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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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WiCell Research Institute Resource Report Resource Website 100+ mentions |
WiCell Research Institute (RRID:SCR_004364) | WiCell | institution | A nonprofit organization offering research and clinical grade pluripotent stem cell lines, cytogenetic testing, quality control testing and cell banking services to researchers worldwide. The organization is focused on enhancing and expanding the study of human pluripotent stem cells by supporting basic research; establishing research protocols; creating and distributing cell lines; providing training to scientists worldwide; and supporting efforts to unlock the therapeutic potential of stem cell technologies. As home to the Wisconsin International Stem Cell (WISC) Bank, and previously the first US National Stem Cell Bank, WiCell serves the worldwide scientific stem cell community through banking, characterization, and distribution of stem cell lines as well as providing technical support. WiCell also offers cytogenetic services, quality control testing services and clinical grade cell lines to researchers across the globe. | stem cell, cell line, iinduced pluripotent stem cell |
is parent organization of: Wisconsin International Stem Cell Bank is parent organization of: National Stem Cell Bank |
ISNI: 0000 0004 0387 4731, Wikidata: Q7997962, grid.439113.d, nlx_38454 | https://ror.org/032ycrz75 | SCR_004364 | 2026-02-07 02:06:23 | 284 | ||||||||
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Roswell Park Cancer Institute Resource Report Resource Website 1+ mentions |
Roswell Park Cancer Institute (RRID:SCR_004471) | RPCI | institution | America''s first cancer center founded by Dr. Roswell Park. His revolutionary model of a multidisciplinary approach to cancer with scientists and clinicians working in concert and in consult has become the standard by which all modern-day comprehensive cancer centers are measured. RPCI is among the first and only upstate New York facility to hold the National Cancer Institute designation of comprehensive cancer center and to serve as a member of the prestigious National Comprehensive Cancer Network. Many RPCI faculty serve on the NCCN panels that create the Clinical Practice Guidelines in OncologyTM the internationally recognized standards for clinical policy in oncology, and the most comprehensive, most frequently updated clinical practice guidelines available in any area of medicine. Over its long history, Roswell Park Cancer Institute has made fundamental contributions to reducing the cancer burden and has successfully maintained an exemplary leadership role in setting the national standards for cancer care, research and education. Over the last decade, RPCI has undergone major growth, adding over 1,000 new jobs, initiating one of the nation''s first hospital facilities dedicated to Phase I cancer research studies, and setting itself apart as a leader in surgical robotics, vitamin D research, immunotherapy and vaccine therapy, studies targeting tumor microenvironment and cancer prevention, and the development and testing of new agents and technology. *Research: From its inception, Roswell Park Cancer Institute identified cancer research as a core element of its mission. Since then, groundbreaking research by RPCI scientists has led to greater understanding of the nature of cancer and to major advances in cancer diagnosis and treatment. * Education: Roswell Park''s excellent faculty and strong alliances with the University at Buffalo, as well as other local and regional colleges and universities, enables the Institute to provide a superior, comprehensive education in several fields. | cancer, research, education |
is parent organization of: RPCI Gene Targeting and Transgenic Shared Resource is parent organization of: Roswell Park Data Bank and BioRepository is parent organization of: RPCI Pathology Resource Network is parent organization of: Blood Group Antigen Gene Mutation Database |
nlx_143749 | SCR_004471 | 2026-02-07 02:06:25 | 2 | |||||||||
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ACT: Artemis Comparison Tool Resource Report Resource Website 10+ mentions |
ACT: Artemis Comparison Tool (RRID:SCR_004507) | ACT | software resource | A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | dna sequence, genome, synteny, pairwise comparison |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | PMID:15976072 | GNU General Public License | OMICS_00928, nlx_48986 | SCR_004507 | Artemis Comparison Tool | 2026-02-07 02:06:48 | 46 | |||||
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Danish Multiple Sclerosis Center Resource Report Resource Website 1+ mentions |
Danish Multiple Sclerosis Center (RRID:SCR_004424) | DMSC | institution | The Danish Multiple Sclerosis Center (DMSC) comprises the MS Clinic and the MS Research Unit including the Neuroimmunology Laboratory. The main research areas are: clinical research including investigator driven trials of new therapies in MS, neuroimaging, neuropsychology and rehabilitation; pathogenesis of MS with focus on immunology, biomarkers and treatment response; as well as studies in the pathology and genetics of MS. DMSC is part of the Department of Neurology, Rigshospitalet, and the Faculty of Medicine, University of Copenhagen. The research facilities are located in sections 6311 and 9392 at the hospital site. DMSC constitutes one of the European MS Centers of Excellence and has extensive collaboration with institutions in Denmark, in other European countries, as well as overseas. DMSC is supported by both national and international grants. | multiple sclerosis |
has parent organization: University of Copenhagen; Copenhagen; Denmark is parent organization of: Danish Multiple Sclerosis Biobank |
nlx_143734, grid.488278.9 | https://ror.org/04anq5q02 | SCR_004424 | 2026-02-07 02:06:24 | 4 | ||||||||
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Squeezambler Resource Report Resource Website |
Squeezambler (RRID:SCR_004385) | Squeezambler | software resource | Software to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells. |
is listed by: OMICtools has parent organization: Wayne State University; Michigan; USA |
PMID:23918251 | OMICS_01503 | SCR_004385 | 2026-02-07 02:06:20 | 0 | |||||||||
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Childhood Brain Tumor Foundation Resource Report Resource Website 1+ mentions |
Childhood Brain Tumor Foundation (RRID:SCR_004421) | CBTF | institution | The Childhood Brain Tumor Foundation (CBTF), an all-volunteer organization, was founded in 1994 by families, friends and physicians of children with brain tumors. Our mission is to raise funds for scientific research and heighten public awareness of this most devastating disease and to improve prognosis and quality of life for those that are affected. Founded and incorporated in Virginia, relocated to Maryland in 1998, the Foundation (a 501(c) (3), strives to meet the goals of our mission. Friends, families, and physicians brought CBTF together and are dedicated to serving the needs of families and children with brain tumors, in hopes of improving the quality of life and find cures for pediatric brain tumors. Annually, CBTF funds basic science or clinical research for pediatric brain tumors; conferences and other programs. We provide informational materials on our website and mail other information (nationally and internationally) upon request. The Childhood Brain Tumor Foundation (CBTF) has funded state-of-the-art research and supported conferences for pediatric brain tumors over the past 17 years. Grants submissions are reviewed thoroughly by our dedicated renown team of scientific advisors to ensure that CBTF selects the highest quality research for pediatric brain tumors. Each year, we receive so many outstanding applications and it is through the support of private and public donations that this is all possible. With your support, together, we will strive to find a cure for children''s brain tumors. | brain tumor, child, human, pediatric, tumor, cancer, brain | grid.478649.0, ISNI: 0000 0004 5902 3100, nlx_143731, Crossref funder ID: 100002725 | https://ror.org/02aqe0j14 | SCR_004421 | 2026-02-07 02:06:24 | 2 | |||||||||
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SNiPer-HD Resource Report Resource Website 1+ mentions |
SNiPer-HD (RRID:SCR_004383) | SNiPer-HD | software resource | Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. | is listed by: OMICtools | PMID:17062589 | OMICS_00735 | SCR_004383 | SNiPer-HD: Improved genotype calling accuracy | 2026-02-07 02:06:44 | 2 | ||||||||
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Vanator Resource Report Resource Website 1+ mentions |
Vanator (RRID:SCR_004370) | Vanator | software resource | A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples. | perl, metagenomic, illumina, alignment, assembly, analysis, profile, virus, clinical, environment, next-generation sequencing, taxonomy, read |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Glasgow; Glasgow; United Kingdom |
PMID:23296970 | OMICS_01505 | SCR_004370 | Vanator-CVR, Vanator-CVR - A metagenomics & virus discovery pipeline, Virus Alignment de Novo Assembly and Taxonomy On Reads, Vanator-CVR: A metagenomics and virus discovery pipeline | 2026-02-07 02:06:23 | 2 | |||||||
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Basic OligoNucleotide Design Resource Report Resource Website 10+ mentions |
Basic OligoNucleotide Design (RRID:SCR_004492) | BOND | software resource | Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs. | dna, oligonucleotide, design, oligonucleotide design |
is listed by: OMICtools has parent organization: Western University; Ontario; Canada |
PMID:23444904 | OMICS_00827 | SCR_004492 | BOND: Basic OligoNucleotide Design | 2026-02-07 02:06:48 | 17 | |||||||
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HelioScan Resource Report Resource Website 10+ mentions |
HelioScan (RRID:SCR_004494) | HelioScan | software resource | HelioScan is a versatile control software for microscopes written in the intuitive graphical programming language LabVIEW. It solves a number of problems observed with custom-built image acquisition systems by providing the following features: * Extendability: both hardware components and software functionality are encapsulated in exchangeable, software components. Additional components can be implemented easily and plugged in at run-time. Components can be independently developed, allowing multiple developers to work in parallel. * Flexibility: Components are independently configurable; each component can have an unlimited number of configurations. * Understandability: The LabVIEW code is well-structured, commented and documented. * High speed: The software supports FPGA-based hardware that enables intelligent and extremely fast signal acquisition and generation. FPGA logic can be easily programmed using LabVIEW. * Tailored to in vivo brain imaging: The software is especially suited for 2-photon Calcium imaging, but can in principle be used for any kind of microscopy. The out-of-the-box software supports different imaging modalities (camera, galvanometric scan mirrors, acusto-optic deflectors) and imaging modes (camera video acquisition, intrinsic optical imaging, two-photon frame scan and tilted frame scan, 2D line scan, 3D spiral scan) and can easily be extended to other imaging modalities (e.g., resonance scanners), imaging modes (e.g., 2D and 3D arbitrary line scans) and associated hardware (e.g., stimulation devices). * Open file-format with extensible meta-data schema: HelioScan saves data in the OME-TIFF file format, which contains image data as multipage TIFF and meta-data as human-readable XML in the TIFF description tag according to the OME schema. | microscopy, two photon, calcium imaging, light microscopy, multiphoton imaging protocol, calcium(2+), imaging, brain, brain imaging | has parent organization: ETH Zurich; Zurich; Switzerland | nlx_143787 | SCR_004494 | Helio Scan | 2026-02-07 02:06:23 | 11 | ||||||||
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Oscar3 Resource Report Resource Website 1+ mentions |
Oscar3 (RRID:SCR_004561) | Oscar | software resource | OSCAR is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries. This tool for shallow, chemistry-specific parsing of chemical documents identifies (or attempts to identify): * Chemical names: singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names. * Ontology terms: if you can do it by string-matching, you can get OSCAR to do it. * Chemical data: Spectra, melting/boiling point, yield etc. in experimental sections. In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing (OPSIN), and with identifiers from the chemical ontology ChEBI Current work on OSCAR3 by Peter Corbett focuses on its use in SciBorg, a framework for the deep parsing of chemical text. OSCAR3 also includes the Oscar Server, a Jetty-powered set of servlets. These provide the following services: * Parsing of text/HTML by OSCAR. * Text/InChI/SMILES/SMILES substructues/SMILES similarity search of papers, coupled with keyword and ontology-based search, using Lucene and the CDK. * List of all names found / all names that co-occur with a search term or terms. * Online management of a chemical/stopword lexicon. * Manual editing of SciXML fragments containing named entities, for creating of gold standards and training data. Oscar3 can be found on SourceForge: http://sourceforge.net/projects/oscar3-chem/ | annotation, chemistry |
is related to: U-Compare has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21999457 | nlx_55584 | SCR_004561 | OSCAR, Open Source Chemistry Analysis Routines | 2026-02-07 02:06:49 | 3 | |||||||
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SOrt-ITEMS Resource Report Resource Website 1+ mentions |
SOrt-ITEMS (RRID:SCR_004716) | SOrt-ITEMS | software resource | Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | metagenome, taxonomy, sequence, orthology, binning | is listed by: OMICtools | PMID:19439565 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01465 | SCR_004716 | Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences, SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences | 2026-02-07 02:06:52 | 6 | ||||||
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National University of Ireland; Galway; Ireland Resource Report Resource Website 1+ mentions |
National University of Ireland; Galway; Ireland (RRID:SCR_004677) | NUI Galway | university | Located in the city of Galway in Ireland. |
is affiliated with: Big Data Public Private Forum is related to: Pharma-Planta Consortium is related to: Biomedical Diagnostics Institute is parent organization of: Digital Enterprise Research Institute |
grid.6142.1, Wikidata:Q644478, Crossref funder ID:501100001634, ISNI:0000 0004 0488 0789, nlx_149500 | https://ror.org/03bea9k73 | SCR_004677 | National University of Ireland, National University of Ireland Galway | 2026-02-07 02:06:26 | 1 | ||||||||
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UnifiedGenotyper Resource Report Resource Website 500+ mentions |
UnifiedGenotyper (RRID:SCR_004710) | UnifiedGenotyper | software resource | A multiple-sample, technology-aware SNP and indel caller. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00080 | SCR_004710 | 2026-02-07 02:06:29 | 561 | ||||||||||
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Capralogics Resource Report Resource Website 1+ mentions |
Capralogics (RRID:SCR_004673) | commercial organization | An Antibody supplier | nlx_152324 | SCR_004673 | Capralogics Inc. | 2026-02-07 02:06:51 | 1 | |||||||||||
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NuChart Resource Report Resource Website 1+ mentions |
NuChart (RRID:SCR_004703) | NuChart | software resource | An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations. | is listed by: OMICtools | OMICS_00525 | SCR_004703 | 2026-02-07 02:06:26 | 2 | ||||||||||
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Pplacer Resource Report Resource Website 10+ mentions |
Pplacer (RRID:SCR_004737) | Pplacer | software resource | Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. | classification, phylogenetic classification |
is listed by: OMICtools has parent organization: Fred Hutchinson Cancer Center |
PMID:21034504 | OMICS_01462 | SCR_004737 | pplacer: phylogenetic placement and downstream analysis | 2026-02-07 02:06:30 | 30 | |||||||
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TETRA Resource Report Resource Website 50+ mentions |
TETRA (RRID:SCR_004573) | TETRA | software resource | Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences. | tetranucleotide, dna sequence |
is listed by: OMICtools has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:15305919 PMID:15507136 |
OMICS_01474 | SCR_004573 | TETRA - Fragment assignment by intrinsic tetranucleotide frequencies | 2026-02-07 02:06:49 | 66 | |||||||
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European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
EMBL member states ; European Union ; NIH ; Wellcome Trust ; UK Research Councils ; Industry Programme partners ; BBSRC |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-02-07 02:06:30 | 3689 | ||||||
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National University of Malaysia; Selangor; Malaysia Resource Report Resource Website 1+ mentions |
National University of Malaysia; Selangor; Malaysia (RRID:SCR_004724) | UKM, NUM | university | UKM affirms integration of faith in Allah and constructive knowledge along with amalgamation of theory and practice as core fundamentals in advancement of knowledge, building of educated society and development of university. |
is parent organization of: ProLysED - Prokaryotic Lysis Enzymes Database is parent organization of: NRESTdb |
nlx_151798 | http://www.ukm.my/v3/ | SCR_004724 | Universiti Kebangsaan Malaysia, National University of Malaysia | 2026-02-07 02:06:52 | 2 |
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