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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)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
GraphPadOrganizationA commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.company, data, graph, scientific, statistical, analysis, curve, fittingSCR_000306(GraphPad, RRID:SCR_000306)Last checked upnlx_156835
Allen Institute for Brain ScienceOrganization, atlas, topical portal, portal, data or information resourceSeattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.Institute, embryonic, gene, expression, data, neuroscience, medical, research, neuroanatomySCR_006491(Allen Institute for Brain Science, RRID:SCR_006491)Allen Institute related to: VisiGene Image Browser, Recombinase (cre) Activity, listed by: Brain Architecture ProjectLast checked upnif-0000-00146
Wellcome Trust Sanger Institute; Hinxton; United KingdomOrganization, institution, data or information resourceNon profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.research, genome, sequence, human, health, project, global, data, treatment, therapySCR_011784(Wellcome Trust Sanger Institute; Hinxton; United Kingdom, RRID:SCR_011784)Wellcome Trustrelated to: Clonalframe, ClonalOrigin, TraCeR, listed by: re3data.org, affiliated with: Open TargetsLast checked upnlx_91258
Center for Expanded Data Annotation and RetrievalOrganization, ontology, portal, data or information resource, controlled vocabularyOrganization that develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.metadata, biomedical, research, data, file, software, applicationSCR_016269(Center for Expanded Data Annotation and Retrieval, RRID:SCR_016269)NIAIDLast checked down
International Neuroinformatics Coordinating FacilityOrganization, organization portal, international standard specification, standard specification, narrative resource, portal, data or information resourceIndependent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.neuroinformatics, neuroscience, neuroimaging, clinical, brain, data, sharing, reuse, globalSCR_002282(International Neuroinformatics Coordinating Facility, RRID:SCR_002282) Royal Institute of Technology; Stockholm; Sweden , Karolinska Institutet; Stockholm; Sweden NSF, Swedish Foundation for Strategic Research, Swedish Research Councilrelated to: Spike Sorting Evaluation Project, Allen Brain Atlas API, SenseLab, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnif-0000-00365
T1D ExchangeOrganization, organization portal, portal, data or information resourceProvides access to resources T1D researchers need to conduct clinical studies. Data sets from their clinic registry is openly available, as are new study results. They also offer use of T1D Discovery Tool, which allows users to search different fields from registry data, and T1D Exchange Biobank, which offers specimen types such as serum, plasma, white blood cells, DNA, and RNA.portal, dataset, type 1 diabetes, t1d, clinical, study, registry, dataSCR_014532(T1D Exchange, RRID:SCR_014532)listed by: NIDDK Information NetworkLast checked up
Stanford Center for Reproducible NeuroscienceOrganization, organization portal, portal, data or information resourceCenter with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects.computing, tools, neuroscience, data, analyze, reproducibility, fMRI, OpenfMRI, OpenNeuro, NeurovaultSCR_016684(Stanford Center for Reproducible Neuroscience, RRID:SCR_016684)Stanford University; Stanford; California Last checked up
European Bioinformatics InstituteOrganization, organization portal, portal, data or information resourceNon-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, proteinSCR_004727(European Bioinformatics Institute, RRID:SCR_004727)European Molecular Biology Laboratory BBSRC, EMBL member states, European Union, Industry Programme partners, NIH, UK Research Councils, Wellcome Trustrelated to: AgedBrainSYSBIO, ProteomeXchange, Open PHACTS, RHEA, TraCeR, used by: Blueprint Epigenome, listed by: re3data.orgLast checked upnlx_72386
European Molecular Biology LaboratoryOrganization, organization portal, training resource, graduate program resource, portal, postdoctoral program resource, data or information resourceIntergovernmental organisation funded by public research money from its member states in Europe. Groups and laboratories perform basic research in molecular biology and molecular medicine, training for scientists, students and visitors. Provides development of services, new instruments and methods, data and technology in its member states.molecular, biology, medicine, data, training, service, organization, data, technology, academicSCR_004473(European Molecular Biology Laboratory, RRID:SCR_004473)related to: GenBank, EU-AIMS, EMIFLast checked upnlx_46173
Stanford Diabetes Research Center Diabetes Clinical and Translational CoreOrganization, service resource, core facility, access service resourceWith the following services from the Diabetes Clinical and Translational Core (DCTC), members will receive training in biospecimen preservation, study design, data analysis, data management, use of statistical software and clinical trial conduct.diabetes, clinical, translation, specimen, study, design, data, statisticSCR_016212(Stanford Diabetes Research Center Diabetes Clinical and Translational Core, RRID:SCR_016212)NIDDKrelated to: Stanford Diabetes Research Center Diabetes Genomics Analysis CoreLast checked down
Stanford Diabetes Research Center Diabetes Immune Monitoring CoreOrganization, service resource, core facility, access service resourceCore facility that provides immune monitoring assays at the RNA, protein, and cellular level, as well as archiving, reporting, and data mining support for clinical and translational studies related to Diabetes. The DIMC is a specialized subcore of the Human Immune Monitoring Center (HIMC) at Stanford.diabetes, assay, immune, system, clinical, translational, human, dataSCR_016210(Stanford Diabetes Research Center Diabetes Immune Monitoring Core, RRID:SCR_016210)NIDDKrelated to: Stanford Diabetes Research Center Diabetes Genomics Analysis CoreLast checked down
Brain ProductsOrganization, service resource, software resource, instrument manufacture, production service resource, material service resourceCommercial organization for hardware and software for neurophysiological research. Provides EEG and ERP amplifier systems, EEG recording caps, Data recording and analysis software, TMS Stimulator for combined EEG/TMS coregistrations and more.manufacture, instruments, hardware, software, neurophysiological, research, EEG, ERP, EEG/fMRI, BCI, amplifier, recording, cap, data, analysis, software, TMS, stimulatorSCR_009443(Brain Products, RRID:SCR_009443)related to: BrainVision AnalyzerLast checked upnlx_155587
Walter Reed Biosystematics UnitOrganization, topical portal, data or information resource, portal, organism-related portalNational resource for systematics research on medically important arthropods and maintainance of the U.S. mosquito collection based in the Smithsonian Institution. Provides an online repository for vector collection data and clearinghouse where individuals and organizations can contribute vector occurrence records, search for vector information, and use tools for the visualization of various vector collections.medically, important, arthropods, maintanace, repository, U.S. mosquito, data, vector, collectionSCR_016729(Walter Reed Biosystematics Unit, RRID:SCR_016729)Last checked up
Africa Centre BiobankResourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented November 30, 2015. Extensive collection of biological specimens of various kinds that are mostly collected from the population around the Africa Centre in northern KwaZulu-Natal, but there are also specimens collected from populations in and around Durban and elsewhere in KwaZulu-Natal. The results of tests carried out on these specimens are generally stored in the main databases of the various studies involved, and are linkable back to the demographic and other data collected from the individuals concerned. The Biobank is curated by staff of the Africa Centre's Virology Laboratory in Durban, where all the specimens are currently stored, mostly in -80C freezers. A particular strength of its holdings are the dried blood spot (DBS), specimens five drops of blood on a filter-paper card, obtained via a finger-prick - of which there are now nearly 115,000. The following is a list of its holdings (May 2011): * 67,700 DBS specimens collected since late 2002 primarily for HIV prevalence estimation of the population covered by the Africa Centre Demographic Surveillance population. All have at least been tested for HIV, and just over 21% give a Positive result. Specimens are collected annually, so for some individuals we might have a sequence of 8-10 specimens covering 2002-2011. * 36,601 DBS specimens collected by the Vertical Transmission Study (VTS) between Sep 2001 and Dec 2006. This study focussed on mother-child pairs and investigated the vertical transmission of HIV from mother to child. DBS specimens were collected from both the mothers (at initial screening, and then from their children at Birth, 6, 10, 14, 18, 22 weeks, and 7, 8, 9, 12, 15, 18, 21 and 24 months. * 6,585 DBS specimens collected as part of the KZN IMPACT study of PMTCT effectiveness in six districts of kwaZulu-Natal. The specimens were collected during 2004-2006 from infants aged 4-8 weeks when mothers brought them to clinics for immunisation. These DBS specimens are stored at room temperature, not in freezers. * 3,524 DBS specimens collected as part of the Kesho Bora study from Sep 2007 . They were collected from mothers at enrollment, and from the infants at delivery, 2 weeks, and at 4, 5, 7, 8 and 15 months. * 50,068 Plasma specimens * 28,775 breastmilk specimens * 11,277 breastmilk products (Pellets and lactoserum). These have all been extracted from the BM specimens in prev. item? * 11,188 RNA and DNA products extracted from DBS and plasma specimens from all our major studies. * 5,735 Serum specimens * 3,505 cell pellets * 1,778 whole blood specimens * 1,284 Peripheral Blood Mononuclear Cells from the Kesho Bora study mothers (665) and their children (619) * 179 skin tissue specimens from the KST study (Kaposi's Sarcoma) * 176 foreskinsmother, child, adult, pediatric, newborn, hiv transmission, dried blood spot, plasma, breastmilk, breastmilk product, rna, dna, serum, cell pellet, blood, peripheral blood mononuclear cell, skin tissue, foreskin, nutrition, resistance, demographic data, dataSCR_000638(Africa Centre Biobank, RRID:SCR_000638)University of KwaZulu-Natal; Durban; South Africa HIVlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_152011
Bulked segregation analysis tools for outbreeding speciesResource, 1d time-series analysis software, data analysis software, data processing software, software application, time-series analysis software, software resourceSoftware tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data.next, generation, sequencing, bulked, segregation, analysis, outbreeting, specie, gene, mapping, dataSCR_017009(Bulked segregation analysis tools for outbreeding species, RRID:SCR_017009)Last checked up
BlixemResource, alignment software, image analysis software, data processing software, software resource, software applicationSoftware for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNASCR_015994(Blixem, RRID:SCR_015994)Wellcome Trust Sanger Institute; Hinxton; United Kingdom NHGRI, Wellcome Trust Grantrelated to: SEQtoolsPMID:26801397Last checked up
star-for-criuResource, alignment software, image analysis software, data processing software, software resource, software applicationSoftware as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability.hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environmentSCR_016294(star-for-criu, RRID:SCR_016294)AMEDD Advanced Medical Technology Initiative, NIGMS, NIHrelated to: STARLast checked uphttps://github.com/paizhang/Hotstarting-For-STAR-Alignment
NOVOPlastyResource, alignment software, image analysis software, data processing software, software resource, software applicationSoftware package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data.de novo, assembler, heteroplasmy, variance, caller, short, circular, genome, organelle, whole, dataSCR_017335(NOVOPlasty, RRID:SCR_017335)Belgian Kids Fund, Hôpital Universitaire des Enfants Reine Fabiola, Interuniversity Institute of Bioinformatics in Brusselslisted by: OMICtoolsPMID:28204566Last checked up
MS BioworksResource, analysis service resource, data analysis service, service resource, production service resourceA protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis.mass spectrometry, protein, data, biomarkers, glycoproteins, proteomics service, analysis service resource, post translational modification, quantitative proteomicsSCR_001043(MS Bioworks, RRID:SCR_001043)listed by: Science ExchangeLast checked downSciEx_4856http://www.scienceexchange.com/facilities/ms-bioworks
DREMEResource, analysis service resource, data analysis service, service resource, production service resourceSoftware tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences).discover, short, ungapped, motif, sequence, compare, shuffled, control, sample, output, recurring, fixed, length, pattern, dataSCR_016860(DREME, RRID:SCR_016860)listed by: MEME Suite - Motif-based sequence analysis toolsLast checked up
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