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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ZFIN Protocol Wiki Resource Report Resource Website 1+ mentions |
ZFIN Protocol Wiki (RRID:SCR_013239) | data or information resource, experimental protocol, wiki, narrative resource | ZFIN Protocol Wiki is where zebrafish researchers can share experimental protocols and tips with the rest of the research community. Protocols are organized into sections corresponding to the chapters of The Zebrafish Book, 5th edition (4th edition on-line). Feel free to add new protocols to the appropriate section or add comments to any existing protocol. Sections * General Methods for Zebrafish Care * Breeding * Embryonic and Larval Culture * Imaging * Cellular Methods * Dissociated Cell Culture * Genetic Methods * Antisense Methods * Histological Methods * in situ Hybridization Techniques * Mapping * Transgenesis * Gene Cloning * DNA Analysis * RNA Analysis * Protein Analysis * Microarray * Recipes | has parent organization: Zebrafish Information Network (ZFIN) | nlx_25072 | SCR_013239 | ZFIN Protocols Wiki, ZFIN Protocol | 2026-08-11 09:42:36 | 3 | ||||||||||
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Mobyle@Pasteur Resource Report Resource Website 100+ mentions |
Mobyle@Pasteur (RRID:SCR_013089) | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | A portal for bioinformatics analyses, including the following: alignment assembly database display genetics hmm information nucleic phylogeny protein sequence structure | FASEB list | has parent organization: Pasteur Institute | nlx_156919 | SCR_013089 | Mobyle@Pasteur | 2026-08-11 09:42:35 | 203 | |||||||||
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GenomeRNAi Resource Report Resource Website 100+ mentions |
GenomeRNAi (RRID:SCR_013088) | service resource, data or information resource, storage service resource, database, data repository | GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome | drosophila genome, caenorhabditis elegans, caenorhabditis elegans genome, c. elegans, drosophila, drosophila cells, human genome, rnai |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases has parent organization: German Cancer Research Center |
nif-0000-02901, r3d100011089 | https://www.ncbi.nlm.nih.gov/gap | SCR_013088 | GenomeRNAi, Genome RNAi | 2026-08-11 09:42:41 | 385 | ||||||||
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NCCN Resource Report Resource Website 500+ mentions |
NCCN (RRID:SCR_012959) | data or information resource, topical portal, portal, disease-related portal | A not-for-profit alliance of 23 cancer centers devoted to patient care, research, and education, is dedicated to improving the quality, effectiveness, and efficiency of cancer care so that patients can live better lives. Through the leadership and expertise of clinical professionals at NCCN Member Institutions, NCCN develops resources that present valuable information to the numerous stakeholders in the health care delivery system. As the arbiter of cancer care, NCCN promotes the importance of continuous quality improvement and recognizes the significance of creating clinical practice guidelines appropriate for use by patients, clinicians, and other health care decision-makers. | nlx_156880 | SCR_012959 | National comprehensive cancer network | 2026-08-11 09:42:41 | 691 | |||||||||||
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minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | data analysis software, software application, software resource, data processing software, data visualization software | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi | SCR_012830 | 2026-08-11 09:42:41 | 417 | ||||||
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affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data analysis software, data processing software, software resource, software application | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-08-11 09:42:30 | 3073 | ||||
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BOOST Resource Report Resource Website 10+ mentions |
BOOST (RRID:SCR_013133) | BOOST | software application, data processing software, software resource, data analysis software | Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies. | gene, genetic, genomic, logistic regression model, gene-gene interactions | is listed by: Genetic Analysis Software | Free, Available for download | nlx_154249 | SCR_013133 | BOolean Operation based Screening and Testing | 2026-08-11 09:42:35 | 33 | |||||||
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AngioCalc Cerebral Aneurysm Calculator Resource Report Resource Website 10+ mentions |
AngioCalc Cerebral Aneurysm Calculator (RRID:SCR_012805) | AngioCalc | data management software, software resource, software application | Providing quality resources for the management of cerebral aneurysms and features an online calculator that calculates cerebral aneurysm volume and percent packing volume after coil embolization. The site also host an imaging Library with neuroanatomy and neurovascular images. | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155693 | SCR_012805 | AngioCalc Cerebral and Peripheral Aneurysm Calculator, AngioCalc Cerebral Aneurysm Calculator | 2026-08-11 09:42:33 | 12 | |||||||||
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USC Multimodal Connectivity Database Resource Report Resource Website 10+ mentions |
USC Multimodal Connectivity Database (RRID:SCR_012809) | UMCD | service resource, data or information resource, storage service resource, database, data repository | Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately. | fmri, dti, dsi, mri, eeg, meg, data set, image, computational hosting, connectivity, neuroimaging, data sharing, brain, rendering, diffusion-weighted mri, functional connectivity, graph theory, resting-state fmri, structural connectivity, image display, magnetic resonance, python, rendering, visualization, connectivity matrix, network, brain network, matrix, de-identified, male, female, apoe, child, adult |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: MGH-USC Human Connectome Project |
Normal, Lesioned, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Obsessive-Compulsive Disorder, BDD, APOE 4/4, APOE 3/4, APOE 3/3, Alzheimer's disease | NRSA ; NIH Blueprint for Neuroscience Research ; NIA F31AG035438-01; NIDA HHSN271200800035C |
PMID:23226127 PMID:20850551 |
The community can contribute to this resource, Some features require an account | nlx_83091 | http://www.nitrc.org/projects/umcd | http://jessebrown.webfactional.com/welcome/default/index | SCR_012809 | UCLA Connectivity Database, UCLA Multimodal Connectivity Database: Web-based brain network analysis and data sharing, UCLA Multimodal Connectivity Database | 2026-08-11 09:42:40 | 26 | ||
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edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | data analysis software, data processing software, software resource, software application | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
NHMRC 406657; Independent Research Institutes Infrastructure Support Scheme 361646; Victorian State Government OIS grant ; Melbourne International Research Scholarship ; Harris and IBS Honours scholarships |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-08-11 09:42:33 | 23868 | ||||
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TGD Resource Report Resource Website 10+ mentions |
TGD (RRID:SCR_012803) | TGD, TGD LOCUS, TGD REF | service resource, wiki, analysis service resource, data or information resource, database, narrative resource, data analysis service, production service resource | TGD Wiki is a user-updatable database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD Wiki provides information on the genome, genes, and proteins of Tetrahymena collected from the scientific literature, research community and many other resources. In order to keep the information in our database as current as possible, we will soon be inviting the members of the Tetrahymena community to add and update these annotations to reflect published research. TGD Wiki currently offers the following features: * Free, unrestricted read access to all available data * Sequence and annotation data for 24,725 genes (TIGR v.2008) * GBrowse genome browser with links to and from each gene page (TIGR v.2006) * BLAST searching of the TIGR gene models and genome sequence (TIGR v.2006) Tetrahymena Genome Database (TGD) Wiki began in 2004 at Stanford University using the schema and programs of its parent project, Saccharomyces Genome Database. TGD Wiki is now a collaboration between Bradley University, Stanford University, and Cornell University. As we begin TGD Wiki at its new home at Bradley University, the TGD Wiki database contains the following data from TGD: * Gene Names and Aliases * Gene Descriptions * Gene Ontology (GO) Annotations * Homologs (similar genes in selected organisms) * Protein Domains * Associated Literature * Paragraphs (longer, free-text descriptions of gene function, structure, and significance) * Coding and Protein Sequences We have updated the following fields to match the newest gene model sequences (TIGR v.2008): Coding and Protein Sequences, Protein Domains and Gene Descriptions. We will also be recalculating the GO Annotations (IEA evidence code) and Homologs as part of our effort to keep the annotations in TGD Wiki as current as possible. We will be relying on members of the Tetrahymena community to maintain high-quality, updated annotations in the remainder of the fields using our annotation interface. Also setting up new database superdb - for unpublished data Look at Ciliate.org for news on this and other new databases | ciliate | has parent organization: Bradley University; Illinois; USA | NIH | nlx_75432 | SCR_012803 | TGD REF, Tetrahymena Genome Database, TGD Wiki, TGD LOCUS, Tetrahymena Genome Database Wiki | 2026-08-11 09:42:30 | 14 | |||||||
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KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | service resource, topical portal, portal, analysis service resource, data or information resource, database, web service, software resource, data analysis service, production service resource, data access protocol | Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies. | model, pathway, functional hierarchy, module, cancer, disease, drug, drug classification, orthology, ortholog, genome, gene, protein, compound, classification, biochemical reaction, pathway, ligand, biosynthesis, pathway prediction, sequence, chemical structure, human, enzyme, database, molecular interaction, metabolism, metabolomics, cellular process, structure, drug development, reaction, cell |
is used by: NIF Data Federation is used by: Arabidopsis Reactome is used by: LIPID MAPS Proteome Database is used by: globaltest is used by: MitoMiner is used by: Database for Annotation Visualization and Integrated Discovery is used by: Biochemical Pathways Reaction Kinetics Database is used by: Ultimate Rough Aggregation of Metabolic Map is used by: GEMINI is used by: In vivo - In silico Metabolite Database is listed by: 3DVC is listed by: OMICtools is affiliated with: Kyoto Encyclopedia of Genes and Genomes Expression Database is related to: PathCase Pathways Database System is related to: ExplorEnz is related to: NCBI BioSystems Database is related to: Allen Institute Neurowiki is related to: eQuilibrator is related to: GeneTrail is related to: KegTools is related to: PRODORIC is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: METLIN is related to: Kidney and Urinary Pathway Knowledge Base is related to: DAVID is related to: ConsensusPathDB is related to: ENZYME is related to: FlyMine is related to: Babelomics is related to: SynSysNet is related to: Cotton EST Database is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: INMEX is related to: BioExtract is related to: ClueGO is related to: MalaCards is related to: TrED is related to: FunTree is related to: MOPED - Model Organism Protein Expression Database is related to: ProOpDB is related to: KOBAS is related to: GeneTerm Linker is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: GeneCodis is related to: FunNet - Transcriptional Networks Analysis is related to: LegumeIP is related to: Algal Functional Annotation Tool is related to: aGEM is related to: DINIES is related to: KEGG PATHWAY Database is related to: ShinyGO is related to: KEGGREST has parent organization: Kyoto University; Kyoto; Japan has parent organization: University of Tokyo; Tokyo; Japan is parent organization of: KegTools works with: DIANA-mirPath works with: MiMeDB |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:22700311 PMID:22130871 PMID:22080510 PMID:19880382 PMID:19172790 PMID:18428742 PMID:18287706 PMID:18077471 PMID:16381885 PMID:16014746 PMID:14681412 PMID:12539951 PMID:11752249 PMID:10928937 PMID:10592173 PMID:9847135 |
Restricted | nlx_31015, OMICS_01583, OMICS_03010, OMICS_01582, OMICS_03974, OMICS_05434, OMICS_05360 | http://www.genome.jp/kegg/ | SCR_012773 | KEGG - Kyoto Encyclopedia of Genes and Genomes, Kyoto Encyclopedia of Genes and Genomes | 2026-08-11 09:42:30 | 81488 | ||||
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Abcam Resource Report Resource Website 10000+ mentions |
Abcam (RRID:SCR_012931) | antibody supplier, reagent supplier, commercial organization, material resource | A commercial antibody supplier which supplies primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits. | antibody supplier, rabmabs, epitomics, immunoassay, primary antibody, secondary antibody |
is affiliated with: MitoScience is parent organization of: Epitomics |
Available to the research community | nlx_152244 | SCR_012931 | 2026-08-11 09:42:41 | 124463 | |||||||||
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Expectation-Maximization Segmentation Resource Report Resource Website 1+ mentions |
Expectation-Maximization Segmentation (RRID:SCR_013228) | software application, data processing software, software resource, data visualization software | EMS is a freely available suite of Matlab functions and subroutines (with some externally compiled C routines) for fully-automated multi-spectral classification of brain tissues in Magnetic Resonance (MR) images. It uses a model based approach (including an explicit model for MR bias fields) in which all the model parameters are automatically estimated for each individual scan. This enables it to process large amounts of data from normal subjects and subjects suffering from Multiple Sclerosis without need for user intervention or preceeding manual training phase. | nif-0000-00295 | SCR_013228 | EMS | 2026-08-11 09:42:42 | 1 | |||||||||||
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IMGT - the international ImMunoGeneTics information system Resource Report Resource Website 500+ mentions |
IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) | IMGT | service resource, topical portal, portal, analysis service resource, data or information resource, database, data analysis service, production service resource | A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. | immunogenetics, immunoinformatics, immunoglobulin, antibody, t cell receptor, major histocompatibility complex, immunoglobulin superfamily, major histocompatibility complex superfamily, protein, immune system, sequence, genome, structure, monoclonal antibody, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IMGT Repertoire has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: IMGT/LIGM-DB is parent organization of: IMGT/GENE-DB is parent organization of: IMGT-ONTOLOGY is parent organization of: IMGT/V-QUEST is parent organization of: IMGT/HLA |
CNRS ; MESR ; Reseau National des Genopoles ; Region Languedoc-Roussillon ; European Union BIOMED1 BIOCT930038; European Union Biotechnology BIOTECH2 BIO4CT960037; European Union 5th PCRDT Quality of Life and Management of Living Resources QLG2-2000-01287; Agence Nationale de la recherche ANR BIOSYS06_135457; EU ImmunoGrid IST-028069 |
PMID:18978023 | nif-0000-03011, biotools:imgt | https://bio.tools/imgt | http://imgt.cines.fr | SCR_012780 | ImMunoGeneTics Information System, IMGT/LIGM, ImMunoGeneTics | 2026-08-11 09:42:33 | 779 | ||||
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Lab Vision Resource Report Resource Website 1+ mentions |
Lab Vision (RRID:SCR_013436) | antibody supplier, reagent supplier, commercial organization, material resource | An Antibody supplier | nlx_152395 | SCR_013436 | 2026-08-11 09:42:36 | 4 | ||||||||||||
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AngioBio Resource Report Resource Website 10+ mentions |
AngioBio (RRID:SCR_013556) | antibody supplier, reagent supplier, commercial organization, material resource | An Antibody supplier | nlx_152271 | SCR_013556 | 2026-08-11 09:42:43 | 28 | ||||||||||||
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B-Bridge International Resource Report Resource Website 1+ mentions |
B-Bridge International (RRID:SCR_013559) | antibody supplier, reagent supplier, commercial organization, material resource | An Antibody supplier | nlx_152289 | SCR_013559 | B-Bridge International Inc., B-Bridge International Inc | 2026-08-11 09:42:39 | 2 | |||||||||||
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Aviva Systems Biology Resource Report Resource Website 1+ mentions |
Aviva Systems Biology (RRID:SCR_013560) | antibody supplier, reagent supplier, commercial organization, material resource | An Antibody supplier | nlx_152288 | SCR_013560 | 2026-08-11 09:42:37 | 4 | ||||||||||||
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L2L Microarray Analysis Tool Resource Report Resource Website 1+ mentions |
L2L Microarray Analysis Tool (RRID:SCR_013440) | L2L | service resource, data analysis software, software application, data repository, analysis service resource, data or information resource, storage service resource, database, software resource, data analysis service, production service resource, data processing software |
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019. Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible |
microarray, gene expression, adipogenesis, biological, biological process, cancer, cell cycle regulator, cellular component, chromatin, cockayne syndrome, dna damage, growth factor, hormone, human biology, hypoxic response, immune mediator, inflammatory mediator, molecular function, molecular neuroanatomy resource, adipocyte, development, hypoxia, immune, inflammation, metabolism, mitogen, neuro, rna, vascular, transcription, tissue, splicing, mouse, human, rat, source code, statistical analysis, gene, chromatin structure |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Washington; Seattle; USA |
Cockayne syndrome, DNA damage, Other, Aging, Cancer | Cora May Poncin Foundation ; NIGMS GM41624 |
PMID:16168088 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10463 | http://depts.washington.edu/l2l/about.html | SCR_013440 | L2L Microarray Database, L2L Microarray Analysis Tool: A simple tool for discovering the hidden biological significance in microarray expression data, L2L MDB | 2026-08-11 09:42:42 | 1 |
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