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SciCrunch: Registry

SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, materials, and more - visit SciCrunch to register your resource.

(last updated: Jul 14, 2018)

Physical Resource or Software Tool Software

15,940 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Linkoping University; Linkoping; SwedenOrganization, university, institutionSCR_004156(Linkoping University; Linkoping; Sweden, RRID:SCR_004156)related to: LifeGeneLast checked upnlx_158604
Echelon BiosciencesResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplierSCR_004169(Echelon Biosciences, RRID:SCR_004169)Last checked upnlx_152350
Cosmo Bio CoResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplierSCR_004296(Cosmo Bio Co, RRID:SCR_004296)Last checked upnlx_152334
EpiGRAPHResource, software resourceA software for genome and epigenome analysis.SCR_004326(EpiGRAPH, RRID:SCR_004326)listed by: OMICtoolsLast checked upOMICS_00633
wFleaBaseResource, data or information resource, databasewFleaBase provides gene and genomic information for species of the genus Daphnia - commonly known as the water flea. It contains the genome of Daphnia pulex and other species, including bulk data files, and all gene pages, plus genomics tools including microsatellites, cDNA, Cosmid and BAC libraries, GSS and ESTs, and microarrays. It also contains maps of the Daphnia genome, and genome annotation tools. The freshwater crustacean Daphnia is a model system for ecology, evolution and the environmental sciences. The rapidly growing genomic data for this organism is stimulating interdisciplinary research to understand the complex interplay between genome structure, gene expression, individual fitness, and population-level responses to chemical contaminants and environmental change.wFleaBase includes data from all species of the genus, yet the primary species are D. pulex and D. magna, because of the broad set of genomic tools that have already been developed for these animals. A complete sequence for Daphnia pulex is now available at this site. Please observe this Data release policy. The data is a first characterization of the crustacean genome, which was made possible by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) in collaboration with the Daphnia Genomics Consortium (DGC) whose members were funded by the National Science Foundation. Category: Genomics Databases (non-vertebrate) Subcategory: Invertebrate genome databasesSCR_006018(wFleaBase, RRID:SCR_006018)Indiana University; Indiana; USA Last checked upnif-0000-03642
QuidelResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplierSCR_006146(Quidel, RRID:SCR_006146)Last checked upnlx_152444
University of Waterloo; Ontario; CanadaResource, university, institutionSCR_006166(University of Waterloo; Ontario; Canada, RRID:SCR_006166)Last checked upnlx_143877
University of Notre Dame; Indiana; USAResource, university, institutionSCR_006191(University of Notre Dame; Indiana; USA, RRID:SCR_006191)Last checked upnlx_51295
University of Western Brittany; Brest; FranceResourceSCR_006232(University of Western Brittany; Brest; France, RRID:SCR_006232)related to: PRECISESADSLast checked upnlx_158277
University of Tunis El Manar; Tunis; TunisiaResource, university, institutionSCR_011736(University of Tunis El Manar; Tunis; Tunisia, RRID:SCR_011736)Last checked upnlx_77337
SchrodingerResourceCommercial ogranization which provides molecular and drug discovery software and services to researchers.software solution, drug discovery, small molecule, computational chemistrySCR_014879(Schrodinger, RRID:SCR_014879)Last checked up
ACCUSA2Resource, software resourceMulti-purpose SNV calling software enhanced by probabilistic integration of quality scores.snvSCR_000558(ACCUSA2, RRID:SCR_000558)listed by: OMICtoolsLast checked downOMICS_01360
University of Twente; Overijssel; NetherlandsResource, university, institutionSCR_011737(University of Twente; Overijssel; Netherlands, RRID:SCR_011737)Last checked upnlx_151953
Epoch Clinical Trial OntologyResource, ontology, data or information resource, controlled vocabularyOntology of clinical trial terminology.owlSCR_000366(Epoch Clinical Trial Ontology, RRID:SCR_000366)listed by: BioPortalLast checked upnlx_157400
GenomeJackResource, software resourceA genome browser specialized in next-generation sequencing data.next-generation sequencing, genome, browser, analysisSCR_012026(GenomeJack, RRID:SCR_012026)listed by: OMICtoolsLast checked upOMICS_02143
ProSpecResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplierSCR_006584(ProSpec, RRID:SCR_006584)Last checked upnlx_152436
NanopolishResource, software resource, software application, data analysis software, data processing softwareSoftware package for signal-level analysis of Oxford Nanopore sequencing data.SCR_016157(Nanopolish, RRID:SCR_016157)Last checked up
International Biobank, Inc.Resource, biomaterial supply resource, material resource, tissue bankNot yet vetted by NIF curatorSCR_010549(International Biobank, Inc., RRID:SCR_010549)Last checked upnlx_32905
Program DynaFitResource, software resourceProgram DynaFit Analysis of (bio)chemical kinetics and equilibria Welcome to the DynaFit home page. Purpose Symbolic Notation Bibliographic Reference Numerical Methods Minimum System Requirements Purpose The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance). Symbolic Notation The main advantage in using the program DynaFit is in the ability to characterize the (bio)chemical reacting system in terms of symbolic, or stoichiometric, equations. For example, the ``slow, tight'''' inhibition of a dissociative dimeric enzyme is described by the following text: Monomer Monomer <==> Enzyme : k1 k2 Enzyme Inhibitor <==> Complex : k3 k4 Enzyme Substrate <==> ReactiveX : k5 k6 ReactiveX --> Product Enzyme : k7 k8 The names of chemical species (Monomer, Enzyme, etc.) are entirely arbitrary and can be freely chosen by the investigator. Bibliographic Reference If you publish any results obtained by using DYNAFIT, plase cite the following reference: Kuzmic, P. (1996) Anal. Biochem. 237, 260-273. Program DYNAFIT for the Analysis of Enzyme Kinetic Data: Application to HIV Proteinase ABSTRACT A computer program with the code name DYNAFIT was developed for fitting either the initial velocities, or the time-course of enzyme reactions, to an arbitrary molecular mechanism represented symbolically by a set of chemical equations. Seven numerical tests and five graphical tests are applied to judge the goodness of fit. Experimental data on the inhibition of the dissociative dimeric proteinase from HIV were used in four test examples. A set of initial velocities was analyzed to see if a tight-binding inhibitor could bind to the HIV proteinase monomer. Three different sets of progress curves were analyzed (i) to determine the kinetic properties of an irreversible inhibitor; (ii) to investigate the dissociation and denaturation mechanism for the protease dimer; and (iii) to investigate the inhibition mechanism for a transient inhibitor. See a MEDLINE abstract with related references concerning the kinetics of HIV-1 protease. Numerical Methods The nonlinear regression module uses the Levenberg-Marquardt algorithm [1]. The time-course of (bio)chemical reactions is computed by the numerical integration of simultaous first-order ordinary differential equations, using the Livermore Solver of ODe Systems (LSODE, [2]). The composition of complex mixtures at equilibrium (e.g., in the concentration jump experiment where a complex mixture is incubated prior to the addition of a reagent) is computed by solving simultaneous nonlinear algebraic equations, namely, the mass balance equations for the component species, by using the multidimensional Newton-Raphson method [3]. References G. A. F. Seber and C. J. Wild (1989) Nonlinear Regression, Wiley, New York, p. 624. A. C. Hindmarsh (1983) ODEPACK: a systematized collection of ODE solvers; in Scientific Computing, ed. R. S. Stepleman et al., North Holland, Amsterdam, pp. 55--64. E. Kreyszig (1993) Advanced Engineering Mathematics; 7th ed., John Wiley, New York, p. 929. Minimum System Requirements DynaFit for Windows Intel Pentium III or Celeron class 800 MHz or faster processor Microsoft Windows XP (SP1) or 2000 (SP2) 128 MB RAM 20 MB Hard Disk Space Ethernet Network Interface Card required for license activation(1) CD/DVD-ROM drive required for software installation(2) (1) The Network Interface Card is used to compute a unique Computer ID, tied to a particular DynaFit license. Essentially the Computer ID required for license activation is an encrypted Media Access Control (MAC address) associated with the given Network Card. (2) CD/DVD-ROM is not required if the software is being installed by using the downloadable installer file dynafit-install.zip. Sponsor. This work has been supported by the NIH, grant No. R43 AI52587-02 and the U.S. Department of Defense, U.S. Army Medical Research and Materials Command, Ft. Detrick, MD, administered by the Pacific Telehealth & Technology Hui, Honolulu, HI, contract No. V549P-6073.SCR_008444(Program DynaFit, RRID:SCR_008444)Last checked upnif-0000-30477
MiniaResource, software resourceA short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.SCR_004986(Minia, RRID:SCR_004986)listed by: OMICtoolsLast checked upOMICS_00022
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