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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: Feb 12, 2018)

Physical Resource or Software Tool Software

15,653 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Beijing: Eyes Open Eyes Closed StudyResource, data set, data or information resourceData set of 48 healthy controls from a community (student) sample from Beijing Normal University in China with 3 resting state fMRI scans each. During the first scan participants were instructed to rest with their eyes closed. The second and third resting state scan were randomized between resting with eyes open versus eyes closed. In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 6-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information and information on the counterbalancing of eyes open versus eyes closed.early adult human, resting state, fmri, diffusion tensor imaging, resting state fmri, eyes open, eyes closed, neuroimaging, mprage, image collection, brainSCR_001507(Beijing: Eyes Open Eyes Closed Study, RRID:SCR_001507)NITRC , NITRC HealthyNational High Technology Program of China (863), National Natural Science Foundation of ChinaLast checked downnlx_152810
Annual Reviews: A Nonprofit Scientific PublisherResource, journal articleAnnual Reviews offers comprehensive, timely collections of critical reviews written by leading scientists. It publishes authoritative, analytic reviews in 37 focused disciplines within the Biomedical, Life, Physical, and Social Sciences. The mission of Annual Reviews is to provide systematic, periodic examinations of scholarly advances in a number of fields of science through critical authoritative reviews. The comprehensive critical review not only summarizes a topic but also roots out errors of fact or concept and provokes discussion that will lead to new research activity. The critical review is an essential part of the scientific method. Sponsors: Annual Reviews is a non-profit organization created and managed by scientists to serve science by publishing reviews in 40 different scientific fields.biomedical, life science, literature, physical science, review, social scienceSCR_001655(Annual Reviews: A Nonprofit Scientific Publisher, RRID:SCR_001655)Last checked upnif-0000-10150
PennSeqResource, software resourceSoftware for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution.isoform, gene expression, rna-seqSCR_001763(PennSeq, RRID:SCR_001763)OMICtools PMID:24362841Last checked upOMICS_01946
BIRDSUITEResource, software resource, software applicationOpen-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.gene, genetic, genomic, snp, genotype, copy number polymorphism, copy number variant, affymetrixSCR_001794(BIRDSUITE, RRID:SCR_001794) Genetic Analysis Software , OMICtools PMID:18776909Last checked upnlx_154245, OMICS_00705
DAVIDResource, data analysis service, data access protocol, database, web service, production service resource, analysis service resource, service resource, software resource, data or information resourceAn integrated biological knowledgebase and comprehensive set of functional annotation tools for investigators to understand biological meaning behind large lists of genes. For any given gene list, DAVID tools are able to: - Identify enriched biological themes, particularly GO terms - Discover enriched functional-related gene groups - Cluster redundant annotation terms - Visualize genes on BioCarta & KEGG pathway maps - Display related many-genes-to-many-terms on 2-D view. - Search for other functionally related genes not in the list - List interacting proteins - Explore gene names in batch - Link gene-disease associations - Highlight protein functional domains and motifs - Redirect to related literatures - Convert gene identifiers from one type to another.functional domain, annotation, motif, protein, ontology enrichment, gene, high-throughput, functional classification, functional annotation, clustering, genome, pathway, gene-disease association, interaction, functional domain, motif, visualizationSCR_001881(DAVID, RRID:SCR_001881) 3DVC , LabWorm , OMICtools NIAIDPMID:19131956Last checked upnif-0000-10451, OMICS_02220, SCR_003033, nif-0000-30408
ABCDreportResource, software resource, software application, data analysis software, data processing softwareSoftware application as a simple system to review study progress. Used in ABCD study.system, simple, review, study, progress, development, adolescence, brain, cognitive, reportSCR_016030(ABCDreport, RRID:SCR_016030)NIDALast checked up
Offline SorterResource, software resource, commercial organizationOffline spike sorting software. This software tool for viewing and classifying action potential waveforms (spikes) previously collected from single electrodes, stereotrodes and tetrodes accepts file types from many data acquisition companies and software xp, windows 7, action potential, waveform, spike, classifySCR_000012(Offline Sorter, RRID:SCR_000012)Last checked upnlx_158484
ProcessDBResource, data or information resource, databaseIt helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a bio-savvy graphical user interface that helps users formulate, visualize, compare, modify, manage and test their own mechanistic theories of cellular function. All models in ProcessDB can be automatically combined with user-specified experimental protocols and exported to the Berkeley Madonna solver for testing against experimental data. ProcessDB allows investigators to know with precision what their theories predict, and speeds discovery of mechanisms that account for all of the available data. ProcessDB, which is accessable from any Internet-connected computer, offers a highly secure and professionally maintained tool that supports mechanistic knowledge management for research laboratories working on complex biological or biomedical problems.cellular, mechanism, molecular cell biologySCR_002111(ProcessDB, RRID:SCR_002111)Last checked upnif-0000-20893
LyonbiopoleResource, organization portal, portal, funding resource, data or information resourceA worldwide competitiveness cluster centered on pharmaceutical activities including the fight against human and animal infectious diseases and cancers. Designed as a tool interface and public / private approximation, the division has implemented measures to encourage collaborative R & D, help in setting up projects and find funding, increase strategic and financial partnerships for economic development and international companies, provide access to reception areas, technological shared platforms such as the Infectious Diseases Center Lyonbiop??le. It aims to strengthen the competitiveness of the sector health and the attractiveness of the Rh??ne-Alpes area, mainly on the Lyon-Grenoble axis. (adapted from the translated Wikipedia)vaccine, diagnostic, pharmaceutical, drug, prevention, treatmentSCR_003733(Lyonbiopole, RRID:SCR_003733)Infectious disease, CancerLast checked downnlx_157924
EGAPPResource, topical portal, portal, data or information resourceInitiative to develop a systematic, evidence-based process for evaluating genetic tests and other applications of genomic technology that are rapidly moving from research to use in clinical practice. A key objective of this process is to provide objective, timely, and credible information that is clearly linked to the scientific evidence on specific applications of genetic and genomic tests. The primary focus of EGAPP activities is an independent, nonfederal expert panel, the EGAPP Working Group. Other components of the EGAPP initiative include a federal interagency, the CDC staff and consultants, and an EGAPP initiative evaluation team.genetic test, genomics, clinical, genomic technology, evaluation, public healthSCR_004189(EGAPP, RRID:SCR_004189)OMICtools Last checked upOMICS_01538
Webvision - The Organization of the Retina and Visual SystemResource, narrative resource, blog, book, image collection, data or information resourceOnline textbook that has evolved into an interactive, dynamic blog that covers all things related to the bioscience of the visual system. It summarizes recent advances in knowledge and understanding of the visual system through dedicated chapters and evolving discussion to serve as a clearing house for all things related to retina and vision science.eye, visual system, vision, retina, neuroanatomySCR_004254(Webvision - The Organization of the Retina and Visual System, RRID:SCR_004254)Last checked upnlx_26732
NeuroTribesResource, blog, narrative resource, data or information resourceSteve Silberman's personal blog highlighting science, culture, politics and neurodiversity. Steve is an investigative reporter for Wired and other national magazines.mind, science, culture, steve silbermanSCR_000019(NeuroTribes, RRID:SCR_000019)Last checked upnlx_91543
PubChem SubstanceResource, database, service resource, d spatial image, storage service resource, data repository, data or information resourceAs one of three primary databases of PubChem (Pcsubstance, Pccompound, and PCBioAssay), PubChem Substance Database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound. A PubChem FTP is available and new data is accepted into the repository. Pcsubstance contains more than 81 million records (2011).small molecule, biological activity, chemical substance, bioactivity, gold standardSCR_004742(PubChem Substance, RRID:SCR_004742)Last checked upnlx_74645
delay-discountingResource, software resource, software applicationSoftware that performs a delay-discounting task measuring impulsivity. Used in ABCD study.abcd, delay, discounting, task, measure, impulsivity, software, application, toolSCR_016031(delay-discounting, RRID:SCR_016031)Last checked up
PRResource, ontology, data or information resource, controlled vocabularyAn ontological representation of protein-related entities by 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. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563).database, obo, proteinSCR_004964(PR, RRID:SCR_004964)BioPortal , BioPortal NIGMS, NIHLast checked upnlx_92849
Wikiversity School of MedicineResource, wiki, narrative resource, training resource, data or information resourceThe Wikiversity School of Medicine is a free online educational resource for the study of medicine. It is a member of the Faculty of Life Sciences and aims to maximize collaboration with other schools within the faculty and elsewhere. Prospective students may study medicine at Wikiversity by registering with the site and joining the school. Students may study via the proposed curriculum pathway, by picking and choosing modules or lessons from the different departments or by joining the school in creating lessons. The school''s medical course is currently divided into pre-clinical and clinical sets of modules. Access to these modules is via the school curriculum. This resource is available in other languages including Deutsch, Espa??ol, Fran??ais, Italiano, Portugu??s, and .life sciences, medicine, medical studentSCR_005008(Wikiversity School of Medicine, RRID:SCR_005008)Last checked upnlx_96772
ScienceBlogs: JobsResource, job resourceScienceBlogs posts about Jobs.employment, career, position, job postingSCR_005200(ScienceBlogs: Jobs, RRID:SCR_005200)Last checked upnlx_144213
GenomicRangesResource, software resourceSoftware package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.genomic intervalSCR_000025(GenomicRanges, RRID:SCR_000025)OMICtools Last checked upOMICS_01161
DONE: Detection of Outlier NEuronsResource, software resource, software applicationSoftware that performs a morphology-based approach for the automatic identification of outlier neurons based on neuronal tree structures. This tool was used by Zawadzki et al. (2012), who reported on and its application to the NeuroMorpho database. For the analysis, each neuron is represented by a feature vector composed of 20 measurements, which are projected into lower dimensional space with PCA. Bivariate kernel density estimation is then used to obtain a probability distribution for cells. Cells with high probabilities are understood as archetypes, while those with the small probabilities are classified as outliers. Further details about the method and its application in other domains can be found in Costa et al. (2009) and Echtermeyer et al. (2011). This version requires Matlab (Mathworks Inc, Natick, USA) and allows the user to apply the workflow using a graphical user interface.neuron, feature-space, archetype, outlier, matlab, neuromorphometry, computational neuroscienceSCR_005299(DONE: Detection of Outlier NEurons, RRID:SCR_005299)NITRC CNPq, EPSRC, FAPESP, FAPESP sponsorship, National Research Foundation of KoreaPMID:22615032Last checked upnlx_144348
KI Biobank - GallstoneResource, disease-related portal, topical portal, research forum portal, biomaterial supply resource, portal, material resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. KI Biobank - Gallstone aims at investigating genetics of gallstone disease on Swedish Twins. Types of samples * EDTA whole blood * DNA * Plasma Number of sample donors: 82gene, geneticsSCR_005664(KI Biobank - Gallstone, RRID:SCR_005664)One Mind Biospecimen Bank Listing Gallstone disease, TwinLast checked downnlx_151297
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