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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.

(last updated: Oct 12, 2019)

Physical Resource or Software Tool Software

16,890 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
NCI ThesaurusResource, ontology, data or information resource, controlled vocabularyA reference terminology and core biomedical ontology for NCI that covers approximately 100,000 key biomedical concepts with terms, codes, definitions, and more than 200,000 inter-concept relationships. It is the reference terminology for NCI, NCI Metathesaurus and NCI informatics infrastructure covering vocabulary for clinical care, translational and basic research, and public information and administrative activities. It includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships. NCIt features: * Stable, unique codes for biomedical concepts; * Preferred terms, synonyms, definitions, research codes, external source codes, and other information; * Links to NCI Metathesaurus and other information sources; * Over 200,000 cross-links between concepts, providing formal logic-based definition of many concepts; * Extensive content integrated from NCI and other partners, much available as separate NCIt subsets * Updated frequently by a team of subject matter experts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP).thesaurus, clinical, treatment, prevention, biomedical, owl, health, drug, chemotherapySCR_003563(NCI Thesaurus, RRID:SCR_003563)National Cancer Institute Cancerrelated to: NCI Metathesaurus, OnEx - Ontology Evolution Explorer, listed by: OBO, BioPortalLast checked upnlx_157698ftp://ftp1.nci.nih.gov/pub/cacore/EVS/, https://cabig.nci.nih.gov/concepts/EVS/, https://wiki.nci.nih.gov/display/EVS/NCI+Thesaurus+%28NCIt%29, http://nciterms.nci.nih.gov, http://purl.bioontology.org/ontology/NCIThttp://ncicb.nci.nih.gov/core/EVS
Physico-Chemical Methods and PropertiesResource, ontology, data or information resource, controlled vocabularyTwo ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties.obo, method, property, biophysical chemistry, physico-chemicalSCR_010407(Physico-Chemical Methods and Properties, RRID:SCR_010407)CHEBI listed by: BioPortal, OBOLast checked upnlx_157552ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo
Physico-Chemical ProcessResource, ontology, data or information resource, controlled vocabularyAn ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. It includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX.obo, physico-chemical process, physico-chemical, microscopic process, molecular entity, subatomic particle, macroscopic process, biochemical processSCR_003530(Physico-Chemical Process, RRID:SCR_003530)CHEBI related to: Gene Ontology, listed by: BioPortal, OBOLast checked upnlx_157639ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/rex.obo, http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=REXhttp://www.ebi.ac.uk/~kirill/REX/
Connecting Overlapped Pair-End readsResource, software resourceAn efficient software tool to connect overlapping pair-end reads using k-mer frequencies.standalone software, c++SCR_012102(Connecting Overlapped Pair-End reads, RRID:SCR_012102)SourceForge listed by: OMICtoolsPMID:23044551Last checked upOMICS_05256ftp://ftp.genomics.org.cn/pub/cope
GCEResource, software resource, software application, data analysis software, data processing softwareSoftware tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.estimation, genomic, characteristic, analysis, k-mer, frequencey, de novoSCR_017332(GCE, RRID:SCR_017332)Last checked upftp://ftp.genomics.org.cn/pub/gce
BMTaggerResource, software resource, software application, data processing softwareA tool that discriminates between human reads and microbial reads without performing an alignment of all reads to the human genome.microbiome, human reads, metagenomics, microbial reads, human genomeSCR_014619(BMTagger, RRID:SCR_014619)listed by: Human Microbiome ProjectLast checked upftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/
RefSeqResource, data or information resource, databaseCollection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.curated, non redundant, genomic, DNA, transcript, RNA, protein, sequence, NCBI, reference, gene, identification, mutation, polymorphism, analysisSCR_016579(RefSeq, RRID:SCR_016579)NCBI related to: INSDCLast checked upftp://ftp.ncbi.nlm.nih.gov/refseq
HIBALResource, software resourceFORTRAN code for a simple hydrologic-isotopic-balance model for application to paleolake d18O records. Inputs to the model include discharge, on-lake precipitation, evaporation, and the d18O values of these fluid fluxes. Benson and Paillet (2002)d18o, hydrologic isotopic balance model, paleolake, hydrology, hydrologic, isotopic, balance, model, fortran, discharge, evaporation, precipitation, fluid flux, recordSCR_002461(HIBAL, RRID:SCR_002461)World Data Center for Paleoclimatology listed by: CINERGILast checked downSciRes_000127ftp://ftp.ncdc.noaa.gov/pub/data/paleo/softlib/hibal/hibal.txt
VaDiRResource, data analysis software, data processing software, software application, sequence analysis software, algorithm resource, software resourceMethod for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets.rna-seq, somatic variant calling, ovarian cancer, cancer genomes transcriptome, orthogonal validation, genetic mutation, sequence variation analysisSCR_015797(VaDiR, RRID:SCR_015797)Biostatistics and Informatics Shared Resource (BISR), Cancer Center Cancer Biology program, Department of Defense Ovarian Cancer Research Program, University of Kansas Cancer Center Support Grant, University of Kansas Endowment AssociationDOI:10.5524/100360Last checked upftp://penguin.genomics.cn/pub/10.5524/100001_101000/100360/
Experimental Conditions OntologyResource, ontology, data or information resource, controlled vocabularyAn ontology designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.obo, clinical, physiology, morphology, measurementSCR_003306(Experimental Conditions Ontology, RRID:SCR_003306)Medical College of Wisconsin; Wisconsin; USA listed by: BioPortal, OBOPMID:22654893Last checked upnlx_157401ftp://rgd.mcw.edu/pub/ontology/experimental_condition/experimental_condition.obo, http://sourceforge.net/projects/phenoonto/
HARPResource, standalone software, data processing software, software application, data visualization software, 3d visualization software, software resource, image processing softwareSoftware as a cross platform application for automating the processing of ?CT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release.MRC Harwell UK, automating, processing, uCT, OPT, image, dataSCR_016546(HARP, RRID:SCR_016546)related to: IMPC, submitted by: Resource Identification PortalLast checked upharp.exe
Bacteriome.orgResource, data or information resource, databaseDatabase integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong.functional interaction, genetics, genome, protein, protein-protein interaction, protein interaction, function, evolution, structure, gene, phylogenetic profile, chromosome, blast, phylogenetic, complex, networkSCR_001934(Bacteriome.org, RRID:SCR_001934)University of Toronto; Ontario; Canada Canadian Institutes of Health Researchlisted by: OMICtoolsReferences (2)Last checked upnif-0000-02592, OMICS_01899http://128.100.134.188/bacteriome/
PRINTSResource, data or information resource, databaseCompendium of protein fingerprints. Diagnostic fingerprint database.compedium, protein, fingerprint, diagnostic, databaseSCR_003412(PRINTS, RRID:SCR_003412)University of Manchester; Manchester; United Kingdom Last checked upnif-0000-03338http://130.88.97.239/PRINTS/index.php
Bremen Cancer RegistryResource, data or information resource, databaseA population based database collecting incident cases of cancer diagnosed since January 1998 in the population of the Federal state of Bremen. The Registry provides data for the analysis of * age specific time trends and geographical patterns of cancer incidence in men and women * cancer causes (e.g. work-related, environmental and personal risk factors) * epidemiological evaluation of screening programs * survival analysis of cancer patients. Since the incidence year of 2001, the Registry has a completeness level of > 95 %, based on expected values provided by the Robert Koch Institute.registry, male, female, ageSCR_004093(Bremen Cancer Registry, RRID:SCR_004093)CancerGerman Federal Ministry of Healthrelated to: Robert Koch Institute, Berlin, GermanyLast checked upnlx_158557http://134.102.3.71/, http://www.krebsregister.bremen.de
CCNY Microscopy FacilityResource, service resource, core facility, access service resourceThe microscopy center is a shared central facility whose primary goal is to promote scientific research by providing training in basic operation of the scanning electron microscope (SEM), the transmission electron microscope (TEM) and the Confocal.RRRRR RRRRR New users of the facility are asked to submit an application then schedule an appointment with the manager to discuss the project or to begin training.SCR_009697(CCNY Microscopy Facility, RRID:SCR_009697)City College of New York; New York; USA listed by: Eagle ILast checked upnlx_156157http://134.74.50.69/em/
MirSNPResource, data or information resource, databaseDatabase of human SNPs in predicted miRNA-mRNA binding sites, based on information from dbSNP135 and mirBASE18. MirSNP is highly sensitive and covers most experiments confirmed SNPs that affect miRNA function. MirSNP may be combined with researchers' own GWAS or eQTL positive data sets to identify the putative miRNA-related SNPs from traits/diseases associated variants. They aim to update the MirSNP database as new versions of mirBASE and dbSNP database become available.single nucleotide polymorphism, mirna, genome-wide association study, expression quantitative trait locus, mirna-mrna binding site, trait, disease, variant, gene, mrnaSCR_001629(MirSNP, RRID:SCR_001629)Peking University; Beijing; China International Science and Technology Cooperation Program of China, National High Technology Research and Development Program of China, National Natural Science Foundation of ChinaPMID:23173617Last checked downnlx_153896http://202.38.126.151/hmdd/mirsnp/search/
miRGatorResource, data or information resource, databaseDatabase of compiled, public, deep sequencing miRNA data and several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data are of great utility for studying iso-miRs, miRNA editing and modifications. miRNA??????target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets.genome, functional annotation, microrna, expression profile, mir-seq, mirna-mrna target relation, expression correlationSCR_007793(miRGator, RRID:SCR_007793)Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea Korean Ministry of Science and Technology, Korean Rural Development Administration, Ministry of Education and Human Resources Developmentlisted by: OMICtoolsReferences (3)Last checked downnif-0000-03136, OMICS_00363http://203.255.191.19/MEXWebApp/, http://genome.ewha.ac.kr/miRGator/miRGator.html
ViewTool Cheng LabResource, software resource, web applicationWeb application viewer for large microscopy data.microscope, microscopy, data, portal, penn, stateSCR_016430(ViewTool Cheng Lab, RRID:SCR_016430)submitted by: Resource Identification PortalLast checked uphttp://3d.fish/
3D-InterologsResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins.interolog, protein-protein interaction, blast, homolog, protein, interaction, functionSCR_003101(3D-Interologs, RRID:SCR_003101)National Chiao Tung University; Hsinchu; Taiwan related to: IntAct, Universal Protein Resource, Gene OntologyPMID:21143789Last checked upnif-0000-00554, OMICS_01896http://3D-interologs.life.nctu.edu.tw
COMPASSResource, software resource, algorithm resourceAlgorithm for MATLAB and the EEGLAB toolbox that enables the automatic detection of independent components from an ICA that represent event-related brain potentials. It performs automatic Independent Component (IC) selection with respect to the contributions of the ICs to a certain ERP.matlab, eeglab, independent component, ica, erp, event-related potentialSCR_015874(COMPASS, RRID:SCR_015874)Gertrud Reemtsma Foundation for Brain Researchused by: MATLABPMID:20965258Last checked uphttp://53450283.de.strato-hosting.eu/jrw/lab/e_compass.htm
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