/10.17616/R3HP8C | SCR_017420 | SciCrunch Registry | Medical Image Repository, SICAS, SICAS Medical Image Repository | 2026-10-10 12:40:48 | 5 | |||||||
|
TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019. | temporal, signal, clocklikeness, molecular, phylogeny, visualization, analysis, temporally, sampled, sequenced, data, identify, genetic, incongruent | is related to: BEAST | ERC Grant ; EU Seventh Framework Programme |
DOI:doi.org/10.1093/ve/vew007 | Restricted | http://tree.bio.ed.ac.uk/software/tempest/ | SCR_017304 | SciCrunch Registry | Path-O-Gen, tempest | 2026-10-10 12:40:47 | 166 | ||||||
|
European Variation Archive (EVA) Resource Report Resource Website 100+ mentions |
European Variation Archive (EVA) (RRID:SCR_017425) | EVA | data or information resource, data repository, database, service resource, storage service resource | Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser. | Collection, genetic, variation, data, chromosomal, location, dbSNP, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:eva | https://bio.tools/eva | SCR_017425 | SciCrunch Registry | EVA, European Variation Archive | 2026-10-10 12:40:08 | 107 | ||||||
|
University of Florida Department of Chemistry Nuclear Magnetic Resonance Core Facility Resource Report Resource Website |
University of Florida Department of Chemistry Nuclear Magnetic Resonance Core Facility (RRID:SCR_017382) | NMR Facility, UF NMR Facility | access service resource, core facility, degree granting program, postdoctoral program resource, service resource, training resource, training service resource, undergraduate program resource | Facility serves students and faculty of University of Florida, and researchers from industry who use facility instruments to check outcome of reactions or characterize compounds. Instruments include Inova 500 MHz magnet with 2 RF Channels, Inova 500 MHz magnet with 3 RF Channels, Mercury 300 MHz (m4n and m8n), Mercury 300 MHz Broadband, Agilent 600 MHZ Magnet, and several NMR probes. | Laboratory portal, Biochemistry, Chemistry, NMR, NMR instrument, NMR Imaging and Localized Spectroscopy, Nuclear Magnetic Resonance, University of Florida, National High Magnetic Field Laboratory | has parent organization: University of Florida; Florida; USA | Restricted | https://nmr.chem.ufl.edu/trainings/, https://nmr.chem.ufl.edu/safety/, https://nmr.chem.ufl.edu/nmr-policies/, | SCR_017382 | SciCrunch Registry | UF Department of Chemistry NMR Facility | 2026-10-10 12:40:02 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
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.
Email: info_at_ dknet.org
