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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Iowa State University Genome Informatics Core Facility Resource Report Resource Website |
Iowa State University Genome Informatics Core Facility (RRID:SCR_017790) | GIF | access service resource, core facility, service resource | Provides help with grant review, information on data management plans,suggestion best practices for bionformatics analyses, advise on experimental design for Next Gen Sequencing (NGS) projects.Services include:Genome assembly and annotation,Transcriptome assembly and annotation,SNP/InDel calling,RNA-Seq analysis,ChiP-seq,Introgression mapping,novel gene discovery,Personalized GBrowse instances for data visualization,Access to high performance computing, Custom big data projects. | Genome, informatics, data, management, analysis, design, grant, service, core | Open | ABRF_422 | SCR_017790 | Genome Informatics Facility | 2026-09-03 05:08:17 | 0 | ||||||||
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Loyola University Genomics Core Facility Resource Report Resource Website |
Loyola University Genomics Core Facility (RRID:SCR_017857) | LGF | access service resource, core facility, service resource | Core provides next-generation sequencing capabilities using Illumina MiSeq. Helps with experimental design, quality control analysis, library preparation, and data analysis. MiSeq desktop sequencer allows to access applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing, and HLA typing.MiSeq is capable of delivering up to 15 Gb of output with 25 million sequencing reads and 2x300 basepair read lengths. | Next, generation, sequencing, Illumina MiSeq, experimental, design, quality, control, analysis, library, preparation, data, targeted, gene, metagenomics, genome, expression, amplicon, HLA, typing, service, core, ABRF | is listed by: ABRF CoreMarketplace | Restricted | ABRF_678 | SCR_017857 | Loyola Genomics Facility | 2026-09-03 05:08:03 | 0 | |||||||
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Oregon State University Center for Quantitative Life Sciences Core Facility Resource Report Resource Website 1+ mentions |
Oregon State University Center for Quantitative Life Sciences Core Facility (RRID:SCR_018373) | CQLS | access service resource, core facility, service resource, training service resource | Formerly Center for Genome Research and Biocomputing Core Facility. Functions and facilities include services in genomics, functional genomics, genotyping and imaging.Biocomputing facilities with computing infrastructure, which includes managed cloud and shared resources, data analyses and training are customized to individual needs, including genome assembly and annotation, analysis of RNAseq, GBS, and metagenomics data, and GPU-enabled deep learning analyses. | Genome, genomic, functional genomic, genotyping, imaging, biocomputing, data analysis, training, core facility, ABRF, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Oregon State University; Oregon; USA |
Open | ABRF_856 | https://coremarketplace.org/?FacilityID=856 | SCR_018373 | CGRB, Center for Genome Research and Biocomputing | 2026-09-03 05:08:27 | 2 | ||||||
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HVSeeker Resource Report Resource Website 1+ mentions |
HVSeeker (RRID:SCR_026120) | software application, software resource | Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. | genome, bacteria, phage, sequence, distinguishing between bacterial and phage sequences, | German Research Foundation INST 37/935-1 FUGG; King Fahd University of Petroleum and Minerals |
Free, Available for download, Freely available, | SCR_026120 | 2026-09-03 05:10:39 | 1 | ||||||||||
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NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects Resource Report Resource Website |
NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects (RRID:SCR_003205) | NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects | data or information resource, portal, project portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. 2012 workshop to establish a Central Resource of Data from Genome Sequencing Projects. The workshop addressed the challenges to aggregating and analyzing data sets from genome sequencing studies, such as: * Data sets being generally hard to access. * Data residing in various databases. * Variant and exposure/phenotype data not being comparable across studies. Participants in the workshop discussed options for dealing with these challenges, along with their costs and tradeoffs. Videos and accompanying slides from the workshop are available. Also available as a video playlist on GenomeTV | genome, sequencing |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_003205 | 2026-09-03 05:12:11 | 0 | |||||||||
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Xenbase Resource Report Resource Website 100+ mentions |
Xenbase (RRID:SCR_003280) | XenBase | data or information resource, data repository, database, image repository, service resource, storage service resource | Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics. | molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standard, bio.tools, FASEB list, RRID Community Authority |
is listed by: OMICtools is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of Calgary; Alberta; Canada is parent organization of: Xenopus Anatomy Ontology |
NICHD P41 HD064556; NICHD R01 HD045776 |
PMID:23125366 PMID:19884130 PMID:36755307 |
Free, Available for download, Freely available | biotools:xenbase, OMICS_01665, nif-0000-01286, r3d100010279 | http://www.xenbase.org/entry/, https://bio.tools/xenbase, https://doi.org/10.17616/R3MP4S | SCR_003280 | Xenbase: Xenopus laevis and tropicalis biology and genomics resource | 2026-09-03 04:46:09 | 484 | ||||
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PoPoolation Resource Report Resource Website 100+ mentions |
PoPoolation (RRID:SCR_003495) | PoPoolation | software resource | A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. | population genetics, next generation sequencing, sliding window, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21253599 | Acknowledgement requested | OMICS_04414, biotools:popoolation | https://bio.tools/popoolation | SCR_003495 | 2026-09-03 04:46:25 | 144 | ||||||
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genomation Resource Report Resource Website 50+ mentions |
genomation (RRID:SCR_003435) | genomation | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters. | genome, genomic interval, genomic feature analysis, GRanges objects, annotate given regions, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:25417204 | Free, Available for download, Freely available | biotools:genomation, OMICS_02306 | https://github.com/al2na/genomation, https://github.com/BIMSBbioinfo/genomation, https://bio.tools/genomation | http://al2na.github.io/genomation/ | SCR_003435 | 2026-09-03 04:46:14 | 62 | |||||
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Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis Resource Report Resource Website 50+ mentions |
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) | CAMERA | analysis service resource, data analysis service, data or information resource, data repository, organization portal, portal, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data. | ecology, energy, environment, gene, analysis, bioinformatics, biological, biology, community, cyberinfrastructure, data, dna, genome, genomics, health care, map, marine, metadata, metagenomic, microbial, microbiology, molecular biology, organism, research, scientific, sequence, sequencing, software, tool, training, viral |
is listed by: OMICtools is related to: VIROME has parent organization: University of California at San Diego; California; USA |
Gordon and Betty Moore Foundation | PMID:21045053 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_011924, OMICS_01476, nif-0000-23292 | SCR_002676 | 2026-09-03 04:45:40 | 83 | ||||||
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Honey Bee Genome Project Resource Report Resource Website 1+ mentions |
Honey Bee Genome Project (RRID:SCR_002890) | data or information resource, portal, topical portal | The HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social organization and behavioral traits. This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly. About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology. Sponsors: Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiple drones from the same queen (strain DH4) were obtained from Danny Weaver of B. Weaver Apiaries. All libraries were made from DNA isolated from these drones. The honey bee BAC library (CHORI-224) was prepared by Pieter de Jong and Katzutoyo Osoegawa at the Children's Hospital Oakland Research Institute. | gene, agricultural, allergy, antibiotic, apis mellifera, array, behavioral, biologist, chromosome, development, disease, genome, heath, honey bee, human, immunity, insect, mental heath, organism, pollination, reaction, resistance, sequence, trait | has parent organization: Baylor University; Texas; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25604 | http://www.hgsc.bcm.tmc.edu/project-species-i-Apis%20mellifera.hgsc?pageLocation=Apis%20mellifera | SCR_002890 | Honey Bee | 2026-09-03 04:45:43 | 4 | |||||||
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Assembly/Alignment/Annotation of 12 Related Drosophila Species Resource Report Resource Website 10+ mentions |
Assembly/Alignment/Annotation of 12 Related Drosophila Species (RRID:SCR_002921) | data or information resource, data set, organism-related portal, portal, topical portal | A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org. | sequence, annotation, analysis, genome, fruitfly, drosophila, research, comparative, alignment, assembly | has parent organization: Lawrence Berkeley National Laboratory | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30021 | SCR_002921 | AAA: 12 Drosophila Genomes | 2026-09-03 04:45:54 | 35 | ||||||||
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Gramene Resource Report Resource Website 500+ mentions |
Gramene (RRID:SCR_002829) | GR | data or information resource, database | Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site. | crop, plant genome, genetic, blast, gene, genome, genetic diversity, pathway, protein, marker, quantitative trait locus, comparative map, phenotype, genomics, physiology, comparative, grain, expressed sequence tag, trait, mutation, environment, taxonomy, web service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Gene Ontology is related to: Plant Ontology is related to: Trait Ontology is related to: EnvO is related to: BioCyc has parent organization: Cold Spring Harbor Laboratory has parent organization: Cornell University; New York; USA is parent organization of: Trait Ontology is parent organization of: Plant Environmental Conditions is parent organization of: Plant Trait Ontology is parent organization of: Cereal Plant Development Ontology is parent organization of: Cereal Plant Gross Anatomy Ontology |
USDA IFAFS 00-52100-9622; USDA 58-1907-0-041; USDA 1907-21000-030; NSF 0321685; NSF 0703908; NSF 0851652 |
PMID:21076153 PMID:17984077 PMID:16381966 |
Free, Freely available | r3d100010856, nif-0000-02926, nlx_65829, biotools:gramene | https://bio.tools/gramene, https://doi.org/10.17616/R3GG7M | SCR_002829 | GR PROTEIN, RiceGenes, GR REF, GR GENE, Gramene: A Resource for Comparative Grass Genomics, GR QTL | 2026-09-03 04:45:46 | 863 | ||||
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Tribolium castaneum Genome Project Resource Report Resource Website 10+ mentions |
Tribolium castaneum Genome Project (RRID:SCR_002848) | data or information resource, database, portal, topical portal | This portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below. The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University). Access to the Data :- Genome Assembly: The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder. A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page. The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change. :- BLAST Searches: The BLAST link is located in the sidebar. :* Linearized chromosome and unplaced scaffold sequences :* Assembled contigs :* Bin0 unassembled reads and Repeat reads Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query. Sponsors: Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338). | genetic, chromosome, coleoptera, drosophila, genome, model, pest, red flour beetle, sequence, tribolium castaneum | has parent organization: Baylor University; Texas; USA | Free, Freely available | nif-0000-25607 | http://www.hgsc.bcm.tmc.edu/project-species-i-Tribolium%20castaneum.hgsc?pageLocation=Tribolium%20castaneum | SCR_002848 | Tribolium | 2026-09-03 04:45:48 | 10 | |||||||
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International HapMap Project Resource Report Resource Website 5000+ mentions |
International HapMap Project (RRID:SCR_002846) | HapMap | data or information resource, database, experimental protocol, narrative resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project. | genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosome, bio.tools |
is used by: BioSample Database at EBI is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SNAP - SNP Annotation and Proxy Search is related to: Haploview is related to: NHGRI Sample Repository for Human Genetic Research is related to: DistiLD - Diseases and Traits in LD is related to: SNP at Ethnos is related to: GBrowse is related to: Broad Institute Genomics Platform has parent organization: NCBI |
Chinese Academy of Sciences ; Chinese Ministry of Science and Technology ; Delores Dore Eccles Foundation ; Genome Canada ; Genome Quebec ; Hong Kong Innovation and Technology Commission ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; National Natural Science Foundation of China ; SNP Consortium ; University Grants Committee of Hong Kong ; Wellcome Trust ; W. M. Keck Foundation ; NIH |
PMID:14685227 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02940, biotools:int_hapmap_project, r3d100011835, OMICS_00273 | http://www.hapmap.org/, https://bio.tools/int_hapmap_project, https://doi.org/10.17616/R3H06Q | http://snp.cshl.org | SCR_002846 | HapMap Project | 2026-09-03 04:45:41 | 6854 | |||
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HemBase Resource Report Resource Website 1+ mentions |
HemBase (RRID:SCR_002880) | data or information resource, database, resource | Database designed for web-based examination of the human erythroid transcriptome. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology. Red blood cells in the circulation arise from hematopoietic stem cells that proliferate as erythroid progenitors and differentiate into erythroid precursor cells in response to the hormone erythropoietin. Messenger RNA was isolated from those cells and used to generate gene libraries. Sequencing several thousand expressed sequence tags (EST) from those libraries was then performed. Those EST and sequences encoding several hundred additional genes with known expression in erythroid cells are compiled here as a database of human erythroid gene activity. The database is organized and linked according to the location of these sequences within the human genome., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | erythroid, erythroid cell, erythroblast, expressed sequenced tag, transcriptome, gene, erythropoiesis, cytogenetic location, hematology, genome, red blood cell, progenitor cell, precursor cell, chromosome |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Anemia, Erythroleukemia, Malaria, Erythroid cell related disease | NIDDK 1ZIADK025098 | PMID:14681483 PMID:10409428 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02949 | SCR_002880 | Hembase | 2026-09-03 04:45:49 | 4 | |||||
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ATGC: Montpellier bioinformatics platform Resource Report Resource Website 100+ mentions |
ATGC: Montpellier bioinformatics platform (RRID:SCR_002917) | ATGC | catalog, data or information resource, database, portal, topical portal | A bioinformatics platform that is a joint project of several South of France laboratories with available services based on their expertise, issued from their research activities which involve phylogenetics, population genetics, molecular evolution, genome dynamics, comparative and functional genomics, and transcriptome analysis. Most of the software and databases on ATGC are (co)authored by researchers from South of France teams. Some are widely used and highly cited. South of France laboratories: * CRBM (transcriptomes and stem cells). * IBC (computational biology). * MiVEGEC (evolution and phylogeny). * LGDP (plant genomics). * LIRMM (computer science). * South Green (plant genomics). | bioinformatics, genome, genetics, molecular evolution, comparative, functional, dynamics, transcriptome, analysis, database, data analysis service, software resource, data set, high-throughput sequencing, binary, phylogenetics, population genetics, genome dynamics, comparative genomics, functional genomics, transcriptome analysis, molecular, evolution, stem cell, computational biology, plant genomics, FASEB list |
is related to: ReNaBi has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: MPscan |
nif-0000-30044 | SCR_002917 | ATGC - South of France bioinformatics platform | 2026-09-03 04:45:52 | 230 | ||||||||
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European Conditional Mouse Mutagenesis Program Resource Report Resource Website 50+ mentions |
European Conditional Mouse Mutagenesis Program (RRID:SCR_003104) | EUCOMM | biomaterial manufacture, material service resource, production service resource, service resource | Generate, archive, and distribute world-wide up to 12.000 conditional mutations across the mouse genome in mouse embryonic stem (ES) cells and Establish a limited number of mouse mutants from this resource. EUCOMM contributes the largest fraction of conditionally trapped and targeted genes in mouse C57BL/6N embryonic stem (ES) cells to the IKMC. EUCOMM vectors, mutant ES cells and mutant mice are distributed worldwide, enabling functional genomics research in a standardized and cost-effective manner by a much wider biomedical research community than has been possible previously. EUCOMM mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMM mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Mutagenesis Strategies * Conditional gene trapping - random approach for expressed genes * Conditional targeted trapping - directed approach, used for expressed genes * Conditional gene targeting - directed approach, used for non-expressed genes | mutant, c57bl/6n, embryonic stem cell, conditionally trapped, targeted gene, gene, functional genomics, vector, mutant embryonic stem cell, mutant mouse, mutagenesis, genome, gene trapping, gene targeting |
is related to: EuMMCR is related to: European Mouse Mutant Archive is related to: Europhenome Mouse Phenotyping Resource has parent organization: International Knockout Mouse Consortium |
European Union FP6 | Free, Freely available | nif-0000-30531 | SCR_003104 | 2026-09-03 04:46:04 | 54 | |||||||
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JASPAR Resource Report Resource Website 5000+ mentions |
JASPAR (RRID:SCR_003030) | JASPAR | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. | structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dna, FASEB list |
is listed by: OMICtools is listed by: re3data.org is related to: Babelomics has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: Karolinska Institute; Stockholm; Sweden |
Carlsberg Foundation ; EMBRACEa Sixth Framework Network of Excellence ; European Union ; Novo Nordisk Foundation ; Sars Centre |
PMID:18006571 PMID:16381983 PMID:14681366 |
Free, Freely available | r3d100010091, OMICS_00538, nif-0000-03061 | https://doi.org/10.17616/R3QC7R | http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se | SCR_003030 | JASPAR, JASPAR CORE, JASPAR CORE database, JASPAR database | 2026-09-03 04:45:57 | 5785 | |||
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ChIPMonk Resource Report Resource Website 1+ mentions |
ChIPMonk (RRID:SCR_002975) | ChIPMonk | software resource | Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided | java, chip, chip-on-chip, plotting, normalization, visualization, genome, annotation, probe, array, analysis |
is listed by: OMICtools has parent organization: Babraham Institute |
Free, Available for download, Freely available | OMICS_02043, nif-0000-30159 | http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/ | SCR_002975 | 2026-09-03 04:45:52 | 4 | |||||||
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BRENDA Resource Report Resource Website 100+ mentions |
BRENDA (RRID:SCR_002997) | BRENDA | data or information resource, database | Database for functional enzyme and ligand-related information maintained as part of the German ELIXIR Node. Provides advanced query systems, evaluation tools, and various visualization options for the detailed assessment of enzyme properties. Enzyme data in BRENDA are classified according to the Enzyme Commission (EC) nomenclature of IUBMB. | enzyme, metabolic pathway, protein sequence, protein structure, genome, structure, function, annotation, kinetics, molecular property, occurrence, preparation, application, mutant, variant, pathway, ligand, web service, sequence, substructure, FASEB list |
is related to: ENZYME is parent organization of: BRENDA Tissue and Enzyme Source Ontology |
European Union SLING 226073; European Union FELICS 021902 (RII3) |
PMID:33211880 PMID:30395242 PMID:28438579 PMID:27924025 PMID:25378310 PMID:23203881 PMID:21062828 PMID:14681450 PMID:12850129 PMID:11796225 PMID:11752250 |
Free, Freely available, | r3d100010616, nif-0000-30222 | http://www.brenda-enzymes.info/, https://doi.org/10.17616/R39W42 | http://www.brenda.uni-koeln.de/ | SCR_002997 | Brenda: The Comprehensive Enzyme Information System, BRaunschweig ENzyme Database, Brenda: Enzyme Database, BRENDA: The Comprehensive Enzyme Information System | 2026-09-03 04:45:49 | 446 |
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Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
