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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Pseudomonas Genome Database
 
Resource Report
Resource Website
100+ mentions
Pseudomonas Genome Database (RRID:SCR_006590) PseudoCAP data analysis service, data or information resource, database, service resource, production service resource, analysis service resource Database of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download. gene, genome, annotation, localization, prokaryote, pseudomonas aeruginosa, sequence, subcellular, cystic fibrosis, ortholog, annotation, dna sequence, intergenic dna, protein sequence, bio.tools, FASEB list is used by: NIF Data Federation
is listed by: Debian
is listed by: bio.tools
is related to: AmiGO
has parent organization: Simon Fraser University; British Columbia; Canada
has parent organization: University of British Columbia; British Columbia; Canada
Cystic Fibrosis Foundation Therapeutics Inc PMID:18978025 nif-0000-03369, r3d100012086, biotools:pseudomonas_genome_database https://bio.tools/pseudomonas_genome_database, https://doi.org/10.17616/R3935H SCR_006590 Pseudomonas Genome Database - Improving Disease Treatment Through Genome Research 2026-07-31 09:26:25 489
Variant Effect Predictor
 
Resource Report
Resource Website
1000+ mentions
Variant Effect Predictor (RRID:SCR_007931) VEP data analysis service, service resource, production service resource, software resource, analysis service resource Data analysis service to predict the functional consequences of known and unknown variants. perl, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Ensembl
biotools:ensembl_variant_effect_predictor https://bio.tools/ensembl_variant_effect_predictor SCR_007931 Ve!P 2026-07-31 09:26:36 1871
eTBlast
 
Resource Report
Resource Website
1+ mentions
eTBlast (RRID:SCR_008188) eTBlast narrative resource, data or information resource, database, service resource eTBLAST is a unique search engine for searching biomedical literature. Our service is very different from PubMed. While PubMed searches for keywords, our search engine lets you input an entire paragraph and returns MEDLINE abstracts that are similar to it. This is something like PubMed''s Related Articles feature, only better because it runs on your unique set of interests. For example, input the abstract of an unpublished paper or a grant proposal into our engine, and with the touch of a button you''ll be able to find every abstract in MEDLINE dealing with your topic. No more guessing whether your set of keywords has found all the right papers. No more sorting through hundreds of papers you don''t care about to find the handful you were looking for--our search engine does it for you. When most people use PubMed to search MEDLINE they pick one or two keywords to describe their topic, then browse through a long list of results. When they find a paper that looks interesting they click on its Related Articles, in hopes of finding more papers like that one. If they find another relevant paper, they explore it''s related articles--and so on. This process of culling long lists of documents by hand makes literature searching tedious and time consuming. We make it easier for you by providing better results the first time, and then allowing you to automatically combine the papers you care about for a second round. Our Iterate feature allows you to checkmark the abstracts you found interesting in the first round and combine them all to create a new query. It''s like rolling several Related Articles lists into one. * We sort our results by relevance, while PubMed sorts by date. * We save you the time and effort of creating a complicated query. * We let you iterate your search over several good papers to narrow your focus. * We provide you the full MEDLINE abstract in our results, and a link to the PubMed page. * We can send your results straight to your email so you never lose a reference or forget where you found it. * This absolutely free service is provided by the University of Texas Southwestern Medical Center. No registration necessary! biomedical, literature, medline interfaces, paper, publish, search engine, unpublished, journal, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: University of Texas Southwestern Medical Center; Texas; USA
has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA
Hudson Foundation ;
P.O'B. Montgomery Distinguished Chair
PMID:16926219 biotools:etblast, nif-0000-21148 https://bio.tools/etblast http://invention.swmed.edu/etblast/index.shtml SCR_008188 eTBLAST: a text-similarity based search engine 2026-07-31 09:26:43 4
tRNAscan-SE
 
Resource Report
Resource Website
1000+ mentions
tRNAscan-SE (RRID:SCR_008637) data analysis service, web application, service resource, production service resource, software resource, analysis service resource Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file). bio.tools, tRNA genes, genomic sequence is listed by: bio.tools
is listed by: Debian
is listed by: OMICtools
has parent organization: University of California at Santa Cruz; California; USA
PMID:15980563
PMID:9023104
DOI:10.1093/nar/25.5.0955
Free, Freely available SCR_010835, OMICS_00385, nif-0000-32031, biotools:trnascan-se https://bio.tools/trnascan-se, https://sources.debian.org/src/trnascan-se/ SCR_008637 Lowe Lab tRNAscan-SE 2026-07-31 09:26:41 2493
Network Analysis, Visualization and Graphing TORonto
 
Resource Report
Resource Website
50+ mentions
Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) NAViGaTOR data visualization software, software application, data processing software, d visualization software, software resource A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches. fly, algorithm, capacity, graphical, graphing, human, interaction, interactome, intersection, mouse, network, node, protein, proteomic, rat, worm, yeast, graphing application, 2d visualization, 3d visualization, visualization, biological network, protein-protein interaction, gene, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: University of Toronto; Ontario; Canada
Genome Canada ;
Ontario Genomics Institute ;
Canada Research Chair Program ;
Ontario Research Fund Research Excellence ;
Canada Foundation for Innovation 12301;
Canada Foundation for Innovation 203383
PMID:19837718 Freely-downloadable for academic and not-for-profit institutions nif-0000-25610, biotools:navigator https://bio.tools/navigator SCR_008373 NAViGaTOR - Network Analysis Visualization and Graphing TORonto, NAViGaTOR - Network Analysis Visualization & Graphing TORonto 2026-07-31 09:26:39 52
EMBOSS
 
Resource Report
Resource Website
1000+ mentions
EMBOSS (RRID:SCR_008493) EMBOSS software toolkit, data analysis software, software application, software resource, sequence analysis software, data processing software Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication. FASEB list is listed by: Debian
is listed by: OMICtools
is listed by: SoftCite
is related to: BioExtract
is related to: pepwheel
DOI:10.1016/S0168-9525(00)02024-2 Free, Freely available OMICS_21165, nif-0000-30488 https://sources.debian.org/src/emboss/ http://www.emboss.org SCR_008493 The European Molecular Biology Open Software Suite, European Molecular Biology Open Software Suite 2026-07-31 09:26:40 4543
Vienna RNA
 
Resource Report
Resource Website
100+ mentions
Vienna RNA (RRID:SCR_008550) software resource, data or information resource, database This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
is related to: ANNOgesic
has parent organization: University of Vienna; Vienna; Austria
DOI:10.1186/1748-7188-6-26 biotools:vienna_rna_package, nif-0000-31411, OMICS_09351 https://bio.tools/vienna_rna_package, https://sources.debian.org/src/vienna-rna/ SCR_008550 Vienna RNA 2026-07-31 09:26:50 404
GMAP
 
Resource Report
Resource Website
500+ mentions
GMAP (RRID:SCR_008992) GMAP image analysis software, alignment software, source code, software application, software resource, data processing software THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing. mrna, est sequence, expressed sequence tag, sequence, cdna sequence, genome, cdna, bio.tools is used by: deFuse
is listed by: Debian
is listed by: bio.tools
has parent organization: Genentech
PMID:15728110 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_15072, biotools:gmap, nlx_152505 https://bio.tools/gmap, https://sources.debian.org/src/gmap/ SCR_008992 2026-07-31 09:26:45 594
STEPS
 
Resource Report
Resource Website
100+ mentions
STEPS (RRID:SCR_008742) STEPS software resource, software application, simulation software STEPS is a package for exact stochastic simulation of reaction-diffusion systems in realistic, complex 3D geometries. Our core simulation algorithm is an efficient implementation of a variation on Gillespie''s SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. While it was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it is a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role. We have implemented STEPS as a set of Python modules, which means STEPS users can use Python scripts to control all aspects of setting up the model, generating a mesh, controlling the simulation and generating and analyzing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution. reaction-diffusion, stochastic, signaling, molecular, python, software, simulator, reaction kinetics, 3d diffusion, signaling pathway, scripting, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Okinawa Institute of Science and Technology
has parent organization: University of Antwerp; Antwerp; Belgium
GOA ;
UA Belgium ;
Human Frontier Science Program ;
Okinawa Institute of Science and Technology
biotools:steps, nlx_143852 https://bio.tools/steps http://steps.sourceforge.net/STEPS/Home.html SCR_008742 STochastic Engine For Pathway Simulation 2026-07-31 09:26:42 336
NetOGlyc
 
Resource Report
Resource Website
500+ mentions
NetOGlyc (RRID:SCR_009026) NetOGlyc data analysis service, service resource, software application, production service resource, software resource, analysis service resource Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins. neural network, predict, mucin, galnac, o-glycosylation site, protein, o-glycosylation, glycoprotein, o-glycoproteome, glycosite, proteome, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: CBS Prediction Servers
PMID:23584533 Acknowledgement requested nlx_153864, biotools:netoglyc https://bio.tools/netoglyc SCR_009026 NetOGlyc Server 2026-07-31 09:26:59 601
elastix
 
Resource Report
Resource Website
100+ mentions
elastix (RRID:SCR_009619) elastix image analysis software, software toolkit, software application, data processing software, registration software, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023. Software toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. A paper describing elastix contains more details: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, elastix: a toolbox for intensity based medical image registration,; IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. reusable library, analyze, c++, console (text based), domain independent, nifti, nrrd, os independent, philips par/rec, registration, resampling, spatial transformation, bio.tools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is listed by: bio.tools
is related to: Insight Segmentation and Registration Toolkit
has parent organization: Utrecht University; Utrecht; Netherlands
PMID:19923044 THIS RESOURCE IS NO LONGER IN SERVICE nlx_155845, biotools:elastix http://www.nitrc.org/projects/elastix, https://bio.tools/elastix, https://sources.debian.org/src/elastix/ SCR_009619 2026-07-31 09:26:48 167
BARS
 
Resource Report
Resource Website
10+ mentions
BARS (RRID:SCR_009123) BARS software resource, software application Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, genetic, genomic, r, linux, bio.tools is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
THIS RESOURCE IS NO LONGER IN SERVICE nlx_154204, biotools:bars, nlx_154228, SCR_009106 https://bio.tools/bars SCR_009123 Bayesian Adaptive Regression Splines 2026-07-31 09:26:45 39
IMGT-ONTOLOGY
 
Resource Report
Resource Website
IMGT-ONTOLOGY (RRID:SCR_010342) IMGT-ONTOLOGY ontology, controlled vocabulary, data or information resource Ontology for immunogenetics and immunoinformatics. Provides semantic specification of terms to be used in immunogenetics and immunoinformatics and manages related knowledge, thus allowing standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. Manages the knowledge through diverse facets relying on seven axioms, IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, LOCALIZATION, ORIENTATION and OBTENTION. These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGT, the international ImMunoGeneTics information system, has been built on IMGT-ONTOLOGY. The version 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION. owl, ontology, immunogenetics, immunoinformatics, terms semantic specification, bio.tools is listed by: BioPortal
is listed by: Debian
is listed by: bio.tools
has parent organization: IMGT - the international ImMunoGeneTics information system
Free, Freely available nlx_157436, biotools:IMGt-ONtOLOGY http://www.imgt.org/IMGTindex/ontology.php, https://bio.tools/IMGT-ONTOLOGY SCR_010342 2026-07-31 09:27:06 0
PSIPRED
 
Resource Report
Resource Website
1000+ mentions
PSIPRED (RRID:SCR_010246) data access protocol, service resource, production service resource, software resource, web service, analysis service resource Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences. Predict Secondary Structure, protein analysis, secondary structure prediction, protein sequence, sequence analysis, protein, analysis is listed by: Debian
is listed by: SoftCite
has parent organization: University College London; London; United Kingdom
Biotechnology and Biological Science Research Council ;
University College London
DOI:10.1093/nar/gkz297 Free, Freely available SCR_018546, nlx_156884 https://sources.debian.org/src/psipred/ SCR_010246 PSIPRED Protein Sequence Analysis Workbench, PSIPRED 4.0 2026-07-31 09:27:05 1688
Evex
 
Resource Report
Resource Website
10+ mentions
Evex (RRID:SCR_010509) data or information resource, text-mining software, database, software application, software resource EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature. gene, protein, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Ghent University; Ghent; Belgium
biotools:evex, nlx_158731 https://bio.tools/evex SCR_010509 2026-07-31 09:26:55 18
Cistrome
 
Resource Report
Resource Website
10+ mentions
Cistrome (RRID:SCR_000242) software resource, data access protocol, web service Web based integrative platform for transcriptional regulation studies. Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: Galaxy
has parent organization: Harvard University; Cambridge; United States
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ;
National Basic Research Program of China ;
NHGRI HG004069;
NIDDK DK074967;
NIDDK DK062434
PMID:21859476 Free, Freely available SCR_017663, biotools:cistrome, OMICS_02173 http://cistrome.org/ap/root, https://bio.tools/cistrome SCR_000242 Galaxy Cistrome 2026-07-31 09:24:52 16
nmrML
 
Resource Report
Resource Website
1+ mentions
nmrML (RRID:SCR_000467) nmrML data or information resource, markup language, narrative resource, standard specification, interchange format An open mark-up language for NMR data. nuclear magnetic resonance, bio.tools is listed by: bio.tools
is listed by: Debian
is parent organization of: nmrCV
nlx_157309, biotools:nmrml_converter https://bio.tools/nmrml_converter SCR_000467 2026-07-31 09:24:55 9
CovalentDock Cloud
 
Resource Report
Resource Website
CovalentDock Cloud (RRID:SCR_000126) CovalentDock Cloud software resource, data access protocol, web service THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor. protein ligand covalent docking, ligand, receptor, covalent linkage, data analysis service, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:23034731 THIS RESOURCE IS NO LONGER IN SERVICE covalentdock_cloud, OMICS_01597 https://bio.tools/covalentdock_cloud SCR_000126 2026-07-31 09:24:51 0
cn.FARMS
 
Resource Report
Resource Website
cn.FARMS (RRID:SCR_000289) cn.FARMS software toolkit, data analysis software, software application, data processing software, software resource Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff. copy number variation analysis, copy number variation, microarray, affymetrix, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:21486749 Free, Available for download, Freely available biotools:cn.farms, OMICS_02060 https://bio.tools/cn.farms SCR_000289 cn.farms - factor analysis for copy number estimation 2026-07-31 09:24:52 0
Dipy
 
Resource Report
Resource Website
10+ mentions
Dipy (RRID:SCR_000029) DIPY software toolkit, data analysis software, software application, data processing software, software resource Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data. MRI, magnetic resonance, diffusion data analysis, diffusion MRI data, diffusion MRI data analysis, is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
has parent organization: Neuroimaging in Python
has parent organization: University of Cambridge; Cambridge; United Kingdom
PMID:24600385 Free, Available for download, Freely available nlx_155745 https://sources.debian.org/src/python-dipy/, http://www.nitrc.org/projects/dipy, http://elef.soic.indiana.edu/, https://github.com/nipy/dipy_web, http://nipy.org/dipy/ SCR_000029 Diffusion Imaging In Python, NIPY Diffusion Imaging Analysis 2026-07-31 09:24:49 15

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