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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
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
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
Accessible Resource for Integrated Epigenomics StudiesResource, topical portal, data access protocol, web service, portal, software resource, data or information resourcePortal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time.Epigenomic, human, tissue, DNA, methylation, data, peripheral, bloodSCR_017492(Accessible Resource for Integrated Epigenomics Studies, RRID:SCR_017492)BBSRC, Medical Research Council, University of Bristol, Wellcome Trustsubmitted by: Resource Identification PortalPMID:25991711Last checked up
Retinal wave repositoryResource, source code, data set, service resource, storage service resource, software resource, data repository, data or information resourceA curated repository (data and code) of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged.hdf5, development, neural circuit, retina, eye, multielectrode, array recording, spontaneous activity, reproducible research, retinal wave, electrophysiology, multielectrode array, developmental age, genotypeSCR_010462(Retinal wave repository, RRID:SCR_010462) University of Cambridge; Cambridge; United Kingdom , Code Analysis Repository and Modelling for e-Neuroscience , GigaScience Developing retina, AgingBBSRC, EPSRC, Wellcome TrustPMID:24666584Last checked upnlx_157664
BioMart ProjectResource, software resource, web service, data access protocolA query-oriented data management system that can be used with any type of data and is particularly suited for providing "data mining" like searches of complex descriptive data. BioMart comes with an "out of the box" website that can be installed, configured and customized according to user requirements. Further access is provided by graphical and text based applications or programmatically using web services or API written in Perl and Java. BioMart has built-in support for query optimization and data federation and in addition can be configured to work as a DAS 1.5 Annotation server. The process of converting a data source into BioMart format is fully automated by the tools included in the package. Currently supported RDBMS platforms are MySQL, Oracle and Postgres.biology, data, management, data mining, search, descriptive, graphical, application, perl, java, gold standardSCR_002987(BioMart Project, RRID:SCR_002987) European Bioinformatics Institute , Ontario Institute for Cancer Research Agence National de la Recherche, Breast Cancer Campaign Tissue Bank, Center for Genome Regulation, Center for Mathematical Modelling, Centre National de la Recherche Scientifique, European Molecular Biology Laboratory, Japanese Ministry of Education Culture Sports Science and Technology MEXT, National Research Foundation of Korea, Sandra Ibarra Foundation for Cancer, Spanish Government, U.S. Department of Energy, Wellcome Trustrelated to: Mouse Genome Informatics (MGI), used by: Blueprint EpigenomeLast checked upnif-0000-30184
EvidenceFinderResource, software resource, web applicationA web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.web application, software resource, literature searchSCR_013764(EvidenceFinder, RRID:SCR_013764)Europe PubMed Central Wellcome Trustrelated to: Connected Researchers, Europe PubMed Central, used by: Europe PubMed Central, listed by: Connected ResearchersDOI:10.1093/nar/gku1061Last checked down
Human Ageing Genomic ResourcesResource, software resource, software toolkit, data or information resource, databaseCollection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses. A major resource in HAGR is GenAge, which includes a curated database of genes related to human aging and a database of ageing- and longevity-associated genes in model organisms. Another major database in HAGR is AnAge. Featuring over 4,000 species, AnAge provides a compilation of data on aging, longevity, and life history that is ideal for the comparative biology of aging. GenDR is a database of genes associated with dietary restriction based on genetic manipulation experiments and gene expression profiling. Other projects include evolutionary studies, genome sequencing, cancer genomics, and gene expression analyses. The latter allowed them to identify a set of genes commonly altered during mammalian aging which represents a conserved molecular signature of aging. Software, namely in the form of scripts for Perl and SPSS, is made available for users to perform a variety of bioinformatic analyses potentially relevant for studying aging. The Perl toolkit, entitled the Ageing Research Computational Tools (ARCT), provides modules for parsing files, data-mining, searching and downloading data from the Internet, etc. Also available is an SPSS script that can be used to determine the demographic rate of aging for a given population. An extensive list of links regarding computational biology, genomics, gerontology, and comparative biology is also available.gene, gerontology, human, model, senescence, genomics, longevity, genetics, perl, spss, demographic analysis, genome, evolution, gene expression, model organism, human aging, dietary restriction, genetic manipulationSCR_007700(Human Ageing Genomic Resources, RRID:SCR_007700)University of Liverpool; Liverpool; United Kingdom Aging, CancerEllison Medical Foundation, European Union FP7 Health Research, Wellcome TrustPMID:23193293Last checked upnif-0000-02938
FLIMfitResource, software resource, software application, software toolkitSoftware package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time.fluorescence, lifetime, imaging, microscopy, dataset, global, analysis, multiwell, plate, routineSCR_016298(FLIMfit, RRID:SCR_016298)United Kingdom Biotechnology and Biological Sciences Research Council, United Kingdom Technology Strategy Board, Wellcome TrustDOI:10.1371/journal.pone.0070687, PMID:23940626Last checked down
Seq-GenResource, software resource, software application, simulation softwareSoftware program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.simulator, simulation software, molecular evolution, nucleotide, amino acid, sequence, phylogeny, phylogenetic treeSCR_014934(Seq-Gen, RRID:SCR_014934)University of Edinburgh; Scotland; United Kingdom BBSRC, Fogarty, The Royal Society, Wellcome Trustsubmitted by: Resource Identification PortalLast checked up
neuroConstructResource, software resource, software application, simulation softwareSoftware for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface.cell, cellular, channel, conductance, data, dendrite, java, mechanism, membrane, model, morphology, network, neuron, neuronal network, pharmacology, physiology, simulation, software, synapse, visualizationSCR_007197(neuroConstruct, RRID:SCR_007197)University College London; London; United Kingdom MRC, Wellcome Trustrelated to: NEURON, Open Source Brain, NeuroML, listed by: 3DVC, NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnif-0000-00105
GubbinsResource, software resource, software application, data processing software, data analysis software, sequence analysis softwareSoftware application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution.rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignmentSCR_016131(Gubbins, RRID:SCR_016131)Wellcome Trust Sanger Institute; Hinxton; United Kingdom Wellcome TrustPMID:25414349Last checked up
SAMTOOLSResource, software resource, software application, data processing softwareSoftware tool for manipulating alignments in SAM format for storing nucleotide sequence alignment, including sorting, merging, indexing and generating alignments in per position format. Parts that are relevant to genetic analysis include SNP and indel callings.gene, genomic, c, c++, java, perl, python, ruby, common, lisp, haskell, read, alignment, nucleotide, sequence, data, processSCR_002105(SAMTOOLS, RRID:SCR_002105)SourceForge NHGRI, Wellcome Trustrelated to: Platypus, shovill, used by: deFuse, Short Read Sequence Typing for Bacterial Pathogens, ROSE, listed by: OMICtools, Genetic Analysis Software, SNVerPMID:19505943Last checked upnlx_154607, OMICS_01074
HappyResource, software resource, software application, data analysis software, data processing software, source codeSoftware package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download). HAPPY's analysis is essentially two stage; ancestral haplotype reconstruction using dynamic programming, followed by QTL testing by linear regression: * Assume that at a QTL, a chromosome originating from the progenitor strain, labelled s, contributes an unknown additive amount Ts to the phenotype, so that the expected genetic effect for a diploid individual with ancestral alleles labelled s,t at the trait locus is Ts+Tt; a test for a QTL is equivalent to testing for differences between the Ts's. * A dynamic-programming algorithm is used to compute the probability Fn(s,t) that a given individual has the ancestral alleles s, t at locus labelled n, conditional upon all the genotype data for that individual. Then the expected phenotype is 2 Sums Ts Sumt Fn(s,t), and the Ts are estimated by a linear regression of the observed phenotypes on these expected values across all individuals, followed by an analysis of variance to test whether the progenitor estimates differ significantly. * The method's power depends on the ability to distinguish ancestral haplotypes across the interval; clearly the power will be lower if all markers in a region have the same type of non-informative allele distribution, but the markers can share information where there is a mixture. HAPPY is written in ANSI C. It has been compiled and tested on various UNIX platforms (Linux, IRIX, SunOS). It requires the NAG C library, so you will need a license for this product in order to compile the program locally. The source code for HAPPY is available for non-commercial users only by anonymous ftp.qtl, quantitative trait locus, r, c, gene, genetic, genomic, ansi c, unix, irix, sunos, linux, animal model, trait, map, genotype, phenotype, haplotype, linear regression, data set, qtl mappingSCR_001395(Happy, RRID:SCR_001395)Wellcome Trust Centre for Human Genetics Wellcome Trustlisted by: Genetic Analysis SoftwarePMID:11050180Last checked upnlx_152594
riboWaltzResource, software resource, software application, data analysis software, data processing software, data visualization softwareSoftware R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates.calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinateSCR_016948(riboWaltz, RRID:SCR_016948)Autonomous Province of Trento, Wellcome Trustrelated to: R Project for Statistical Computing, uses: ggplot2, Biostrings, GenomicFeatures, GenomicRanges, IRanges, devtoolsPMID:30102689Last checked up
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
Gaussian-Copula Mutual Information (GCMI)Resource, software resource, software application, data analysis software, data processing softwareSoftware package of functions for calculating mutual information and other information theoretic quantities using a parametric Gaussian copula.gaussian, copula, parametric, equation, calculation, python, matlab, repository, statisticSCR_016450(Gaussian-Copula Mutual Information (GCMI), RRID:SCR_016450)European Research Council, UK Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome TrustLast checked up
PALMResource, software resource, software application, data analysis software, data processing softwareSoftware tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools.statistics, permutation, bootstrap, non parametric, combination, inferenceSCR_017029(PALM, RRID:SCR_017029)Brazilian National Research Council, GlaxoSmithKline, Marie Curie ITN, Medical Research Council, MRC, NIBIB, Wellcome TrustDOI:10.1002/hbm.23115, PMID:24530839, PMID:26074200, PMID:27288322Last checked up
EagleResource, software resource, software application, data analysis software, data processing softwareOpen source software tool for haplotype phasing. Estimates haplotype phase either within genotyped cohort or using phased reference panel.haplotype, phasing, estimate, genotype, cohort, reference, panelSCR_017262(Eagle, RRID:SCR_017262)Broad Institute Austrian Science Fund, Dutch Brain Foundation, Fannie and John Hertz Foundation, NCRR, Netherlands Scientific Organization, NHGRI, NHLBI, NIMH, VU University Amsterdam, Wellcome TrustPMID:27694958Last checked up,
Alien-hunterResource, software resource, software applicationSoftware for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome, gene, transfer, interpolated, variable, motif, prediction, hgt, ivomSCR_015967(Alien-hunter, RRID:SCR_015967)Wellcome Trustworks_with: Artemis: Genome Browser and Annotation ToolPMID:16837528Last checked up
SC3Resource, software resource, data processing software, data analysis software, sequence analysis software, software applicationSoftware tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.scRNA-seq, interactive, cluster, clustering, cell, single, rna, rnaseqSCR_015953(SC3, RRID:SCR_015953)ARC (Action de Recherche Concerte), Belgian Network DYSCO, Belgian State Science Policy Office, Bloodwise, Cambridge Experimental Cancer Medicine Centre, Cambridge NIHR Biomedical Research Center, EPSRC, FRS-FNRS, Kay Kendall Leukaemia Fund, Leukemia and Lymphoma Society of America, MRC, Sanger Institute, University of Edinburgh, Wallonia-Brussels Federation, Wellcome TrustPMID:28346451Last checked up
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