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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
Zebrafish Brain AtlasResource, reference atlas, service resource, storage service resource, atlas, image repository, data repository, data or information resourceCollates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.brain, neuroanatomy, developing, transgene, antibody, confocal, section, reconstruction, high-resolution, developmental stage, embryo, brain structure, confocal imaging, comparative anatomy, transgenic, 3d spatial image, video, embryonic zebrafish, development, annotation, narrative resource, training material, cell repositorySCR_000606(Zebrafish Brain Atlas, RRID:SCR_000606)University College London; London; United Kingdom BBSRC, European Union, Wellcome Trustrecommends: Zebrafish Anatomical Ontology, listed by: One Mind Biospecimen Bank ListingLast checked upnlx_149455http://zebrafishucl.org/
Worldwide Protein Data Bank Resource, data or information resource, resource, databaseA free and public single global PDB archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standardSCR_006555( Worldwide Protein Data Bank , RRID:SCR_006555)BBSRC, DOE, European Molecular Biology Laboratory; Heidelberg; Germany, European Union, Japan Science and Technology Agency, NBDC - National Bioscience Database Center, NCI, NIDDK, NIGMS, NIH, NINDS, NLM, NSF, Wellcome Trustrelated to: Biological Magnetic Resonance Data Bank, Proteopedia - Life in 3D, NRG-CING, Research Collaboratory for Structural Bioinformatics Protein Data Bank, DDBJ - DNA Data Bank of Japan, PDBe - Protein Data Bank in Europe, PDBe - Protein Data Bank in Europe, PDBj - Protein Data Bank Japan, Biological Magnetic Resonance Data Bank, Research Collaboratory for Structural Bioinformatics Protein Data Bank, used by: Ligand ExpoPMID:14634627Last checked upnif-0000-23903
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
Wellcome Trust Centre for Human GeneticsResource, topical portal, portal, data or information resourceAn international leader in genetics, genomics and structural biology, and research institute of the Nuffield Department of Medicine at the University of Oxford, whose objective is to extend our understanding on how genetic inheritance makes us who we are in order to gain a clearer insight into mechanisms of health and disease. Looking across all three billion letters of the human genetic code, they aim to pinpoint variant spellings and discover how they increase or decrease an individual's risk of falling ill. They collaborate with research teams across the world on a number of large-scale studies in these areas.genetics, genomics, structural biologySCR_003307(Wellcome Trust Centre for Human Genetics, RRID:SCR_003307)University of Oxford; Oxford; United Kingdom other sponsors, University of Oxford; Oxford; United Kingdom, Wellcome TrustLast checked upnif-0000-31897
Wellcome Trust Case Control ConsortiumResource, data or information resourceConsortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in African populations. The same approach has been used to type 2,000 cases of tuberculosis (TB) and 2,000 cases of malaria, as well as 2,000 shared controls. As well as addressing diseases of major global significance, and extending WTCCC coverage into the area of infectious disease, the inclusion of samples of African origin has obvious benefits with respect to methodological aspects of genome-wide association analysis. Second, the WTCCC has, for four additional diseases (autoimmune thyroid disease, breast cancer, ankylosing spondylitis, multiple sclerosis), completed an analysis of 15,000 SNPs designed to represent a large proportion of the known non-synonymous coding SNPs across the genome. This analysis has been performed at the WTSI using a custom Infinium chip (Illumina). Data release The genotypic data of the control samples (1958 British Birth Cohort and UK Blood Service) and from seven diseases analyzed in the main study are now available to qualified researchers. Summary genotype statistics for these collections are available directly from the website. Access to the individual-level genotype data and summary genotype statistics is by application to the Consortium Data Access Committee (CDAC) and approval subject to a Data Access Agreement. WTCCC2: A further round of GWA studies were funded in April 2008. These include 15 WTCCC-collaborative studies and 12 independent studies be supported totaling approximately 120,000 samples. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC2 will perform genome-wide association studies in 13 disease conditions: Ankylosing spondylitis, Barrett's oesophagus and oesophageal adenocarcinoma, glaucoma, ischaemic stroke, multiple sclerosis, pre-eclampsia, Parkinson's disease, psychosis endophenotypes, psoriasis, schizophrenia, ulcerative colitis and visceral leishmaniasis. WTCCC2 will also investigate the genetics of reading and mathematics abilities in children and the pharmacogenomics of statin response. Over 60,000 samples will be analyzed using either the Affymetrix v6.0 chip or the Illumina 660K chip. The WTCCC2 will also genotype 3,000 controls each from the 1958 British Birth cohort and the UK Blood Service control group, and the 6,000 controls will be genotyped on both the Affymetrix v6.0 and Illumina 1.2M chips. WTCCC3: The Wellcome Trust has provided support for a further round of GWA studies in January 2009. These include 5 WTCCC-collaborative studies to be carried out in WTCCC3 and 5 independent studies, across a range of diseases. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC3 will perform genome-wide association studies in the following 4 disease conditions: primary biliary cirrhosis, anorexia nervosa, pre-eclampsia in UK subjects, and the interactions between donor and recipient DNA related to early and late renal transplant dysfunction. The WTCCC3 will also carry out a pilot in a study of the genetics of host control of HIV-1 infection. Over 40,000 samples will be analyzed using the Illumina 660K chip. The WTCCC3 will utilize the 6,000 control genotypes generated by the WTCCC2.gene, genomic, genetics, microarray, genome-wide association study, snp, genome-wide association, blood, dna, genotype, variation, genome, sequence variant, copy number variation, genetic variation, phenotype, diseaseSCR_001973(Wellcome Trust Case Control Consortium, RRID:SCR_001973)Wellcome Trust Sanger Institute; Hinxton; United Kingdom Bipolar Disorder, Coronary artery disease, Crohn's disease, Rheumatoid arthritis, Type 1 diabetes, Type 2 diabetes, Hypertension, Control, Multiple sclerosis, Breast cancer, Ankylosing spondylitis, Autoimmune thyroid disease, Malaria, Tuberculosis, Inflammatory bowel disease, Barrett's esophagus, Esophageal adenocarcinoma, Glaucoma, Ischemic stroke, Pre-eclampsia, Parkinson's disease, Psychosis endophenotypes, Psoriasis, Schizophrenia, Ulcerative colitis, Visceral leishmaniasis, Primary biliary cirrhosis, Anorexia nervosa, Human immunodeficiency virus, Renal transplant dysfunctionBill and Melinda Gates Foundation, Wellcome Trust, Wellcome Trust Sanger Institute; Hinxton; United Kingdomrelated to: Psychiatric Genomics ConsortiumPMID:17554300Last checked downnif-0000-10551
Wellcome ImagesResource, database, image collection, service resource, storage service resource, image repository, data repository, data or information resourceDigital collection of images, with themes ranging from medical and social history to contemporary healthcare and biomedical science. The collection contains historical images from the Wellcome Library collections, Tibetan Buddhist paintings, ancient Sanskrit manuscripts written on palm leaves, beautifully illuminated Persian books and much more. The Biomedical Collection holds over 40 000 high-quality images from the clinical and biomedical sciences. Selected from the UK''s leading teaching hospitals and research institutions, it covers disease, surgery, general healthcare, sciences from genetics to neuroscience including the full range of imaging techniques. They are always looking for new high quality biomedical images from scientific researchers, clinical photographers and artists in any field of science or medicine. As a contributor you retain your original material and copyright, and receive commission and full credit each time your images are used. The annual Wellcome Images awards (previously known as Biomedical Images Awards) reward contributors for their outstanding work and winners are chosen by a panel of experts. The resulting public exhibitions are always extremely popular and receive widespread acclaim. All images on the Wellcome Images site are available free for use in: * private study and non-commercial research * examination papers * criticism and review, this applies only where there are no multiple copies made * theses submitted by a student at a higher or further education institution for the purposes of securing a degree * personal use by private individualsbiomedical, clinical, disease, surgery, healthcare, genetics, neuroscience, imaging, science, medicine, history, painting, manuscriptSCR_004181(Wellcome Images, RRID:SCR_004181)Wellcome TrustLast checked downnlx_143611
Wellcome-CTC Mouse Strain SNP Genotype SetResource, data set, data or information resourceData set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34.genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strainSCR_003216(Wellcome-CTC Mouse Strain SNP Genotype Set, RRID:SCR_003216)Wellcome Trust Centre for Human Genetics NCRR, NIAAA, NIGMS, NIMH, NINDS, Wellcome TrustLast checked upnlx_156947
Virtual Fly BrainResource, atlas, neurons, expression, data or information resourceAn interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.Drosophila, brain, neurons, innervation patterns, gene expression, transgene expression, phenotypes, neuroanatomy, neurobiologySCR_004229(Virtual Fly Brain, RRID:SCR_004229) University of Cambridge; Cambridge; United Kingdom , European Bioinformatics Institute , University of Edinburgh; Scotland; United Kingdom Wellcome Trustrelated to: FlyBase, Flycircuit, Janelia Research, uses: Drosophila Gross Anatomy Ontology, Drosophila Development OntologyPMID:22180411Last checked upnlx_143644http://www.virtualflybrain.org/site/vfb_site/home.htm
VGNCResource, service resource, data or information resource, databaseSoftware resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.Vertebrate, gene, nomenclature, data, symbolSCR_017514(VGNC, RRID:SCR_017514)NGRIH, Wellcome Trustrelated to: HGNCLast checked up
VasoTrackerResource, software resource, data acquisition software, data analysis software, data processing software, software applicationOpen source and stand alone software for assessing vascular reactivity. Used in pressure myograph system.vascular, reactivity, pressure, myograph, systemSCR_017233(VasoTracker, RRID:SCR_017233)University of Strathclyde; Glasgow; United Kingdom British Heart Foundation, Wellcome Trustrelated to: Durham University, Durham, EnglandPMID:30846942Last checked uphttps://github.com/VasoTracker/VasoTracker
University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility Resource, service resource, core facility, access service resourceFacility provides regular training sessions, tools, advice and data analysis services to Centre members.core, facility, bioinformaticsSCR_017151(University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility , RRID:SCR_017151)University of Edinburgh; Scotland; United Kingdom Wellcome Trustsubmitted by: Resource Identification PortalLast checked up
UK BiobankResource, biomaterial supply resource, material resource, data or information resourceBiobank resource to improve the prevention, diagnosis and treatment of a wide range of serious and life-threatening illnesses including cancer, heart diseases, diabetes, arthritis and forms of dementia. This long-term national project to build the world's most detailed resource for health researchers has followed the health of 500,000 volunteers aged 40-69 years in the UK for up to 30 years. The project will help approved researchers to develop new and better ways of preventing, diagnosing and treating common illnesses. Scientists will be able to register online to use the UK Biobank Resource soon. Health assessments include blood, urine and saliva collection, lifestyle questionnaire including a detailed web-based diet questionnaire. There is also a section to assess cognitive function and psychological status. A hearing test is undertaken while wearing headphones. In an interview participants have been asked questions about birth (if they knew it), serious illnesses they may have had, operations and any medication they might be taking. Blood pressure and some body measurements have been taken including: Hand grip, Waist and hip circumference, Standing height, Sitting height, Weight and bioimpedance, Spirometry, Bone density, Use of an infra red finger probe (that goes over the end of your finger) to measure the stiffness of your arteries, Eye measurements and a fitness assessment.diet, questionnaire, blood, urine, saliva, cognitive function, psychological status, hearing test, interview, serious illness, operation, medication, blood pressure, body measurementSCR_012815(UK Biobank, RRID:SCR_012815)Alzheimer's disease, Aging, Cancer, Dementia, Diabetes, Heart disease, ArthritisMRC, Scottish Government, UK Department of Health, Wellcome Trust, Welsh Assembly Governmentlisted by: One Mind Biospecimen Bank ListingLast checked upnlx_95741
UCL Motor Control GroupResource, topical portal, portal, data or information resourceUsing robotic devices to investigate human motor behavior, this group develops computational models to understand the underlying control and learning processes. By simulating novel objects or dynamic environments they study how the brain recalibrates well-learned motor skills or acquires new ones. These insights are used to design fMRI studies to investigate how these processes map onto the brain. They have developed a number of novel techniques of how to study motor control in the MRI environment, and how to analyze MRI data of the human cerebellum. They also study patients with stroke or neurological disease to further determine how the brain manages to control the body.motor cortex, motor control, brain, human, neurological disease, stroke, fmri, cerebellum, mriSCR_005271(UCL Motor Control Group, RRID:SCR_005271)University College London; London; United Kingdom Neurological disease, StrokeBBSRC, James S. McDonnell Foundation, Marie-Curie Program, Wellcome TrustLast checked upnlx_144299
TriTrypDBResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceAn integrated genomic and functional genomic database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ''''User Comments'''' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate. TriTrypDB provides programmatic access to its searches, via REST Web Services. The result of a web service request is a list of records (genes, ESTs, etc) in either XML or JSON format. REST services can be executed in a browser by typing a specific URL. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).kinetoplastid parasite, pathogen, genome, gene chromosome, annotation, trypanosomatidae, parasite, blastSCR_007043(TriTrypDB, RRID:SCR_007043)Eukaryotic Pathogen Database Resources (EuPathDB) Bill and Melinda Gates Foundation, Wellcome Trustrelated to: GeneDB, GeneDB Lmajor, GeneDB TbruceiPMID:19843604Last checked upnlx_152064
TREES toolboxResource, software resourceSoftware package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance.neuronal branching, microscopy, neuron, matlab, visualization, rendering, reconstruction, analysis, modeling, morphology, dendrite, axon, computational neuroanatomy, treeSCR_010457(TREES toolbox, RRID:SCR_010457)University College London; London; United Kingdom Alexander von Humboldt-Stiftung, European Research Council, Gatsby Charitable Foundation, Max Planck Society, Wellcome Trustlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:20700495Last checked upnlx_157723http://www.nitrc.org/projects/treestoolbox
T1DBase Resource, resource, database, service resource, storage service resource, data repository, data or information resourceNO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://beta.immunobase.org). Database focused on the genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data.genetics, beta cell, gene, variant, region, genomics, gene expression, genome-wide association study, data analysis serviceSCR_007959( T1DBase , RRID:SCR_007959)University of Cambridge; Cambridge; United Kingdom Type 1 diabetes, DiabetesJuvenile Diabetes Research Foundation, NIDDK, Wellcome Trustrelated to: dkCOIN, used by: NIF Data Federation, NIDDK Information Network, listed by: NIDDK Information NetworkPMID:20937630Last checked upnif-0000-03531
SUPFAMResource, data or information resource, databaseSUPFAM is a database that consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies. The present release (Release 3.0) of SUPFAM uses homologous families in Pfam (Version 23.0) and SCOP (Release 1.69) which are examples of sequence -alignment and structure classification databases respectively. The two steps involved in setting up of SUPFAM database are * Relating Pfam and SCOP families using a new profile-profile alignment algorithm AlignHUSH. This results in identifying many Pfam families which could be related to a family or superfamily of known structural information. * An all-against-all match among Pfam families with yet unknown structure resulting in identification of related Pfam families forming new potential superfamilies. The SUPFAM database can be used in either the Browse mode or Search mode. In Browse mode you can browse through the Superfamilies, Pfam families or SCOP families. In each of these modes you will be presented with a full list which can be easily browsed. In Search mode, you can search for Pfam families, SCOP families or Superfamilies based on keywords or SCOP/Pfam identifiers of families and superfamilies.duf/upf connections, 3-d structure, alignment, amino acid sequence, bioinformatics, clustering, homologous protein family, multiple sequence alignment, nmr, pali, pfam, phylogeny, protein classification, protein domain database, protein families, protein sequence database, rps_blast, scop, structural genomics, structure determination, superfamily, three-dimensional, x-ray crystalographySCR_005304(SUPFAM, RRID:SCR_005304)Indian Institute of Science; Bangalore; India Council of Scientific and Industrial Research New Delhi, Wellcome Trustrelated to: Pfam, SCOP: Structural Classification of ProteinsReferences (2)Last checked upnif-0000-03517http://pauling.mbu.iisc.ernet.in/~supfam
StimfitResource, software resource, software application, data analysis software, data processing softwareSoftware for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy.electrophysiology, python, numpy, scipy, numerical, library, stimulus, analysisSCR_016050(Stimfit, RRID:SCR_016050)European Research Council, Gatsby Charitable Foundation, Wellcome Trustuses: NumPy, SciPyPMID:24600389Last checked up
SHERPA RoMEOResource, database, data or information resourceA database which houses publisher policies regarding the self- archiving of journal articles on the web and in Open Access repositories. RoMEO contains publishers' general policies on self-archiving of journal articles and certain conference series. Each entry provides a summary of the publisher's policy, including what version of an article can be deposited, where it can be deposited, and any conditions that are attached to that deposit.database, publisher policy, open accessSCR_013815(SHERPA RoMEO, RRID:SCR_013815)University of Nottingham; Nottingham; United Kingdom JISC, Wellcome Trustrelated to: Connected Researchers, listed by: Connected ResearchersLast checked up
ShARMResource, organism supplier, database, biomaterial supply resource, biospecimen repository, tissue bank, service resource, portal, storage service resource, data or information resource, material resource, community building portal, material storage repositoryA not for profit organization to accelerate research into aging by sharing resources: providing access to cost and time effective, aged murine tissue through a biorepository and database of live ageing colonies, as well as promoting the networking of researchers and dissemination of knowledge through its online collaborative environment; MiCEPACE. ShARM will provide valuable resources for the scientific community while helping to reduce the number of animals used in vital research into aging. The biobank of tissue and networking facility will enable scientists to access shared research material and data. By making use of collective resources, the number of individual animals required in research experiments can be minimized. The project also has the added value of helping to reduce the costs of research by connecting scientists, pooling resource and combining knowledge. ShARM works in partnership with MRC Harwell and the Centre for Intergrated Research into Musculoskeletal Ageing (CIMA).data sharing, female, male, gut, heart, kidney, livers, lung, mammary fat, muscle, pancreas, bat, bladder, bone, brain, femur, skin, spleen, thymus, tibia, wat, aged tissue, aged mouse, murine modelSCR_003120(ShARM, RRID:SCR_003120)Aging, Control, Young controlWellcome Trustlisted by: One Mind Biospecimen Bank ListingPMID:24085518Last checked downnlx_156767
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