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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
Alien-hunter
 
Resource Report
Resource Website
1+ mentions
Alien-hunter (RRID:SCR_015967) software application, software resource, standalone software Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer. Horizontal Gene Transfer, Interpolated Variable Order Motifs, gene, transfer, interpolated, variable, motif, prediction, hgt, ivom is listed by: Debian
is listed by: OMICtools
works with: Artemis: Genome Browser and Annotation Tool
Wellcome Trust PMID:16837528
DOI:10.1093/bioinformatics/btl369
Free, Available for download OMICS_08280 https://sources.debian.org/src/alien-hunter/, https://sources.debian.org/src/alien-hunter/ SCR_015967 2026-09-03 05:05:02 6
FLIMfit
 
Resource Report
Resource Website
1+ mentions
FLIMfit (RRID:SCR_016298) software application, software resource, software toolkit Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. fluorescence, lifetime, imaging, microscopy, dataset, global, analysis, multiwell, plate, routine United Kingdom Biotechnology and Biological Sciences Research Council BBSRC BB/E003621/1;
United Kingdom Technology Strategy Board Technology Award CHBT/007/00030;
Wellcome Trust WT 095931/Z/11/Z
PMID:23940626
DOI:10.1371/journal.pone.0070687
THIS RESOURCE IS NO LONGER IN SERVICE https://github.com/flimfit/FLIMfit SCR_016298 2026-09-03 05:05:13 6
POAS4SPM
 
Resource Report
Resource Website
1+ mentions
POAS4SPM (RRID:SCR_010469) POAS4SPM software resource Software toolbox for SPM to denoise diffusion MRI data. Used for diffusion weighted magnetic resonance imaging data enhancement based on structural adaptive smoothing in both voxel space and diffusion-gradient space.Part of the ACID-toolbox. denoise diffusion MRI data, diffusion weighted, magnetic resonance imaging data, MRI data, is related to: ACID
works with: SPM
Deutsche Forschungsgemeinschaft ;
Wellcome Trust
PMID:24993814 nlx_157718 http://www.diffusiontools.com/ SCR_010469 Position Orientation Adaptive Smoothing for SPM 2026-09-03 04:50:29 9
NeuronVisio
 
Resource Report
Resource Website
1+ mentions
NeuronVisio (RRID:SCR_006839) Neuronvisio d visualization software A Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections'''' properties and it offers easy integration with matplotlib for plotting the results. The geometry can be saved using NeuroML and the computational results in a customized and extensible HDF5 format; the results can then be reload in the software and analyzed in a later stage, without re-running the simulation. Featuring 3D visualization of the model with the possibility to change it runtime; creation of vectors to record any variables present in the section; pylab integration to plot directly the result of the simulation; exploration of the timecourse of any variable among time using a color coded scale; saving the results simulation for later analysis; automatic download and running of models in ModelDB. 3d visualization, electrophysiological model, hdf storage, matplotlib integration, neuron model, visualization, neuron, visualization, electrophysiology is related to: INCF Software Center
is related to: NEURON
is related to: ModelDB
has parent organization: European Bioinformatics Institute
Wellcome Trust PMID:22685429 GNU General Public License, Acknowledgement requested nlx_156723 SCR_006839 Neuron visio 2026-09-03 04:48:50 3
Bio-tradis
 
Resource Report
Resource Website
50+ mentions
Bio-tradis (RRID:SCR_015993) TraDIS:Transposon Directed Insertion Sequencing data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Alexander von Humboldt Stiftung/Foundation ;
Medical Research Council G1100100/1;
Wellcome Trust WT098051
PMID:26794317
DOI:10.1093/bioinformatics/btw022
Free, Available for download, Freely available OMICS_11083, biotools:bio-tradis https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ SCR_015993 2026-09-03 04:53:18 56
SC3
 
Resource Report
Resource Website
10+ mentions
SC3 (RRID:SCR_015953) data analysis software, data processing software, sequence analysis software, software application, software resource Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients. scRNA-seq, interactive, cluster, clustering, cell, single, rna, rnaseq, bio.tools is listed by: Debian
is listed by: bio.tools
ARC (Action de Recherche Concerte) ;
Belgian Network DYSCO ;
Belgian State Science Policy Office ;
Bloodwise 13003;
Cambridge Experimental Cancer Medicine Centre ;
Cambridge NIHR Biomedical Research Center ;
EPSRC EP/N014529/1;
FRS-FNRS ;
Kay Kendall Leukaemia Fund ;
Leukemia and Lymphoma Society of America 07037;
MRC ;
Sanger Institute ;
University of Edinburgh ;
Wallonia-Brussels Federation ;
Wellcome Trust 104710/Z/14/Z
PMID:28346451 Free, Available for download biotools:sc3 https://bio.tools/sc3 SCR_015953 SC3 package, Single-Cell Consensus Clustering 2026-09-03 04:53:28 23
Stimfit
 
Resource Report
Resource Website
10+ mentions
Stimfit (RRID:SCR_016050) data analysis software, data processing software, software application, software resource Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy. electrophysiology, python, numpy, scipy, numerical, library, stimulus, analysis uses: NumPy
uses: SciPy
European Research Council ;
Gatsby Charitable Foundation ;
Wellcome Trust
PMID:24600389 Free, Available for download SCR_016050 2026-09-03 04:53:31 41
Clonalframe
 
Resource Report
Resource Website
100+ mentions
Clonalframe (RRID:SCR_016060) data analysis software, data processing software, sequence analysis software, software application, software resource Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome is listed by: Debian
is listed by: OMICtools
is related to: Imperial College London; London; United Kingdom
is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Wellcome Trust DOI:10.1534/genetics.106.063305 Free, Available for download OMICS_14623 https://github.com/xavierdidelot/ClonalFrameML, https://sources.debian.org/src/clonalframe/ SCR_016060 ClonalFrameML 2026-09-03 04:53:45 407
Gubbins
 
Resource Report
Resource Website
500+ mentions
Gubbins (RRID:SCR_016131) data analysis software, data processing software, sequence analysis software, software application, software resource Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment is listed by: Debian
is listed by: OMICtools
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Wellcome Trust 098051 PMID:25414349 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_14386 https://sources.debian.org/src/gubbins/ SCR_016131 Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences 2026-09-03 04:53:35 604
Brain Imaging Data Structure (BIDs)
 
Resource Report
Resource Website
100+ mentions
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) BIDS data or information resource, narrative resource, portal, 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
European Regional Development Fund ;
German federal state of Sachsen-Anhalt ;
International Neuroinformatics Coordinating Facility ;
Laura and John Arnold Foundation ;
Medical Research Council United Kingdom ;
NIAAA U01 AA021697;
NIGMS P20 GM103472;
NIMH Intramural Research Program ;
NSF 1429999;
Wellcome Trust
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 2026-09-03 04:53:35 235
Jpred
 
Resource Report
Resource Website
100+ mentions
Jpred (RRID:SCR_016504) data analysis software, data analytics software, data processing software, sequence analysis software, software application, software resource Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region Biotechnology and Biological Sciences Research Council ;
Wellcome Trust 106370Z14;
Wellcome Trust 355804783;
Wellcome Trust WT083481;
Wellcome Trust WT092340
DOI:10.1093/nar/gkn238 Free, Available for download, Freely available,Tutorial available SCR_016504 Jprotein secondary structure PREDiction 2026-09-03 04:53:40 133
SpydrPick
 
Resource Report
Resource Website
1+ mentions
SpydrPick (RRID:SCR_018176) data analysis software, data processing software, software application, software resource Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools is listed by: Debian
is listed by: bio.tools
COIN Center of Excellence ;
Academy of Finland ;
European Research Council ;
Wellcome Trust
PMID:31361894 Free, Available for download, Freely available biotools:SpydrPick https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick SCR_018176 2026-09-03 04:54:53 3
SuperDCA
 
Resource Report
Resource Website
1+ mentions
SuperDCA (RRID:SCR_018175) data analysis software, data processing software, software application, software resource Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis. Protein, sequence, alignment, analysis, genome, loci, epistasis Academy of Finland ;
European Research Council ;
Royal Society ;
Wellcome Trust
PMID:29813016 Free, Available for download, Freely available SCR_018175 Super Direct Coupling Analysis 2026-09-03 04:54:59 1
genomics resource for animal lectins
 
Resource Report
Resource Website
1+ mentions
genomics resource for animal lectins (RRID:SCR_018122) data or information resource, portal, topical portal Resource presents information about animal lectins involved in various sugar recognition processes. Genomic, animal lectin, sugar recognition process has parent organization: Imperial College London; London; United Kingdom BBSRC ;
Consortium for Functional Glycomics ;
Wellcome Trust
Free, Freely available SCR_018122 2026-09-03 04:54:57 3
mousebrain.org
 
Resource Report
Resource Website
50+ mentions
mousebrain.org (RRID:SCR_018356) atlas, data or information resource Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Atlas, brain cell, cell type, single cell RNA seq data, taxon, tissue, gene, marker, anatomical location, data has parent organization: Karolinska Institutet; Stockholm; Sweden Knut and Alice Wallenberg Foundation ;
Swedish Foundation for Strategic Research ;
Wellcome Trust ;
Swedish Research Council ;
European Research Council ;
Ollie and Elof Ericssons Foundation ;
Åke Wiberg Foundation
PMID:30096314 Free, Freely available SCR_018356 2026-09-03 04:55:01 64
EnteroBase
 
Resource Report
Resource Website
100+ mentions
EnteroBase (RRID:SCR_019019) data access protocol, data or information resource, database, software resource, web service Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
has parent organization: University of Warwick; Coventry; United Kingdom
Biotechnology and Biological Sciences Research Council ;
Wellcome Trust
Restricted biotools:Enterobase https://bio.tools/EnteroBase SCR_019019 2026-09-03 04:55:26 317
BoxPlotR
 
Resource Report
Resource Website
100+ mentions
BoxPlotR (RRID:SCR_015629) data processing software, data visualization software, software application, software resource, web application Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. Box plot generation, customized box plot, data, plot, analysis is listed by: SoftCite
is related to: PlotsOfData
is related to: vioplot
ERC ;
Genome Québec International Recruitment Award ;
Wellcome Trust ;
WTCCB
PMID:24481215 Free, Available for download, Freely available SCR_018327 https://github.com/VizWizard/BoxPlotR.shiny SCR_015629 2026-09-03 04:53:15 370
InterMine
 
Resource Report
Resource Website
10+ mentions
InterMine (RRID:SCR_001772) software resource An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data. mac os x, unix/linux, windows, java, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Cambridge; Cambridge; United Kingdom
Wellcome Trust PMID:24753429 Free, Freely available OMICS_03840, biotools:intermine https://github.com/intermine/intermine, https://bio.tools/intermine http://intermine.github.io/intermine.org/ SCR_001772 2026-09-03 04:44:55 25
Wellcome Trust Case Control Consortium
 
Resource Report
Resource Website
100+ mentions
Wellcome Trust Case Control Consortium (RRID:SCR_001973) WTCCC data or information resource Consortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in African populations. The same approach has been used to type 2,000 cases of tuberculosis (TB) and 2,000 cases of malaria, as well as 2,000 shared controls. As well as addressing diseases of major global significance, and extending WTCCC coverage into the area of infectious disease, the inclusion of samples of African origin has obvious benefits with respect to methodological aspects of genome-wide association analysis. Second, the WTCCC has, for four additional diseases (autoimmune thyroid disease, breast cancer, ankylosing spondylitis, multiple sclerosis), completed an analysis of 15,000 SNPs designed to represent a large proportion of the known non-synonymous coding SNPs across the genome. This analysis has been performed at the WTSI using a custom Infinium chip (Illumina). Data release The genotypic data of the control samples (1958 British Birth Cohort and UK Blood Service) and from seven diseases analyzed in the main study are now available to qualified researchers. Summary genotype statistics for these collections are available directly from the website. Access to the individual-level genotype data and summary genotype statistics is by application to the Consortium Data Access Committee (CDAC) and approval subject to a Data Access Agreement. WTCCC2: A further round of GWA studies were funded in April 2008. These include 15 WTCCC-collaborative studies and 12 independent studies be supported totaling approximately 120,000 samples. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC2 will perform genome-wide association studies in 13 disease conditions: Ankylosing spondylitis, Barrett's oesophagus and oesophageal adenocarcinoma, glaucoma, ischaemic stroke, multiple sclerosis, pre-eclampsia, Parkinson's disease, psychosis endophenotypes, psoriasis, schizophrenia, ulcerative colitis and visceral leishmaniasis. WTCCC2 will also investigate the genetics of reading and mathematics abilities in children and the pharmacogenomics of statin response. Over 60,000 samples will be analyzed using either the Affymetrix v6.0 chip or the Illumina 660K chip. The WTCCC2 will also genotype 3,000 controls each from the 1958 British Birth cohort and the UK Blood Service control group, and the 6,000 controls will be genotyped on both the Affymetrix v6.0 and Illumina 1.2M chips. WTCCC3: The Wellcome Trust has provided support for a further round of GWA studies in January 2009. These include 5 WTCCC-collaborative studies to be carried out in WTCCC3 and 5 independent studies, across a range of diseases. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC3 will perform genome-wide association studies in the following 4 disease conditions: primary biliary cirrhosis, anorexia nervosa, pre-eclampsia in UK subjects, and the interactions between donor and recipient DNA related to early and late renal transplant dysfunction. The WTCCC3 will also carry out a pilot in a study of the genetics of host control of HIV-1 infection. Over 40,000 samples will be analyzed using the Illumina 660K chip. The WTCCC3 will utilize the 6,000 control genotypes generated by the WTCCC2. gene, genomic, genetics, microarray, genome-wide association study, snp, genome-wide association, blood, dna, genotype, variation, genome, sequence variant, copy number variation, genetic variation, phenotype, disease is related to: Psychiatric Genomics Consortium
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Bipolar disorder, Coronary artery disease, Crohn's disease, Rheumatoid arthritis, Type 1 diabetes, Type 2 diabetes, Hypertension, Control, Multiple sclerosis, Breast cancer, Ankylosing spondylitis, Autoimmune thyroid disease, Malaria, Tuberculosis, Inflammatory bowel disease, Barrett's esophagus, Esophageal adenocarcinoma, Glaucoma, Ischemic stroke, Pre-eclampsia, Parkinson's disease, Psychosis endophenotypes, Psoriasis, Schizophrenia, Ulcerative colitis, Visceral leishmaniasis, Primary biliary cirrhosis, Anorexia nervosa, Human immunodeficiency virus, Renal transplant dysfunction, Diabetes Wellcome Trust ;
Bill and Melinda Gates Foundation ;
Wellcome Trust Sanger Institute; Hinxton; United Kingdom
PMID:17554300 Access to summary data and individual-level genotype data is available by application to the Wellcome Trust Case Control Consortium Data Access Committee. Access to data will be granted to qualified investigators for appropriate use. nif-0000-10551 SCR_001973 Wellcome Trust Case-Control Consortium (WTCCC) 2026-09-03 04:45:07 221
Virtual Fly Brain
 
Resource Report
Resource Website
10+ mentions
Virtual Fly Brain (RRID:SCR_004229) VFB atlas, data or information resource, expression, neurons An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain. Drosophila, brain, neurons, innervation patterns, gene expression, transgene expression, phenotypes, neuroanatomy, neurobiology uses: Drosophila Gross Anatomy Ontology
uses: Drosophila Development Ontology
is related to: FlyBase
is related to: Flycircuit
is related to: Janelia Research
has parent organization: University of Edinburgh; Scotland; United Kingdom
has parent organization: University of Cambridge; Cambridge; United Kingdom
has parent organization: European Bioinformatics Institute
Wellcome Trust PMID:22180411 nlx_143644 http://www.virtualflybrain.org/site/vfb_site/home.htm SCR_004229 VirtualFlyBrain.org, VFB, Virtual Fly Brain 2026-09-03 05:00:38 47

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