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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: Sep 14, 2019)

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16,820 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Global Catalogue of MicroorganismsResource, topical portal, data or information resource, portal, organism-related portal, databaseDatabase and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.research, deep, mining, genomic, data, retrival, analysis, visualisation, microbial, resourceSCR_016460(Global Catalogue of Microorganisms, RRID:SCR_016460)the 13th Five-year Informatization Plan of the Chinese Academy of Sciences, the Bureau of International Cooperation of the Chinese Academy of Sciences, the National Key Research Program of China, the National Science Foundation for Young Scientists of China, the Strategic Priority Research Program of the Chinese Academy of SciencesPMID:29718202Last checked up
clusterProfilerResource, software resource, software application, data analysis software, data processing software, data visualization softwareSoftware R package for statistical analysis and visualization of functional profiles for genes and gene clusters.data, statistical, analysis, visualization, gene, clusterSCR_016884(clusterProfiler, RRID:SCR_016884)2007 Chang-Jiang Scholars Program, Fundamental Research Funds for the Central Universities, Guangdong Natural Science Research Grant, National 973 Projects of China, National Natural Science Foundation of Chinarelated to: R Project for Statistical Computing, listed by: BioconductorPMID:22455463Last checked uphttps://github.com/GuangchuangYu/clusterProfiler, https://guangchuangyu.github.io/software/clusterProfiler/
1000 Genomes: A Deep Catalog of Human Genetic VariationResource, organization portal, database, consortium, data set, portal, data or information resourceInternational collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomesgenetic variation, gene, next-generation sequencing, sequence, alignment, genome, single-nucleotide polymorphism, structural variant, haplotype, genome-wide association study, pharmacology, genetics, biomarker, consortium, data sharing, genotype, phenotypeSCR_006828(1000 Genomes: A Deep Catalog of Human Genetic Variation, RRID:SCR_006828) European Bioinformatics Institute , NCBI , Broad Institute , Harvard Medical School; Massachusetts; USA , National Human Genome Research Institute , Wellcome Trust Sanger Institute; Hinxton; United Kingdom 454 Life Sciences Roche, Beijing Genomics Institute; Shenzhen; China, Illumina, Life Technologies, NHGRI, Wellcome Trust Sanger Institute; Hinxton; United Kingdomrelated to: MOSAIK, ART, SNAP - SNP Annotation and Proxy Search, used by: BioSample Database at EBI, uses: NHGRI Sample Repository for Human Genetic Research, listed by: OMICtools, re3data.org, Consortia-pediaLast checked upnlx_143819, OMICS_00261
Vocal Inventory Clustering Engine (VoICE)Resource, software resource, software application, data analysis software, data processing softwareSoftware that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations.bird, song, birdsong, vocal, audio, analysis, vocalization, spectral similarity, avian, matlabSCR_016004(Vocal Inventory Clustering Engine (VoICE), RRID:SCR_016004)5T32HC00722834, Autism Speaks, NICHD, NIMH, UCLAuses: MATLABLast checked up
Malaria Parasite Metabolic PathwaysResource, data set, image collection, data or information resourceData set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database.enzyme, gene, genome, map, metabolic, mosquito, parasite, pathway, plasmodium falciparum, protein, reaction, sequence, metabolic pathway, chemical structure, cell-cell interaction, transport, morphology, mitochondria, apicoplastSCR_007072(Malaria Parasite Metabolic Pathways, RRID:SCR_007072)Hebrew University of Jerusalem; Jerusalem; Israel Malaria6th FP- BioMalPar Network of Excellence on Biology and Pathology of the Malaria Parasite, European Union, NIAID, UNDP/World Bank/WHO Special ProgrammeLast checked upnif-0000-21249
Dr.VIS - Human Disease-Related Viral Integration SitesResource, data or information resource, databaseDr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free.disease, virus, viral integration, viral integration site, integration site, malignant disease, chromosome region, genomic position, viral-host junction sequence, junction sequence, oncogene, chromosome, catalog, graphic interfaceSCR_005965(Dr.VIS - Human Disease-Related Viral Integration Sites, RRID:SCR_005965)Tongji University; Shanghai; China 863 Hi-Tech Program of China, Major State Basic Research Development Program, Major State Basic Research Development Program of China, National Key Technology R&D Program in the 11th Five Year Plan of China, National Natural Science Foundation of China, State Key Basic Research Program 973PMID:22135288Last checked downnlx_151323http://www.scbit.org/dbmi/drvis
HLAsupEResource, data or information resource, databaseDatabase of HLA supertype-specific epitopes. It describes major histocompatibility complex (MHC) molecules that bind short peptides derived from endogenous or exogenous antigens and present them onto the surface of antigen-presenting cells (APCs) for T-cell receptor (TCR) recognition.hla, supertype, epitope, t cell, immunology, immune, mhc, antigen, histocompatibilitySCR_016277(HLAsupE, RRID:SCR_016277)863 Project, National Natural Science Foundation of China, National Science and Technology Major Projectsubmitted by: NIDDK Information NetworkPMID:27307005Last checked up
PANDAResource, workflow software, data processing software, software application, software resource, software toolkit, image processing softwareA matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography. Particularly, there are 3 types of resultant diffusion parameter data: WM atlas-level, voxel-level and TBSS-level. The brain network generated by PANDA has various edge definitions, e.g. fiber number, length, or FA-weighted. The key advantages of PANDA are as follows: # fully-automatic processing from raw DICOM/NIFTI to final outputs; # Supporting both sequential and parallel computation. The parallel environment can be a single desktop with multiple-cores or a computing cluster with a SGE system; # A very friendly GUI (graphical user interface).analyze, computational neuroscience, connectivity analysis, dicom, format conversion, gnome, linux, macos, matlab, modeling, magnetic resonance, nifti, posix/unix-like, tensor metric, tractography, workflow, xnat pipeline, diffusion mri, chinese, connectome, diffusion metrics, network, pipeline, structural connectivitySCR_002511(PANDA, RRID:SCR_002511)Beijing Normal University; Beijing; China 973 program, Beijing Nova Program, National Natural Science Foundation of China, State Key Laboratory of Cognitive Neuroscience and Learninglisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnlx_155911http://www.nitrc.org/projects/panda
Saskatoon Arabidopsis T-DNA mutant population SK CollectionResource, biomaterial supply resource, material resourcePopulation of almost 50,000 activation tagged Arabidopsis thaliana lines that have been archived as individual lines to the T3 generation. The population is an excellent tool for both reverse and forward genetic screens and has been used successfully to identify a number of novel mutants. Flanking sequence tags (FST) have been generated and mapped for 15,507 lines to enable further application of the population, while providing a clear distribution of T-DNA insertions across the genome. The population is being screened for a number of biochemical and developmental phenotypes. The population provides an additional tool for plant researcher's to assist with determining gene function for the many as yet uncharacterized genes annotated within the Arabidopsis genome sequence. The presence of enhancer elements on the inserted T-DNA element (pSKI015) allows both knock-out and dominant activation phenotypes to be identified for traits of interest.arabidopsis thaliana, genetics, mutant, biochemical, developmental, phenotype, gene function, flanking sequence tag, trait, t-dnaSCR_004939(Saskatoon Arabidopsis T-DNA mutant population SK Collection, RRID:SCR_004939)AAFC Canadian Crop Genomics Initiative, NSERCrelated to: TAIRReferences (2)Last checked upnlx_91019
SGCResourceA not-for-profit, public-private partnership that carries out basic science of relevance to drug discovery whose core mandate is to determine 3D structures on a large scale and cost-effectively - targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets.basic science, drug discovery, drug, structural genomics, genomics, 3d structure, protein, human parasite, drug target, structure, human protein, protocol, phylogenetic tree, histone tail, high-throughput protein crystallization, lex bubbling system, reagent, epigenetic probe, antibody, vector, plasmid, constructSCR_003890(SGC, RRID:SCR_003890)University of Oxford; Oxford; United Kingdom , University of Toronto; Ontario; Canada Cancer, Diabetes, Obesity, Psychiatric disorderAbbVie, Boehringer Ingelheim, Canada Foundation for Innovation, Canadian Institutes of Health Research, Genome Canada, GlaxoSmithKline, Janssen, Lilly Canada, Novartis Research Foundation, Ontario Ministry of Economic Development Employment and Infrastructure, Pfizer, Takeda, Wellcome Trustrelated to: AbbVie, Canada Foundation for Innovation, Canadian Institutes of Health Research, Genome Canada, Janssen Research and Development, Ontario Ministry of Economic Development Employment and Infrastructure, Pfizer Animal Genetics, Wellcome Trust, uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank, Addgene, GenBankLast checked upnlx_158220
Protocol Online - Your labs reference bookResource, narrative resource, experimental protocol, data or information resourceDatabase of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert).bioinformatics, molecular biology, immunology, microbiology, proteomics, cell biology, databaseSCR_004937(Protocol Online - Your labs reference book, RRID:SCR_004937)Abcam, Chang Bioscience, Eppendorf, Invitrogen, KPL, Mirus, Nature Publishing Group, Oligomasterused by: NIF Data Federation, Integrated BlogsLast checked upnlx_90492
TI PharmaResource, funding resource, organization portal, portal, consortium, data or information resourceA not-for-profit organization that initiates and manages drug development consortia that involve the pharmaceutical industry, academia, and the Dutch Government. The aim of all their consortia is to conduct pre-competitive research while strengthening the Netherlands' international reputation for drug development. The consortia are focused on addressing therapeutic areas that are listed as priority areas by the World Health Organization including: autoimmune diseases, cardiovascular diseases, cancer, infectious diseases, and diseases of the brain. The consortia are also focused on enabling: therapeutic target discovery, validation, and animal models; lead selection and in-silico modeling; predictive drug disposition and toxicology; biomarkers and biosensors; drug formulation, delivery, and targeting; and, production technologies. TI Pharma consortia aim to improve the efficiency of the drug-development process, with a focus on advancing regulatory science. In addition to research, TI Pharma also has objectives to train and educate scientists in the Netherlands on the drug discovery and development processes, as well as on entrepreneurship. Participants include: all Dutch universities and academic medical centers, more than 30 industrial partners, small-to-medium sized companies, and representatives from the Dutch Medicines Evaluation Board (Netherlands regulatory body for drugs).consortium, biomarker, drug, drug development, tool development, pharmaceutics, drug discovery, animal model, biosensor, drug formulation, drug delivery, drug target, medicineSCR_003758(TI Pharma, RRID:SCR_003758)academia, Dutch government, industryrelated to: European Lead Factory, Kinetics for Drug Discovery, listed by: Consortia-pediaLast checked upnlx_157987
GENESIS Neural Database and Modelers WorkspaceResource, software resource, service resourceSoftware system to assist computational neuroscientists in interacting with databases of models and with neural simulation packages such as GENESIS. There are three components in the system: a user interface, a database server, and a global registry and repository. The collection of software tools with a graphical user interface enables users to interact over the WWW with databases of models and data. It provides facilities for searching multiple remote databases for model components based on various criteria; visualizing the characteristics of the components retrieved; creating new components, either from scratch or derived from existing models; combining components into new models; linking models to experimental data as well as online publications; and interacting with simulation packages such as GENESIS to simulate the new constructs. Although the initial version uses GENESIS as the simulator, the design permits the use of multiple simulation systems, with or without the use of a database. This allows modeling at multiple levels of scale from the molecular level, through the subcellular (e.g. ion channel), single cell, and network levels, to the systems level (e.g. relating models to fMRI studies). The system is intended to help users create and organize models and to interact with databases of models and neuronal simulation software. More specifically, the Modeler's Workspace is designed to provide the following: * Search and retrieval facilities for interacting with databases of models and other information; * Facilities for creating, editing and visualizing the characteristics of models; * Facilities for combining model components together and translating them into formats suitable for simulation systems such as GENESIS and NEURON; * Facilities for managing a personal database where a user can collect models and other objects; and * Collaboration facilities for connecting one or more users together, to allow them to simultaneously edit objects in a shared database and communicate with each other using real-time chat. The Modeler's Workspace is written in Java for portability and extensibility. It is modular in design and uses pluggable components for supporting different data formats, which means that new data types can be supported by loading an appropriate plug-in. To increase the probability that the Modeler's Workspace will be compatible with future databases and tools, they are using the eXtensible Markup Language (XML) as the interchange format for communicating with databases.channel, ion, model, neuron, simulation, visualization, xml, neural model, neural simulation, data sharing, database, neuronal cell, voltage-gated channel, data repository, registrySCR_002357(GENESIS Neural Database and Modelers Workspace, RRID:SCR_002357)University of Texas at San Antonio; Texas; USA Academic Equipment, Human Brain Project, Sun Microsystems Inc.related to: NeuroML, General Neural Simulation System, Neuroscience GatewayLast checked downnif-0000-21168http://www.modelersworkspace.org/
dendsortResource, software resource, software application, data analysis software, data processing software, data visualization softwareSoftware R package from CRAN as a modular leaf ordering methods for dendrogram nodes. Used as sorting methods to improve readability and interpretability of tree structure. Used for comparison of different distance measures or linkage types, identification of tight clusters and outliers, and for coupled heatmap visualization.modular, leaf, ordering, method, dendrogram, node, sorting, tree, structure, cluster, heatmap, visualizationSCR_016693(dendsort, RRID:SCR_016693)Academische Stichting Leuven, iMinds ICON b-SLIM, KU Leuven Research Council CoEaffiliated with: CRAN, R Project for Statistical ComputingPMID:25232468Last checked uphttps://bitbucket.org/vda-lab/dendsort/wiki/Home, https://github.com/cran/dendsort/blob/master/R/dendsort-package.R
LoRDECResource, software resource, software application, sequence analysis software, data analysis software, data processing softwareSoftware that performs hybrid error correction for long, PacBio reads. LoRDEC can correct insertions, deletions, and substitutions in PacBio reads.hybrid error correction, pacbio read, long error correction, real-time sequencingSCR_015814(LoRDEC, RRID:SCR_015814)Academy of Finland, ANR Colib’readPMID:25165095Last checked up
doGlycansResource, software resource, software application, software toolkit, simulation software, source codeSoftware toolkit for atomistic simulations to explore how carbohydrates function. \\nApplications include the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins.carbohydrate, atomistic simulation, glycoprotein, glycolipid, carbohydrate polymer, GROMACSSCR_015758(doGlycans, RRID:SCR_015758)Academy of Finland, European Research Council, Sigrid Juselius FoundationPMID:28906114Last checked up
DRIFTERResource, software resource, image analysis software, data processing software, software applicationModel based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data.bayesian, physiological noise, fMRI, algorithm, cardiac, respiratory, image anaylsis, bold signalSCR_014937(DRIFTER, RRID:SCR_014937)Aalto University; Espoo; Finland Academy of Finland, National Health Research Institute Taiwan, National Science Council Taiwan, NCR, NIBIB, NICHD, NIDCD, NIMH, NINDSsubmitted by: Resource Identification PortalPMID:22281675Last checked down
ICASSOResource, data visualization software, software application, algorithm resource, data processing software, software resourceSoftware implementing a method for assessing both the algorithmic and statistical reliability of estimated independent components developed by Himburg et al in their 2004 paper. The method is based on running the ICA algorithm many times with slightly different conditions and visualizing the clustering structure of the obtained components in the signal space. In experiments with magnetoencephalographic (MEG) and functional magnetic resonance imaging (fMRI) data, the method was able to show that expected components are reliable; furthermore, it pointed out components whose interpretation was not obvious but whose reliability should incite the experimenter to investigate the underlying technical or physical phenomena.independent component analysis, ica, ica estimate, visualization method, tight clusterSCR_014981(ICASSO, RRID:SCR_014981)Academy of Finland, Nokia Foundationuses: FastICA, MATLAB, submitted by: Neuroscience Information FrameworkPMID:15219593Last checked up
Cardiovascular Disease Knowledge PortalResource, disease-related portal, topical portal, portal, data or information resourcePlatform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data.genetic, data, cardiovascular, disease, humanSCR_016536(Cardiovascular Disease Knowledge Portal, RRID:SCR_016536)cardiovascular disease, myocardial infarction, atrial fibrillationAccelerating Medicines Partnership in Type 2 Diabetes, National Institute of Cardiovascular Diseases and StrokeLast checked up
Cerebrovascular Disease Knowledge Portal Resource, disease-related portal, topical portal, portal, data or information resourcePlatform for searching and analysis of human genetic information linked to cerebrovascular disease while protecting the integrity and confidentiality of the data.human, genetic, information, cerebrovascular, disease, data, knowledgeSCR_016535(Cerebrovascular Disease Knowledge Portal , RRID:SCR_016535)Broad Institute of MIT and Harvard , Massachusetts General Hospital cerebrovascular diseaseAccelerating Medicines Partnership in Type 2 Diabetes, National Institute of Neurological Disorders and StrokeLast checked up
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