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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Genomatix Software: Understanding Gene Regulation Resource Report Resource Website 500+ mentions |
Genomatix Software: Understanding Gene Regulation (RRID:SCR_008036) | data processing software, short course material, portal, data or information resource, data analysis software, software application, software resource, narrative resource, training material, topical portal, database | Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc. | effect, expression, functional, gene, genome, alignment, analysis, annotation, biological, cascade, cell, data, dna, in-silico analysis, mechanism, metabolic pathway, microarray, mining, molecular, network, pathway, promoter, protein, region, regulation, scientific, sequence, signaling, software, stimulus, systems biology, technology, text mining, transcription, FASEB list | has parent organization: Genomatix Solutions | nif-0000-10236 | http://www.genomatix.de/products/index.html | SCR_008036 | Genomatix | 2026-02-14 02:01:37 | 868 | ||||||||
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AraCyc Resource Report Resource Website 50+ mentions |
AraCyc (RRID:SCR_008109) | data repository, storage service resource, data or information resource, service resource, database | Curated species-specific database present at the Plant Metabolic Network. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways. | enzyme, gene, arabidopsis thaliana, biochemical, pathway, reaction, metabolism, metabolic pathway, data set, data analysis service, web service, FASEB list |
is used by: Arabidopsis Reactome is listed by: 3DVC has parent organization: Plant Metabolic Network |
NSF | PMID:12805578 PMID:15888675 |
The community can contribute to this resource | nif-0000-20811 | http://www.arabidopsis.org/biocyc/index.jsp http://www.plantcyc.org |
SCR_008109 | Arabidopsis enzymes and biochemical pathways database | 2026-02-14 02:01:29 | 69 | |||||
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Department of Psychiatry, Turner Laboratory Resource Report Resource Website |
Department of Psychiatry, Turner Laboratory (RRID:SCR_008067) | Turner Lab | laboratory portal, data or information resource, organization portal, portal | Dr. Eric Turner''s laboratory studies the mechanisms underlying the development of the nervous system. The vertebrate brain is comprised of a tremendous variety of neurons, each class exhibiting a unique phenotype characterized by the expression of specific neurotransmitter receptors, ion channels, patterns of axonal growth, and synapse formation. The research we conduct focuses on the critical role transcription factors play in the specification of neuronal cell type during development. We are particularly interested in transcription factors of the homeodomain family that bind to DNA and in doing so activate or repress gene expression. One area of study is the role of POU-domain transciption factor Brn3a in axon growth and survival. The primary research areas are: * Neuronal cell fate determination: The expression of regulatory genes is manipulated in living chick embryos using microsurgery and electroporation and the effects on neural marker genes studied. * Molecular mechanisms of gene regulation: Target DNA binding sites of neural transcription factors are biochemically characterized and findings coordinated with sequence data from the mouse and human genomes. * Targeted misexpression of regulatory genes: Transgenic and knockout mouse technology is used to misexpress genes of interest, and the effects on neural marker genes, axonal growth, and cell survival studied. * Global analysis of neural gene expression: Micro-arrays (GeneChips) are employed in conjunction with other areas of study to understand the coordinated regulation of gene expression in the nervous system. Dr. Turner is a member of the University of California, San Diego''s Graduate Program in Neuroscience and Biomedical Sciences Program and accepts students from these two programs. Interesting rotation projects are available using methods ranging from biochemistry and molecular biology to embryology. Additionally, Dr. Turner is also the Director of this NIMH-funded training program for research-oriented psychiatrists, psychologists, and basic neuroscientists working in areas relevant to psychiatry. Typically Fellows spend two years in the program, during which they develop a research project under the close supervision of one of the highly productive members of the UCSD Department of Psychiatry, or another investigator in the La Jolla (UCSD/Salk/Scripps) research community. | electroporation, embryo, embryology, expression, gene, axon, biochemistry, biomedical science, cell, c hick, development, dna, dna binding site, homeodomain, human, knockout technology, microarray, microsurgery, misexpression, molecular biology, molecular mechanism, mouse, nervous system, neural gene, neural marker gene, neural transcription factor, neuronal cell, neuroscience, neuroscientist, psychiatrist, psychologist, regulation, regulatory gene, transcription factor, transgenic technology | has parent organization: University of California at San Diego Department of Psychiatry | nif-0000-10507 | SCR_008067 | UCSD Turner Laboratory, UCSD Psychiatry (Turner''s Lab), Turner Laboratory, Turner Laboratory Developmental Neurobiology Research | 2026-02-14 02:01:37 | 0 | ||||||||
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GeneWindow Resource Report Resource Website 1+ mentions |
GeneWindow (RRID:SCR_008183) | data analysis software, software resource, data processing software, software application | Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible | gene, genetic, analysis, annotation, archive, bioinformatic, cancer, genome, genomic, genotype, genotyping, human, human genome databases, maps, polymorphism, position, variation, data set |
is listed by: 3DVC has parent organization: National Cancer Institute |
nif-0000-21173 | SCR_008183 | GeneWindow | 2026-02-14 02:01:37 | 1 | |||||||||
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RIKEN Omics Science Center Resource Report Resource Website |
RIKEN Omics Science Center (RRID:SCR_008241) | portal, data or information resource, research forum portal, disease-related portal, topical portal | Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level. | expression, gene, genome, human, intracellular, life, living, model organisms and comparative genomics databases, molecule, omics, organism, pathway, protein, proteome, science, sequence, technology, transcriptome | is parent organization of: FANTOM DB | RIKEN Yokohama Institute Yokohama Research Promotion Division of Japan | nif-0000-21361 | SCR_008241 | RIKEN OSC | 2026-02-14 02:01:39 | 0 | ||||||||
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repairGenes Resource Report Resource Website 1+ mentions |
repairGenes (RRID:SCR_008240) | data or information resource, portal, topical portal | The aim of the repairGenes site is to be a source of information about DNA repair genes and a useful resource for research on DNA repair. At the moment, the site contains information about a number of DNA repair genes from a set of selected species. The information is organized by organism and by biological process term as defined by the Gene Ontology (GO) project. The coverage of DNA repair genes is not complete, but hopefully it satisfies to demonstrate the concept and generate ideas for future versions of the system. At present, the raw data about DNA repair genes is extracted from the SWISS-PROT database, and categorized using the GO system. SWISS-PROT entries are being annotated by the Gene Ontology Annotation project at EBI. GOA is an ongoing project which will become more complete with time. As more data is released, this will be fed into repairGenes to keep it up-to-date. In future versions, the user will be able to search freely among organisms and categories of repair genes, enabling easy comparisons between species. For a taste of this, please have a look at the overview of repair genes from five major organisms. The amount of information in the system will be increased and the quality will be improved in the future. So will the features of the system. | gene, gene-, biological, dna, or disease- specific databases, organism, repair, specie, system- | has parent organization: University of Oslo; Oslo; Norway | nif-0000-21359 | SCR_008240 | repairGenes | 2026-02-14 02:01:35 | 1 | |||||||||
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DiseaseMeth Resource Report Resource Website 10+ mentions |
DiseaseMeth (RRID:SCR_005942) | data repository, storage service resource, data or information resource, service resource, database | Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. | disease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylome, bio.tools |
is listed by: 3DVC is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Harbin Medical University; Heilongjiang; China |
National Natural Science Foundation of China ; Natural Science Foundation of Heilongjiang Province ; State Key Laboratory of Urban Water Resource and Environment ; Scientific Research Fund of Heilongjiang Provincial Education Department |
PMID:22135302 PMID:27899673 |
Free,Freely available | OMICS_01838, nlx_151289, biotools:diseasemeth, SCR_017488 | http://bioinfo.hrbmu.edu.cn/diseasemeth https://bio.tools/diseasemeth |
http://202.97.205.78/diseasemeth/ | SCR_005942 | , Disease Meth-The Human Disease Methylation Database, DiseaseMeth database, DiseaseMeth version 2.0 | 2026-02-14 02:01:12 | 34 | ||||
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DistiLD - Diseases and Traits in LD Resource Report Resource Website 1+ mentions |
DistiLD - Diseases and Traits in LD (RRID:SCR_005943) | DistiLD | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database performs three important tasks: # published GWAS are collected from several sources and linked to standardized, international disease codes ICD10 codes) # data from the International HapMap Project are analyzed to define linkage disequilibrium (LD) blocks onto which SNPs and genes are mapped # the web interface makes it easy to query and visualize disease-associated SNPs and genes within LD blocks. Users can query the database by diseases, SNPs or genes. No matter which of the three query modes was used, an intermediate page will be shown listing all the studies that matched the search with a link to the corresponding publication. The user can select either all studies related to a certain disease or one specific study for which to view the related LD blocks. The DistiLD resource integrates information on: * Associations between Single Nucleotide Polymorphisms (SNPs) and diseases from genome-wide association studies (GWAS) * Links between SNPs and genes based on linkage disequilibrium (LD) data from HapMap For convenience, we provide the complete datasets as two (zipped) tab-delimited files. The first file contains GWAS results mapped to LD blocks. The second file contains all SNPs and genes assigned to each LD block. | disease, mutation, gene, linkage disequilibrium, trait, genome-wide association study, single nucleotide polymorphism, chromosomal region, chromosome, linkage disequilibrium block, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: International HapMap Project has parent organization: University of Copenhagen; Copenhagen; Denmark |
Novo Nordisk Foundation Center for Protein Research | PMID:22058129 | Files are published under the Creative Commons Attribution v3 License | biotools:distild, nlx_151291 | https://bio.tools/distild | SCR_005943 | DistiLD - Diseases & Traits in LD, Diseases and Traits In Linkage Disequilibrium blocks, Diseases and Traits In Linkage Disequilibrium, DistiLD Database, DistiLD - Diseases Traits in LD | 2026-02-14 02:01:00 | 5 | ||||
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NEMBASE Resource Report Resource Website 10+ mentions |
NEMBASE (RRID:SCR_006070) | NEMBASE | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets. | nematode, transcriptome, expressed sequence tag, protein, cluster, library, sequence, peptide prediction, functional annotation, gene family, gene, annotation, pathway, genome, partigene, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: nematodes.org |
Wellcome Trust ; Hospital for Sick Children ; BBSRC ; MRC ; NERC |
PMID:21550347 PMID:14681449 |
Public | nlx_151476, biotools:nembase4 | https://bio.tools/nembase4 | SCR_006070 | NEMBASE4, NEMBASE4 - Nematode Transcriptome Analyses | 2026-02-14 02:01:04 | 25 | ||||
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VBRC Resource Report Resource Website 10+ mentions |
VBRC (RRID:SCR_005971) | VBRC | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | One of eight Bioinformatics Resource Centers nationwide providing comprehensive web-based genomics resources including a relational database and web application supporting data storage, annotation, analysis, and information exchange to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. These centers serve the scientific community and conduct basic and applied research on microorganisms selected from the NIH/NIAID Category A, B, and C priority pathogens that are regarded as possible bioterrorist threats or as emerging or re-emerging infectious diseases. The VBRC provides a variety of analytical and visualization tools to aid in the understanding of the available data, including tools for genome annotation, comparative analysis, whole genome alignments, and phylogenetic analysis. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. | virus, arenaviridae, bunyaviridae, filoviridae, flaviviridae, paramyxoviridae, poxviridae, togaviridae, blast, ortholog, variation, sequence analysis, genome, gene, epidemiology, bioinformatics resource center, phenotype, pathogenesis, pathogen, annotation, genomics |
has parent organization: University of Alabama at Birmingham; Alabama; USA has parent organization: University of Victoria; British Columbia; Canada is parent organization of: Hepatitis C Virus Database (HCVdb) |
NIAID contract HHSN266200400036C | r3d100012088, nif-0000-03632 | https://doi.org/10.17616/R31M1P | SCR_005971 | Viral Bioinformatics Resource Center | 2026-02-14 02:01:12 | 18 | ||||||
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HFV Database Resource Report Resource Website 1+ mentions |
HFV Database (RRID:SCR_006017) | HFV Database | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | The Hemorrhagic Fever Viruses (HFV) sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. | gene, hemorrhagic fever virus, biothreat, virus, sequence, nucleotide sequence, reference sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: RefSeq has parent organization: HIV Databases |
United States Department of Defense contract HDTRA B084498I | PMID:22064861 | biotools:hfv, nlx_151408 | https://bio.tools/hfv | SCR_006017 | HFV Sequence Database, Hemorrhagic Fever Viruses Database, Hemorrhagic Fever Viruses (HFV) Database, LANL hemorrhagic fever virus database, Hemorrhagic Fever Viruses (HFV) Database Project | 2026-02-14 02:01:13 | 1 | |||||
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GWASdb Resource Report Resource Website 10+ mentions |
GWASdb (RRID:SCR_006015) | GWASdb | web service, data or information resource, data access protocol, software resource, database | Combines collections of genetic variants (GVs) from GWAS and their comprehensive functional annotations, as well as disease classifications. Used to maximize utilility of GWAS data to gain biological insights through integrative, multi-dimensional functional annotation portal. In addition to all GVs annotated in NHGRI GWAS Catalog, we manually curate GVs that are marginally significant (P value < 10-3) by looking into supplementary materials of each original publication and provide extensive functional annotations for these GVs. GVs are manually classified by diseases according to Disease Ontology Lite and HPO (Human Phenotype Ontology) for easy access. Database can also conduct gene based pathway enrichment and PPI network association analysis for those diseases with sufficient variants. SOAP services are available. You may Download GWASdb SNP. (This file contains all of the significant SNP in GWASdb. In the pvalue column, 0 means this P-value is not reported in the study but it is significant SNP. In the source column, GWAS:A represents the original data in GWAS catalog, while GWAS:B is our curation data which P-value < 10-3) | genetic variant, genome-wide association study, functional annotation, disease classification, snp, gene, chromosome region, annotation, pathway, protein-protein interaction, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: GWASrap is related to: Human Phenotype Ontology is related to: IKMB GWAS Association Testing Pipeline is related to: GWAS Quality Control Pipeline is related to: Human Disease Ontology |
University of Hong Kong Small Project Fund 201007176262; Research Grants Council of Hong Kong 781511M; Research Grants Council of Hong Kong 778609M; Research Grants Council of Hong Kong N_HKU752/10; Food and Health Bureau of Hong Kong 10091262; NCI |
PMID:22139925 | biotools:gwasdb, nlx_151404 | https://bio.tools/gwasdb | SCR_006015 | 2026-02-14 02:01:12 | 43 | ||||||
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Allen Brain Atlas API Resource Report Resource Website 10+ mentions |
Allen Brain Atlas API (RRID:SCR_005984) | Allen Brain Atlas API | portal, data or information resource, source code, software application, software resource, topical portal | API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service | atlas application, expression data, 3d volume, 3d coordinate, gene, reference atlas, connectivity, histology, microarray, brain, rna sequencing, mri, dti, api, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics, ish, high resolution image, nissl, annotation, atlas, image, web service, neuroblast, gene expression, gene, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Mouse Brain Reference Atlas is related to: Allen Developing Mouse Brain Atlas is related to: International Neuroinformatics Coordinating Facility is related to: Brain Explorer Atlas and Teaching Tool is related to: CellTax vignette is related to: Allen Mouse Brain Common Coordinate Framework has parent organization: Allen Institute for Brain Science |
Other/Commercial license License | nlx_151358 | http://www.nitrc.org/projects/incf_allen-brai | SCR_005984 | 2026-02-14 02:01:13 | 13 | |||||||
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GeneVito Resource Report Resource Website |
GeneVito (RRID:SCR_006211) | GeneVito | data visualization software, software resource, data processing software, software application | A JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of poor annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. GeneViTo has already been applied to visualize the genomes of two microbial organisms: the bacterion Chlamydia trachomatis and the archaeon Methanococcus jannaschii. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment (Java 1.4.1) is already installed in the system. | java, genome-wide analysis, genome, visualization, gene, function, structure, dna, protein sequence, genomic, proteomic | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | PMID:14594459 | Free for academic use, Acknowledgement requested | nlx_151776 | SCR_006211 | GeneVito: Genome Visualization Tool, GeneViTo (Genome Visualization Tool), Genome Visualization Tool | 2026-02-14 02:01:15 | 0 | ||||||
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Mammalian Adult Neurogenesis Gene Ontology Resource Report Resource Website 50+ mentions |
Mammalian Adult Neurogenesis Gene Ontology (RRID:SCR_006176) | MANGO | data or information resource, ontology, controlled vocabulary, database | Database of genes concerning adult neurogenesis mapped to cell types and processes that have been curated from the literature. In its present state, the database is restricted to neurogenesis in the hippocampus. | adult neurogenesis, adult, neurogenesis, hippocampus, gene, annotation, cell type, process, FASEB list | has parent organization: Dresden University of Technology; Saxony; Germany | nlx_151684 | SCR_006176 | 2026-02-14 02:01:05 | 63 | |||||||||
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Deciphering Developmental Disorders Resource Report Resource Website 10+ mentions |
Deciphering Developmental Disorders (RRID:SCR_006171) | DDD | material storage repository, storage service resource, biospecimen repository, portal, data or information resource, service resource, research forum portal, disease-related portal, topical portal | The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 23 NHS Regional Genetics Services throughout the UK and scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. It has a Scientific Advisory Board consisting of scientists, doctors, a lawyer and patient representative, and has received National ethical approval in the UK. Over the next few years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed children in the UK with developmental disorders and their parents. The results of the DDD study will provide a unique, online catalogue of genetic changes linked to clinical features that will enable clinicians to diagnose developmental disorders. Furthermore, the study will enable the design of more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with developmental disorders. Over time, the work will also improve understanding of how genetic changes cause developmental disorders and why the severity of the disease varies in individuals. The Sanger Institute will contribute to the DDD study by performing genetic analysis of DNA samples from patients with developmental disorders, and their parents, recruited into the study through the Regional Genetics Services. Using microarray technology and the latest DNA sequencing methods, research teams will probe genetic information to identify mutations (DNA errors or rearrangements) and establish if these mutations play a role in the developmental disorders observed in patients. The DDD initiative grew out of the groundbreaking DECIPHER database, a global partnership of clinical genetics centres set up in 2004, which allows researchers and clinicians to share clinical and genomic data from patients worldwide. The DDD study aims to transform the power of DECIPHER as a diagnostic tool for use by clinicians. As well as improving patient care, the DDD team will empower researchers in the field by making the data generated securely available to other research teams around the world. By assembling a solid resource of high-quality, high-resolution and consistent genomic data, the leaders of the DDD study hope to extend the reach of DECIPHER across a broader spectrum of disorders than is currently possible. | microarray, sequencing, child, genome, chromosome, dna sequencing, ethics, interview, dna, saliva, clinical, genetics, gene, diagnosis, phenotype, clinical data, FASEB list |
is related to: DECIPHER has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Genetic disorder, Parent, Neurodevelopmental disorder, Congenital anomaly, Abnormal growth, Dysmorphic feature, Unusual behavioral phenotype | Wellcome Trust ; Health Innovation Challenge Fund |
PMID:21679367 | nlx_151673 | SCR_006171 | Deciphering Developmental Disorders (DDD) | 2026-02-14 02:01:03 | 42 | |||||
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ScerTF Resource Report Resource Website 10+ mentions |
ScerTF (RRID:SCR_006121) | ScerTF | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Catalog of over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors (TFs). They've curated 11 literature sources, benchmarked the published position-specific scoring matrices against in-vivo TF occupancy data and TF deletion experiments, and combined the most accurate models to produce a single collection of the best performing weight matrices for Saccharomyces cerevisiae. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors. Enter a TF name to find the recommended matrix for a particular TF, or enter a nucleotide sequence to identify all TFs that could bind a particular region. | binding site, transcription factor, regulatory site, gene, regulation, regulatory interaction, matrix, nucleotide sequence, dna sequence, yeast, position weight matrix, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIGMS R01 GM078222; NHGRI HG00249 |
PMID:22140105 | biotools:scertf, nlx_151599, OMICS_00542 | http://ural.wustl.edu/ScerTF https://bio.tools/scertf |
http://ural.wustl.edu/TFDB/ | SCR_006121 | 2026-02-14 02:01:03 | 19 | |||||
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SitEx Resource Report Resource Website 1+ mentions |
SitEx (RRID:SCR_006122) | SitEx | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2019. Analyzing protein structure projection on exon-intron structure of corresponding gene through years led to several fundamental conclusions about structural and functional organization of the protein. According to these results we decided to map the protein functional sites. So we created the database SitEx that keep the information about this mapping and included the BLAST search and 3D similar structure search using PDB3DScan for the polypeptide encoded by one exon, participating in organizing the functional site. This will help: # to study the positions of the functional sites in exon structure; # to make the complex analysis of the protein function; # to exposure the exons that took part in exon shuffling and came from bacterial genomes; # to study the peculiarities of coding the polypeptide structures. Currently, SitEx contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms. | projection, protein, functional site, exon, blast, structure, function, gene, amino acid, encoding gene, proteome, ligand, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Ministry of Science and Education 14.740.11.0001; Ministry of Science and Education 07.514.11.4003; Interdisciplinary Integrative Project 35 of SB RAS ; Russian Foundation for Basic Research 11-04-92712; EU-FP7 260429; Program of RAS ; DAAD Leonard Euler Program Grant |
PMID:22139920 | THIS RESOURCE IS NO LONGER IN SERVICE. | biotools:sitex, nlx_151602 | https://bio.tools/sitex | SCR_006122 | SitEx Database | 2026-02-14 02:01:13 | 1 | ||||
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Predictive Networks Resource Report Resource Website |
Predictive Networks (RRID:SCR_006110) | PN | data analysis service, analysis service resource, data or information resource, production service resource, source code, service resource, software resource, database | A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model. | gene interaction network, gene, interaction, gene expression, graph, visualization, gene interaction, gene network, predictive network analysis, model, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: SourceForge |
NLM 1R01LM010129 | PMID:22096235 | Apache License, v2 | nlx_151582, biotools:predictivenetworks | https://bio.tools/predictivenetworks | SCR_006110 | 2026-02-14 02:01:13 | 0 | |||||
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NHMRC Australian PhenomeBank Resource Report Resource Website 1+ mentions |
NHMRC Australian PhenomeBank (RRID:SCR_006149) | APB | biomaterial supply resource, organism supplier, cell repository, material resource | The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. | RIN, Resource Information Network, murine, mutation, gene, strain, transgenic, alteration, phenotype, live mouse, sperm, embryo, transgene, database, allele, chromosome, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network has parent organization: Australian Phenomics Network works with: International Mouse Strain Resource |
Public | nlx_151640 | http://pb.apf.edu.au/phenbank/foreignPageImport.html?page=http://pbstatic.apf.edu.au:80/phenbank/home.htm | SCR_006149 | Australian Phenome Bank, Phenome Bank, Australian PhenomeBank, NHMRC Australian Phenome Bank, PhenomeBank | 2026-02-14 02:01:05 | 3 |
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