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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software application, software resource, source code | Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer. | Cancer Genes, SNV, indel, gene-specific probabilistic estimates, strength of negative and positive selection, cancer | NCI U54 CA143874; NIGMS R01 GM078598; NIMH R01 MH101244 |
PMID:29106416 | Free, Available for download, Freely available | https://github.com/weghornlab/CBaSE, http://genetics.bwh.harvard.edu/cbase | SCR_027765 | SciCrunch Registry | Cancer Bayesian SElection estimation | 2026-10-24 12:54:30 | 0 | |||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software library, software resource, software toolkit, source code | Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots. | genomic DNA, phenotype, visualizing genomic and phenotypic information, comutation plots, | NCI R01 CA227388; NCI R37 CA222574; NCI U01 CA233100; NIGMS T32 GM008313; NSF |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | SciCrunch Registry | 2026-10-24 12:54:27 | 4 | |||||||||
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HiTIMED Resource Report Resource Website |
HiTIMED (RRID:SCR_028180) | software application, software resource, source code | Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens. | estimate cell proportions, cell type resolution, tumor microenvironment, tumor-type-specific DNA methylation data, | NCI P30 CA168524; NCI P50 CA097257; NCI R01 CA207360; NCI R01CA216265; NIGMS P20 GM130423; NIGMS P20GM103428; NIGMS P20GM104416 |
PMID:36348337 | Free, Available for download, Freely available | SCR_028180 | SciCrunch Registry | Hierarchical Tumor Immune Microenvironment Epigenetic Deconvolution | 2026-10-24 12:54:37 | 0 | ||||||||
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OncoDB Resource Report Resource Website 50+ mentions |
OncoDB (RRID:SCR_028340) | data or information resource, database | Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival. | cancer patients data, gene expression, DNA methylation, somatic mutations, proteomic profiles, chromatin accessibility, | NCI R01CA287778; NIDCR R01DE026471; NIGMS R35GM141535 |
PMID:34718715 PMID:40995640 |
Free, Freely available, | SCR_028340 | SciCrunch Registry | OncoDB2.0 | 2026-10-24 12:54:43 | 84 | ||||||||
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Mitochondrial Function and In Vivo Imaging Core Resource Report Resource Website |
Mitochondrial Function and In Vivo Imaging Core (RRID:SCR_028891) | MF-II Core | access service resource, core facility, service resource | The Mitochondrial Function and In Vivo Imaging (MF-II) Core provides specialized expertise, advanced instrumentation, and comprehensive services for assessing mitochondrial function, metabolism, cardiopulmonary physiology, and in vivo structure and function. The Core supports cardiovascular, pulmonary, and vascular research through high-resolution metabolic and mitochondrial analyses, noninvasive imaging, hemodynamic assessment, and established preclinical disease models. The MF-II Core works collaboratively with investigators to provide experimental design consultation, technical expertise, data acquisition, and analysis to generate high-quality, reproducible data. | Mitochondrial Function, Mitochondrial Bioenergetics, Cellular Metabolism, Oxygen Consumption, Glycolysis, High-Resolution Respirometry, Seahorse XFe96, Oroboros, Echocardiography, Cardiac Function, Hemodynamics, In Vivo Imaging, Micro-CT, PET Imaging, Laser Doppler, Cardiopulmonary Physiology, Preclinical Imaging, Animal Models, Pulmonary Hypertension, Cardiovascular Biology | NIGMS P30GM149398 | SCR_028891 | SciCrunch Registry | 2026-10-24 12:54:52 | 0 | ||||||||||
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spaCR Resource Report Resource Website |
spaCR (RRID:SCR_029041) | spaCR | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software Python framework that links pooled CRISPR-Cas9 perturbations to single-cell spatial phenotypes. It segments cells, nuclei, pathogens and organelles in high-content microscopy images with Cellpose, measures morphology, intensity, texture, spatial and colocalization features into a single SQLite project, supports keyboard-driven annotation and active learning, trains image and measurement-based classifiers with held-out performance recorded per checkpoint, maps sequencing reads to wells and gRNA barcodes, and estimates per-guide and per-gene effects by multiple linear regression to produce a ranked hit list. It runs as a Qt desktop application or headlessly on a workstation, server or cluster, on Linux, macOS and Windows, with CUDA, ROCm, Metal and Intel XPU acceleration. | CRISPR screen; pooled screen; image-based screening; high-content screening; spatial phenotype; single-cell; cell segmentation; Cellpose; deep learning; image classification; barcode mapping; regression; host-pathogen; Toxoplasma gondii; microscopy; Python; SQLite | NIAID AI007413; NIAID AI180278; NIGMS GM151129; NIH Office of the Director OD034245; Swedish Research Council 2021-06749 |
PMID:42465465 | Free, Available for download, Freely available | https://pypi.org/project/spacr/ | SCR_029041 | SciCrunch Registry | , spacr; spaCR: spatial phenotype analysis of CRISPR screens | 2026-10-24 12:54:55 | 0 | ||||||
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NIGMS Multimedia Resource Report Resource Website |
NIGMS Multimedia (RRID:SCR_005712) | NIGMS Multimedia | data or information resource, narrative resource, podcast, video resource | As part of its multimedia outreach, the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health -- the United States'' medical research agency -- offers audio and video podcasts and other multimedia resources that explore the exciting world of basic biomedical research. | basic research, biomedical research, biomedical | has parent organization: National Institute of General Medical Sciences | NIGMS | nlx_149379 | SCR_005712 | SciCrunch Registry | NIGMS Media Gallery, NIGMS - Multimedia, NIGMS - Media Gallery | 2026-10-24 12:45:31 | 0 | |||||||
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TOPSAN Resource Report Resource Website 10+ mentions |
TOPSAN (RRID:SCR_005758) | TOPSAN | data or information resource, data repository, database, image collection, service resource, storage service resource | Collect, share, and distribute information about protein three-dimensional structures. It serves as a portal for the scientific community to learn about protein structures solved by SG centers, and also to contribute their expertise in annotating protein function. The premise of the TOPSAN project is that, no matter how much any individual knows about a particular protein, there are other members of the scientific community who know more about certain aspects of the same protein, and that the collective analyses from experts will be far more informative than any local group, let alone individual, could contribute. They believe that, if the members of the biological community are given the opportunity, authorship incentives, and an easy way to contribute their knowledge to the structure annotation, they would do so. Therefore, borrowing elements from successful, distributed, collaborative projects, such as Wikipedia (the free encyclopedia anyone can edit) and from other open source software development projects, TOPSAN will be a broad, collaborative effort to annotate protein structures, initially, those determined at the JCSG. They believe that the annotation of proteins solved by structural genomics consortia offers a unique opportunity to challenge the extant paradigm of how biological data is collected and distributed, and to connect structural genomics and structural biology to the entire biological research community. TOPSAN is designed to be scalable, modular and extensible. Furthermore, it is intended to be immediately useful in a simplistic way and will accommodate incremental improvements to functionality as usage becomes more sophisticated. Their annotation pages will offer the end user a combination of automatically generated as well as expert-curated annotations of protein structures. They will use available technology to increase the speed and granularity of the exchange of scientific ideas, and use incentive mechanisms that will encourage collaborative participation. | protein, structure, 3d, protein structure, protein function, annotate, crowd sourcing, image, annotation, genomics, collaboration |
has parent organization: Sanford Burnham Prebys Medical Discovery Institute has parent organization: University of California at San Diego; California; USA |
NIGMS U54 GM074898; NIGMS P20 GM076221 |
PMID:20961957 PMID:20716366 PMID:20944203 PMID:20961957 |
Creative Commons Attribution v3 License, The community can contribute to this resource | nlx_149221 | SCR_005758 | SciCrunch Registry | he Open Protein Structure Annotation Network, TOPSAN Project, TOPSAN - The Open Protein Structure Annotation Network | 2026-10-24 12:45:32 | 10 | |||||
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ChemHealthWeb Resource Report Resource Website |
ChemHealthWeb (RRID:SCR_005851) | ChemHealthWeb | data or information resource, narrative resource, portal, topical portal, training material, video resource | Visit ChemHealthWeb for research highlights, chemist profiles, games and videos and other Web extras. The NIGMS Chemistry of Health booklet describes basic chemistry and biochemistry research that spurs a better understanding of human health. | chemistry, health, chemistry, biochemistry, research, human, game, puzzle, chemist, molecule, medicine, teacher | has parent organization: National Institute of General Medical Sciences | NIGMS | nlx_149382 | SCR_005851 | SciCrunch Registry | 2026-10-24 12:45:33 | 0 | ||||||||
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Polbase Resource Report Resource Website |
Polbase (RRID:SCR_006107) | data or information resource, data repository, database, service resource, storage service resource | Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software. | dna polymerase repository, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PubMed is related to: UniProt has parent organization: New England Biolabs |
Small Business Innovation Research ; NIGMS 1R44GM087021 |
PMID:21993301 | Free, Open unspecified license, Acknowledgement required | biotools:polbase, nlx_151580 | https://bio.tools/polbase | SCR_006107 | SciCrunch Registry | DNA Polymerase Database | 2026-10-24 12:45:38 | 0 | |||||
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QTL Archive Resource Report Resource Website 1+ mentions |
QTL Archive (RRID:SCR_006213) | QTL Archive | data or information resource, data repository, data set, service resource, storage service resource | Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive. | quantitative trait locus, inbred rat strain, phenotype, cross, genetics, inbreeding, genetic marker, quantitative genetics |
is listed by: re3data.org has parent organization: Jackson Laboratory |
NIGMS R01 GM070683 | The community can contribute to this resource | r3d100010571, nlx_151757 | https://doi.org/10.17616/R3C02Z | http://qtlarchive.org/ | SCR_006213 | SciCrunch Registry | Quantitative Trait Loci (QTL) Archive, Quantitative Trait Loci Archive | 2026-10-24 12:45:39 | 6 | ||||
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PSICQUIC Registry Resource Report Resource Website 10+ mentions |
PSICQUIC Registry (RRID:SCR_006389) | PSICQUIC | data access protocol, software resource, web service | Web service with well defined methods to enable programmatic access to molecular interactions. Standard for computational access to molecular interaction data resources. | molecular interaction, soap, rest, miql, programmatic access to molecular interactions |
is used by: mentha is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: Reactome is related to: InnateDB has parent organization: HUPO Proteomics Standards Initiative |
European Bioinformatics Institute for Chemogenomics Databases ; European Union Apoptosis Systems Biology Applied to Cancer and AIDS ; European Union Experimental Network for Functional Integration ; European Union Proteomics Standards Initiative and International Molecular Exchange ; European Union Serving Life-science Information for the Next Generation ; Foundation for the National Institutes of Health and Genome British Columbia ; German National Genome Research Network ; Italian Association for Cancer Research ; NIGMS R01GM071909; Wellcome Trust Strategic Award to the European Molecular Biology Laboratory |
PMID:21716279 | Free, Freely available | nlx_152188, nlx_152189, SCR_006392 | http://code.google.com/p/psicquic/ | SCR_006389 | SciCrunch Registry | Protemics Standard Initiative Common QUery InterfaCe, PSI common query interface | 2026-10-24 12:45:41 | 30 | ||||
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LIPID Metabolites And Pathways Strategy Resource Report Resource Website 1000+ mentions |
LIPID Metabolites And Pathways Strategy (RRID:SCR_006579) | LIPID MAPS | data or information resource, database, narrative resource, standard specification | Multi-institutional supported website and database that provides access to large number of globally used lipidomics resources. Internationally led the field of lipid curation, classification, and nomenclature since 2003. Produces new open-access databases, informatics tools and lipidomics-focused training activities will be generated and made publicly available for researchers studying lipids in health and disease. | lipid, pathway, classification, metabolomics, metabolite, FASEB list |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of California at San Diego; California; USA is parent organization of: LIPID MAPS Proteome Database is parent organization of: LIPID MAPS Structure Database |
Glue Grant ; NIGMS |
Free, Freely available | nif-0000-00368, SCR_026208, r3d100012315 | https://doi.org/10.17616/R3WW7G | SCR_006579 | SciCrunch Registry | , LIPID Maps database, LIPID Metabolites And Pathways Strategy database, LIPID Maps | 2026-10-24 12:45:47 | 1473 | |||||
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RNA Modification Database Resource Report Resource Website 10+ mentions |
RNA Modification Database (RRID:SCR_003535) | RNAmods | data or information resource, data repository, database, service resource, storage service resource | The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA. Information provided for each nucleoside includes: the type of RNA in which it occurs and phylogenetic distribution; common chemical name and symbol; Chemical Abstracts registry number and index name; chemical structure; initial literature citations for structural characterization or occurrence, and for chemical synthesis. Both the structural diversity and extent of posttranscriptional modification in RNA is remarkable, with 107 different nucleosides presently known in all types of RNA. The discovery of new modified nucleosides as well as increasing knowledge of the array of functional roles of modification, based largely on extensive studies of tRNA, mandates a need for a comprehensive database of RNA nucleosides. The RNA Modification Database is maintained as an extension of the initial version published in mid-1994. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. The information provided permits access to the modified nucleoside literature through provision of both computer-searchable Chemical Abstracts registry numbers and key literature citations. This database also provides an historical record of the initial reports of occurrence, characterization and chemical synthesis of modified nucleosides from RNA. It is our judgement that the total number of RNA nucleosides listed, and the chemical structures reported, are very accurate. However, the distributions listed are in some cases a matter of concern, due primarily to the possibility of inhomogeneity of the RNA isolate and the use of methods of nucleoside identification that are not sufficiently rigorous. Reinvestigation of some of the unusual or single-report source distributions is warranted, and will likely lead to future refinements in the listings. The authors invite comments concerning new entries, errors or omissions and on the format presently used for electronic access to the database. |
has parent organization: University at Albany; New York; USA has parent organization: University of Utah; Utah; USA |
NIGMS GM29812 | PMID:9399834 PMID:9016519 |
nif-0000-03414 | http://medlib.med.utah.edu/RNAmods/ | SCR_003535 | SciCrunch Registry | 2026-10-24 12:44:59 | 24 | |||||||
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UCSF Chimera Resource Report Resource Website 1000+ mentions |
UCSF Chimera (RRID:SCR_004097) | Chimera | d visualization software, data processing software, software application, software resource | Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials. | molecular modeling, electron microscopy, interactive visualization and analysis, molecular structures |
is used by: Structure-function linkage database is listed by: 3DVC is listed by: SoftCite is related to: Integrative Modeling Platform is related to: UCSF ChimeraX is related to: UCSF ChimeraX has parent organization: Resource for Biocomputing Visualization and Informatics |
NCRR P41 RR001081; NIGMS P41 GM103311 |
PMID:15264254 | Restricted | nlx_143560 | http://plato.cgl.ucsf.edu/chimera/ | SCR_004097 | SciCrunch Registry | Chimera - an Extensible Molecular Modeling System, UCSF Chimera - an Extensible Molecular Modeling System | 2026-10-24 12:45:07 | 2257 | ||||
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Simtk.org Resource Report Resource Website 10+ mentions |
Simtk.org (RRID:SCR_002680) | SimTK | simulation software, software application, software repository, software resource | A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code. | model, modeling, rna folding, protein folding, myosin dynamics, neuromuscular biomechanics, cardiovascular dynamics, biomolecular simulation, biomedical computing, repository, cardiovascular, neuromuscular, myosin, rna, simulation, biocomputation |
is used by: NIF Data Federation lists: Adaptively Sampled Particle Fluids lists: OpenMM lists: CPODES numerical integrator is listed by: Biositemaps is listed by: Integrated Models is listed by: DataCite is listed by: re3data.org is related to: OpenSim is related to: Simbody(tm): SimTK Multibody Dynamics Toolset is related to: SimVascular is related to: SAFA Footprinting Software is related to: Ion Simulator Interface is related to: LAPACK linear algebra library is related to: Neuromuscular Models Library has parent organization: Simbios is parent organization of: FEATURE is parent organization of: Cardiovascular Model Repository is parent organization of: ConTrack is parent organization of: Allopathfinder is parent organization of: Molecular Simulation Trajectories Archive of a Villin Variant is parent organization of: LAPACK linear algebra library is parent organization of: SimTKCore |
NIH ; NIGMS U54 GM072970 |
Free, Available for download, Freely available | nif-0000-23302, DOI:10.17616/R3QJ4B, DOI:10.18735 | https://doi.org/10.17616/R3QJ4B, https://doi.org/10.17616/r3qj4b, https://doi.org/10.18735/, https://dx.doi.org/10.18735/ | SCR_002680 | SciCrunch Registry | Simulation Toolkit, SimTK - the Simulation Toolkit | 2026-10-24 12:44:50 | 20 | |||||
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BioPortal Resource Report Resource Website 100+ mentions |
BioPortal (RRID:SCR_002713) | BioPortal | controlled vocabulary, data or information resource, data repository, ontology, repository, service resource, storage service resource | Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services. | biomedical, thesaurus, ontology mapping, annotation, metadata standard, ontology repository, portal, web service, obo, owl, rdf, rrf protege frame, lexgrid xml |
lists: MeGO lists: Porifera Ontology lists: EnvO lists: Research Network and Patient Registry Inventory Ontology lists: Semantic DICOM Ontology lists: Time Event Ontology lists: Variation Ontology lists: Vertebrate Skeletal Anatomy Ontology lists: Epoch Clinical Trial Ontology lists: Gazetteer lists: Human Disease Ontology lists: Information Artifact Ontology lists: NCBITaxon lists: Amphibian Taxonomy Ontology lists: Anatomic Pathology Lexicon lists: HIV ontology lists: International Classification of Primary Care - 2 PLUS lists: Mathematical Modelling Ontology lists: Nursing Interventions Classification lists: Phylogenetic Ontology lists: Bleeding History Phenotype Ontology lists: Body System Terms from ICD11 lists: Synthetic Biology Open Language Visual Ontology lists: Teleost Anatomy Ontology lists: Teleost Taxonomy Ontology lists: ECO lists: Bioassay Ontology lists: RightField lists: Gene Ontology lists: HGNC lists: Interaction Ontology lists: International Classification for Nursing Practice lists: Spider Ontology lists: Vertebrate Trait Ontology lists: Mental Functioning Ontology lists: Ascomycete Phenotype Ontology lists: Beta Cell Genomics Ontology lists: Biological Collections Ontology lists: Chemical Methods Ontology lists: Chemical Information Ontology lists: Common Anatomy Reference Ontology lists: Experimental Conditions Ontology lists: Dictyostelium Discoideum Anatomy Ontology lists: Fission Yeast Phenotype Ontology lists: Fly Taxonomy lists: FlyBase Controlled Vocabulary lists: Hymenoptera Anatomy Ontology lists: Influenza Ontology lists: Lipid Ontology lists: Kinetic Simulation Algorithm Ontology lists: Malaria Ontology lists: FMA lists: Minimal Anatomical Terminology lists: NEMO Ontology lists: Ontology for Genetic Interval lists: Ontology for Parasite LifeCycle lists: Ontology of Adverse Events lists: Ontology of Medically Related Social Entities lists: Ontology of Vaccine Adverse Events lists: Rat Strain Ontology lists: Plant Environmental Conditions lists: Plant Trait Ontology lists: Population and Community Ontology lists: RNA Ontology lists: Rat Strain Ontology lists: Subcellular Anatomy Ontology lists: Software Ontology lists: Suggested Ontology for Pharmacogenomics lists: Vertebrate Taxonomy Ontology lists: PharmGKB Ontology lists: Physico-Chemical Process lists: International Classification for Patient Safety lists: Adverse Event Reporting Ontology lists: Experimental Factor Ontology lists: Mass Spectrometry Ontology lists: Master Drug Data Base Clinical Drugs lists: Medaka Fish Anatomy and Development Ontology lists: Medical Diagnostic Categories - Diagnosis Related Groups lists: Medical Dictionary for Regulatory Activities lists: Minimal Standard Terminology of Digestive Endoscopy lists: Minimal Standard Terminology of Digestive Endoscopy - French lists: Ontology of Physical Exercises lists: Mosquito Gross Anatomy Ontology lists: Systematized Nomenclature of Medicine - International Version lists: Mosquito Insecticide Resistance Ontology lists: Mouse Experimental Design Ontology lists: Mouse Gross Anatomy and Development Ontology lists: Systematized Nomenclature of Medicine - Clinical Terms lists: Systems Chemical Biology and Chemogenomics Ontology lists: Mouse Pathology Ontology lists: NIF Cell Ontology lists: NHS Quality Indicators lists: Neural-Immune Gene Ontology lists: Ontology of Physics for Biology lists: Cell Type Ontology lists: Xenopus Anatomy Ontology lists: SO lists: Ontology of Pneumology lists: Open Biological and Biomedical Ontologies Relationship Types lists: Biomedical Resource Ontology lists: MGED Ontology lists: Pharmacovigilance Ontology lists: PhenX Phenotypic Terms lists: Bioinformatics Web Service Ontology lists: SysMO JERM Ontology of Systems Biology for Micro-Organisms lists: MeSH lists: PATO lists: BFO lists: MPO lists: PR lists: Cereal Plant Development Ontology lists: PhenomeBLAST Ontology lists: VIVO lists: Computer Assisted Brain Injury Rehabilitation Ontology lists: Computer Retrieval of Information on Scientific Projects Thesaurus lists: NIFSTD lists: Cell Line Ontology lists: Student Health Record Ontology lists: Zebrafish Anatomical Ontology lists: Physical Medicine and Rehabilitation lists: Randomized Controlled Trials Ontology lists: Human Phenotype Ontology lists: Read Codes Clinical Terms Version 3 lists: Reference Sequence Annotation lists: Regulation of Gene Expression Ontolology lists: Neurobehavior Ontology lists: Regulation of Transcription Ontology lists: Reproductive Trait and Phenotype Ontology lists: Skin Physiology Ontology lists: Vaccine Ontology lists: OMIM lists: MedlinePlus lists: Adult Mouse Anatomy Ontology lists: Bone Dysplasia Ontology lists: Bone and Cartilage Tissue Engineering Ontology lists: Botryllus schlosseri anatomy and development ontology lists: EDAM Ontology lists: LexGrid lists: RxNorm lists: Breast Cancer Grading Ontology lists: Breast Tissue Cell Lines Ontology lists: SBO lists: Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology lists: Brucellosis Ontology lists: Sleep Domain Ontology lists: C. elegans Development Vocabulary lists: Physician Data Query lists: C. elegans Gross Anatomy Vocabulary lists: Plant Ontology lists: C. elegans Phenotype Vocabulary lists: CPTAC Proteomics Pipeline Infrastructure Ontology lists: Cancer Research and Management ACGT Master Ontology lists: Cancer Chemoprevention Ontology lists: Cell Behavior Ontology lists: Cereal Plant Gross Anatomy Ontology lists: Cardiac Electrophysiology Ontology lists: Cerebrotendinous Xanthomatosis Ontology lists: Cell Cycle Ontology lists: Cell Culture Ontology lists: Cerrado concepts and plant community dynamics lists: Clinical Signs and Symptoms Ontology lists: Clusters of Orthologous Groups Analysis Ontology lists: Computational Neuroscience Ontology lists: BIRNLex lists: Computer-Based Patient Record Ontology lists: Congenital Heart Defects Ontology lists: Drug Interaction Knowledge Base Ontology lists: Healthcare Common Procedure Coding System lists: Host Pathogen Interactions Ontology lists: Human Dermatological Disease Ontology lists: Solanaceae Phenotype Ontology lists: Soy Ontology lists: Spatial Ontology lists: Surgical Secondary Events lists: eagle-i research resource ontology lists: Biological Pathways Exchange lists: Autism Spectrum Disorder Phenotype Ontology lists: BRENDA Tissue and Enzyme Source Ontology lists: BioTop Ontology lists: Family Health History Ontology lists: International Classification of Diseases Version 9 - Clinical Modification lists: BioModels Ontology lists: Bilingual Ontology of Alzheimer lists: BioPortal Metadata Ontology lists: Biochemical Substructure Ontology lists: Biodiversity Ontology lists: Biological Imaging Methods Ontology lists: International Classification of Functioning Disability and Health lists: Biologie Hors Nomenclature lists: International Classification of Primary Care lists: Biomedical Research Integrated Domain Group Model lists: KB Bio 101 lists: Bionutrition Ontology lists: Artificial Intelligence Rheumatology Consultant System Ontology lists: Leukocyte Surface Marker Ontology lists: Cell Line Ontology by Mahadevan lists: Cellular microscopy phenotype ontology lists: ABA Adult Mouse Brain Ontology lists: AEO lists: African Traditional Medicine Ontology lists: Alzheimer's disease ontology lists: Amino Acid Ontology lists: Amphibian Gross Anatomy Ontology lists: Animal Natural History and Life History Ontology lists: Coding Symbols for a Thesaurus of Adverse Reaction Terms lists: Cognitive Atlas Ontology lists: Common Terminology Criteria for Adverse Events lists: Comparative Data Analysis Ontology lists: Content Archive Resource Exchange Lexicon lists: Crop Ontology lists: Current Procedural Terminalogy Hierarchy lists: Current Procedural Terminology lists: DICOM Controlled Terminology lists: Dataset processing lists: Dengue Fever Ontology lists: Dermatology Lexicon lists: Diagnosis Ontology of Clinical Care Classification lists: Diagnostic Ontology lists: Disease core ontology applied to Rare Diseases lists: Dispedia Core Ontology lists: Drosophila Development Ontology lists: Drosophila Gross Anatomy Ontology lists: EDDA Study Design Terminology lists: Electrocardiography Ontology lists: Eligibility Feature Hierarchy lists: Enzyme Mechanism Ontology lists: Enzyme Reaction Ontology for partial chemical perspectives lists: Epilepsy Ontology lists: Loggerhead Nesting Ontology lists: Fanconi Anemia Ontology lists: Fire Ontology lists: Flora Phenotype Ontology lists: Fungal Gross Anatomy Ontology lists: Human Developmental Anatomy Ontology abstract version 1 lists: G Protein-Coupled Receptor BioAssays Ontology lists: Galen Ontology lists: Gene Expression Ontology lists: Gene Ontology Extension lists: General Formal Ontology lists: General Formal Ontology for Biology lists: Genome Component Ontology lists: Genomic Clinical Decision Support Ontology lists: GeoSpecies Ontology lists: Glycomics Ontology lists: Habronattus Courtship Ontology lists: Health Indicator Ontology lists: Health Level Seven Reference Implementation Model Version 3 lists: Human Developmental Anatomy Ontology abstract version 2 lists: Human Developmental Anatomy Ontology timed version lists: Human Interaction Network Ontology lists: Human Physiology Simulation Ontology lists: Logical Observation Identifier Names and Codes lists: IMGT-ONTOLOGY lists: Image and Data Quality Assessment Ontology lists: Immune Disorder Ontology lists: Infectious Disease Ontology lists: InterNano Nanomanufacturing Taxonomy lists: Interaction Network Ontology lists: International Classification of External Causes of Injuries lists: International Classification of Diseases Version 10 lists: International Classification of Diseases Version 10 - Clinical Modification lists: International Classification of Diseases Version 10 - Procedure Coding System lists: MR dataset acquisition lists: Maize Gross Anatomy Ontology lists: Major Histocompatibility Complex Ontology lists: Medical image simulation lists: Menelas Project Top-Level Ontology lists: Mental State Assessment lists: Metagenome Sample Vocabulary lists: Metagenome and Microbes Environmental Ontology lists: MicroRNA Ontology lists: Microbial Culture Collection Vocabulary lists: Microbial Typing Ontology lists: Minimal Information about any Sequence Controlled Vocabularies lists: Minimal Information about any Sequence Ontology lists: NIF Dysfunction Ontlogy lists: NIF Subcellular Ontology lists: NMR-Instrument Component of Metabolomics Investigations Ontology lists: Name Reaction Ontology lists: NanoParticle Ontology lists: National Cancer Institute Thesaurus lists: National Drug Data File lists: National Drug File - Reference Terminology lists: Natural Products Ontology lists: Neglected Tropical Disease Ontology lists: Neomark Oral Cancer Ontology version 3 lists: Neomark Oral Cancer Ontology version 4 lists: Neural Motor Recovery Ontology lists: NeuroMorpho.Org species ontology lists: NeuroMorpho.Org species ontology old lists: Non-Randomized Controlled Trials Ontology lists: Nursing Care Coordination Ontology lists: Ontological Knowledge Base Model for Cystic Fibrosis lists: Ontology for Drug Discovery Investigations lists: Ontology for General Medical Science lists: Ontology for Genetic Disease Investigations lists: Ontology for Genetic Susceptibility Factor lists: Ontology for MicroRNA Target Prediction lists: Symptom Ontology lists: Ontology for Newborn Screening Follow-up and Translational Research lists: Ontology of Alternative Medicine French lists: Ontology of Biological and Clinical Statistics lists: Ontology of Clinical Research lists: Ontology of Core Data Mining Entities lists: Ontology of Data Mining Investigations lists: Pediatric Terminology lists: Ontology of Experimental Variables and Values lists: Ontology of General Purpose Datatypes lists: Ontology of Geographical Region lists: Ontology of Glucose Metabolism Disorder lists: Ontology of Homology and Related Concepts in Biology lists: Ontology of Language Disorder in Autism lists: Orphanet Rare Disease Ontology lists: Parasite Experiment Ontology lists: Pathogen Transmission Ontology lists: Pathogenic Disease Ontology lists: Pharmacogenomic Relationships Ontology lists: Physico-Chemical Methods and Properties lists: Plant Anatomy lists: Syndromic Surveillance Ontology lists: Plant Structure Development Stage lists: Portfolio Management Application lists: Protein Modification Ontology lists: Protein-Protein Interaction Ontology lists: Proteomics Data and Process Provenance Ontology lists: Provenance Ontology lists: QUDT lists: Quantitative Imaging Biomarker Ontology lists: Radiology Lexicon lists: Robert Hoehndorf Version of MeSH lists: Role Ontology lists: STATistics Ontology lists: Sage Bionetworks Synapse Ontology lists: Sample Processing and Separation Techniques Ontology lists: Santa Barbara Coastal Observation Ontology lists: Semantic Types Ontology lists: Semantic Web for Earth and Environment Technology Ontology lists: Semanticscience Integrated Ontology lists: Single-Nucleotide Polymorphism Ontology lists: Situation-Based Access Control Ontology lists: Taxonomic Rank Vocabulary lists: Taxonomy for Rehabilitation of Knee Conditions lists: Terminological and Ontological Knowledge Resources Ontology lists: Tick Gross Anatomy Ontology lists: Tissue Microarray Ontology lists: Traditional Medicine Constitution Value Set lists: Traditional Medicine Meridian Value Sets lists: Traditional Medicine Other Factors Value Set lists: Traditional Medicine Signs and Symptoms Value Set lists: Translational Medicine Ontology lists: Tribolium Ontology lists: Units Ontology lists: Units of Measurement Ontology lists: Upper-Level Cancer Ontology lists: Vertebrate Homologous Organ Group Ontology lists: Veterans Health Administration National Drug File lists: Vital Sign Ontology lists: WHO Adverse Reaction Terminology lists: Web-Service Interaction Ontology lists: Wheat Trait Ontology lists: XEML Environment Ontology lists: suicideo lists: suicideonto lists: Pseudogene lists: Terminology for the Description of Dynamics lists: Gene Regulation Ontology lists: UBERON lists: CHEBI lists: Cognitive Paradigm Ontology lists: Emotion Ontology lists: Clinical Measurement Ontology lists: Measurement Method Ontology lists: NCI Thesaurus lists: Ontology for Biomedical Investigations lists: Biological Pathways Exchange is listed by: Biositemaps is listed by: FORCE11 is related to: Provisional Cell Ontology has parent organization: National Center for Biomedical Ontology has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Biomedical Informatics Research is parent organization of: NCBO Annotator |
NIGMS U24 GM143402 | PMID:19483092 PMID:21672956 PMID:18999306 |
Free, Available for download, Freely available | nif-0000-23346, r3d100012344 | https://www.force11.org/node/4646, https://doi.org/10.17616/R3J362 | SCR_002713 | SciCrunch Registry | BioPortal Knowledgebase | 2026-10-24 12:44:46 | 363 | ||||
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Molecular Simulation Trajectories Archive of a Villin Variant Resource Report Resource Website |
Molecular Simulation Trajectories Archive of a Villin Variant (RRID:SCR_002704) | Molecular Simulation Trajectories Archive of a Villin Variant | d spatial image, data or information resource, data set | An archive of hundreds of all-atom, explicit solvent molecular dynamics simulations that were performed on a set of nine unfolded conformations of a variant of the villin headpiece subdomain (HP-35 NleNle). It includes scripts for accessing the archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided. The simulations were generated using a distributed computing method utilizing the symmetric multiprocessing paradigm for individual nodes of the Folding_at_home distributed computing network. The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8. Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into frames, also known as a generation. Each frame contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1. The goal is to allow researchers to analyze and benefit from the many trajectories produced through the simulations. | dynamic, atom, headpiece, molecular, simulation, solvent, protein folding, villin, molecule, trajectory, simulation, molecular dynamics trajectory |
is listed by: Biositemaps has parent organization: Simtk.org |
Stanford University; California; USA ; Graduate Fellowship ; NIH ; NIGMS R01-GM062868; NSF MCB-0317072 |
PMID:17950314 | Acknowledgement requested, Available in Gromacs and PDB formats. | nif-0000-23331 | SCR_002704 | SciCrunch Registry | 2026-10-24 12:44:51 | 0 | ||||||
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PRO Resource Report Resource Website 1+ mentions |
PRO (RRID:SCR_002902) | controlled vocabulary, data or information resource, ontology | An ontological representation of protein-related entities, explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. PRO encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). | protein |
is listed by: OMICtools has parent organization: Protein Information Resource |
NIGMS 5R01GM080646-09 | PMID:21929785 | OMICS_06200 | SCR_002902 | SciCrunch Registry | Protein Ontology | 2026-10-24 12:44:55 | 4 | |||||||
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Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | data analysis software, data processing software, data visualization software, software application, software resource | Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. | biological, network, visualization, analysis, data, gene, pathway, molecular, interaction, FASEB list |
is used by: CytoSPADE is used by: HDBase is used by: DisGeNET is used by: categoryCompare lists: PEPPER is listed by: Debian is listed by: SoftCite is related to: PhosphoSitePlus: Protein Modification Site is related to: TRIP Database is related to: CoryneRegNet is related to: AltAnalyze - Alternative Splicing Analysis Tool is related to: MiMI Plugin for Cytoscape is related to: Network Data Exchange (NDEx) is related to: GeneMANIA is related to: DroID - Drosophila Interactions Database is related to: Network-based Prediction of Human Tissue-specific Metabolism is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: DaTo is related to: PiNGO is related to: iBIOFind is related to: cPath is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: ClueGO is related to: RamiGO is related to: EGAN: Exploratory Gene Association Networks has parent organization: Institute for Systems Biology; Washington; USA has parent organization: University of California at San Diego; California; USA is parent organization of: JEPETTO has plug in: CluePedia Cytoscape plugin has plug in: CytoSPADE has plug in: EnrichmentMap has plug in: cytoHubba has plug in: iRegulon works with: NetCirChro works with: IMEx - The International Molecular Exchange Consortium works with: yFiles Layout Algorithms works with: RCy3 |
National Resource for Network Biology ; NCRR RR031228; NIGMS GM070743 |
PMID:21149340 PMID:14597658 |
Free, Available for download, Freely available | nif-0000-30404 | https://sources.debian.org/src/cytoscape/ | SCR_003032 | SciCrunch Registry | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-10-24 12:44:51 | 25317 |
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