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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
University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIROrganization, service resource, core facility, access service resourceBiomedical Technology Research Center to develop methods and analytical approaches to 3D microscopy. Applicable to neurobiology and cell biology, incorporating equipment and implementing software that expand the analysis of 3D structure.method, analytical, 3D microscopy, imaging, neurobiology, cell biology, structureSCR_016627(University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR, RRID:SCR_016627)NIGMS, NIHrelated to: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked up
National Resource for Translational and Developmental ProteomicsOrganization, service resource, organization portal, training resource, portal, data or information resourceOrganization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists.protein, mass, spectrometry, proteomics, measurement, targeted, untargeted, analysisSCR_016907(National Resource for Translational and Developmental Proteomics, RRID:SCR_016907)Northwestern University; Illinois; USA NIGMSprovides: ProSight LiteLast 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
bioPIXIEResource, analysis service resource, data analysis service, service resource, production service resourcebioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it).prediction, bayesian network, probabilistic, interaction, networkSCR_004182(bioPIXIE, RRID:SCR_004182)Princeton University; New Jersey; USA NHGRI, NIGMS, NSFPMID:16420673Last checked downnlx_20893
ProFuncResource, analysis service resource, data analysis service, service resource, production service resourceThe ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein''''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time.gold standardSCR_004450(ProFunc, RRID:SCR_004450)European Bioinformatics Institute DOE, European Union FP6, NIGMSrelated to: PDBsumReferences (2)Last checked upnlx_44430
PILGRMResource, analysis service resource, data analysis service, service resource, production service resourcePILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis.data mining, gene expression, user directed data miningSCR_004749(PILGRM, RRID:SCR_004749)Princeton University; New Jersey; USA NCI, NIGMS, NSFPMID:21653547Last checked upnlx_75372
ESEfinder 3.0Resource, analysis service resource, data analysis service, service resource, production service resourceA web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.exonic splicing enhancer, sr proteinSCR_007088(ESEfinder 3.0, RRID:SCR_007088)Cold Spring Harbor Laboratory NCI, NHGRI, NIGMSPMID:12824367Last checked upnif-0000-30496http://rulai.cshl.edu/tools/ESE2/http://exon.cshl.edu/ESE/
miniTUBAResource, analysis service resource, service resource, storage service resource, production service resourceminiTUBA is a web-based modeling system that allows clinical and biomedical researchers to perform complex medical/clinical inference and prediction using dynamic Bayesian network analysis with temporal datasets. The software allows users to choose different analysis parameters (e.g. Markov lags and prior topology), and continuously update their data and refine their results. miniTUBA can make temporal predictions to suggest interventions based on an automated learning process pipeline using all data provided. Preliminary tests using synthetic data and laboratory research data indicate that miniTUBA accurately identifies regulatory network structures from temporal data. miniTUBA represents in a network view possible influences that occur between time varying variables in your dataset. For these networks of influence, miniTUBA predicts time courses of disease progression or response to therapies. minTUBA offers a probabilistic framework that is suitable for medical inference in datasets that are noisy. It conducts simulations and learning processes for predictive outcomes. The DBN analysis conducted by miniTUBA describes from variables that you specify how multiple measures at different time points in various variables influence each other. The DBN analysis then finds the probability of the model that best fits the data. A DBN analysis runs every combination of all the data; it examines a large space of possible relationships between variables, including linear, non-linear, and multi-state relationships; and it creates chains of causation, suggesting a sequence of events required to produce a particular outcome. Such chains of causation networks - are difficult to extract using other machine learning techniques. DBN then scores the resulting networks and ranks them in terms of how much structured information they contain compared to all possible models of the data. Models that fit well have higher scores. Output of a miniTUBA analysis provides the ten top-scoring networks of interacting influences that may be predictive of both disease progression and the impact of clinical interventions and probability tables for interpreting results. The DBN analysis that miniTUBA provides is especially good for biomedical experiments or clinical studies in which you collect data different time intervals. Applications of miniTUBA to biomedical problems include analyses of biomarkers and clinical datasets and other cases described on the miniTUBA website. To run a DBN with miniTUBA, you can set a number of parameters and constrain results by modifying structural priors (i.e. forcing or forbidding certain connections so that direction of influence reflects actual biological relationships). You can specify how to group variables into bins for analysis (called discretizing) and set the DBN execution time. You can also set and re-set the time lag to use in the analysis between the start of an event and the observation of its effect, and you can select to analyze only particular subsets of variables.analysis, analyze, bayesian, causation, clinical, linear, medical, structure, temporal, network analysis, network, molecule, information refining, gene expression regulation, bioinformatics, statistical package, interaction network, prediction, pathway, inference, biomedical, interventionSCR_003447(miniTUBA, RRID:SCR_003447)National Center for Integrative Biomedical Informatics , University of Michigan; Michigan; USA NIAID, NIDA, NIGMS, Society of University Surgeons Foundationlisted by: BiositemapsPMID:17644819Last checked upnif-0000-33272
SRMAtlasResource, atlas, database, data or information resourceResource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome.collection, proteomic, assay, detect, quantify, protein, mass, spectrometry, peptideSCR_016996(SRMAtlas, RRID:SCR_016996)American Recovery and Reinvestment Act, European Research Council, Luxembourg Centre for Systems Biomedicine University Luxembourg, NCRR, NHGRI, NIGMS, Swiss National Science FoundationPMID:27453469Last checked up
Zebra Finch Expression Brain AtlasResource, atlas, database, data or information resource, expression atlasExpression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches.gene, expression, brain, in-situ, hybridization, taeniopygia, vocal learning, anatomical, atlas, data set, molecular neuroanatomy, adult, male, gene, image, bird, image, avianSCR_012988(Zebra Finch Expression Brain Atlas, RRID:SCR_012988)Oregon Health and Science University; Oregon; USA NIGMS, NINDSLast checked upnif-0000-24345, SCR_000641, nlx_152091http://ignrhnet.ohsu.edu/finch/songbird/index.php
Zebrafinch Brain Architecture ProjectResource, atlas, data or information resourceAtlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing provides a useful atlas in user-chosen planes, which are otherwise unavailable in the paper-based version. * It can be made available on the internet. High resolution histological datasets can be independently evaluated in light of new experimental anatomical, physiological and molecular studies.nissl stain, sagittal, horizontal plane, transverse plane, myelin stain, brainSCR_004277(Zebrafinch Brain Architecture Project, RRID:SCR_004277)Brain Architecture Project Crick-Clay Professorship, NIGMS, NINDS, W. M. Keck FoundationLast checked upnlx_143663
Rhesus Macaque Atlases for Functional and Structural Imaging StudiesResource, atlas, data or information resourceNO LONGER AVAILABLE. Documented on September 17, 2019.\\nA set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.magnetic resonance imaging, macaca mulatta, neuroscience, rhesus macaque, structure, neuroimaging, t1-weighted atlas, t2-weighted atlas, mri, brain, neuroanatomySCR_008650(Rhesus Macaque Atlases for Functional and Structural Imaging Studies, RRID:SCR_008650)University of Wisconsin-Madison; Wisconsin; USA AgingIntramural Research Program, NCRR, NIA, NIGMSPMID:19059346Last checked upnif-0000-33003
NIGMS Human Genetic Cell RepositoryResource, biomaterial supply resource, biospecimen repository, service resource, storage service resource, cell repository, material resource, material storage repositoryHighly characterized cell lines and high quality DNA for cell and genetic research representing a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. The NIGMS Repository contains more than 10,600 cell lines, primarily fibroblasts and transformed lymphoblasts, and over 5,500 DNA samples. The NIGMS Repository has a major emphasis on heritable diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, and many apparently healthy controls. Human induced pluripotent stem cell lines, many of which were derived from NIGMS Repository fibroblasts, have recently become available through the NIGMS Repository. Sample donation facilitates all areas of research by making available well-characterized materials to any qualified researcher who might have otherwise been unable to invest the time and resources to collect needed samples independently. Donations to the Repository have created a resource of unparalleled scope. Samples from the collection have been used in more than 5,500 publications and are distributed to scientists in more than 50 countries. This resource is continuously expanding to support new directions in human genetics.cell, gene, cell line, dna, fibroblast, transformed lymphoblast, lymphoblast, induced pluripotent stem cell line, chromosomal abnormality, healthy, single-gene disorder, complex polygenic disorder, multifactorial birth defect, unaffected first-degree relatives of individuals with genetic disease, heritable disease, genetic disease, human variation, control, clinical data, bloodSCR_004517(NIGMS Human Genetic Cell Repository, RRID:SCR_004517)Coriell Cell Repositories Chromosomal abnormality, Healthy, Single-gene disorder, Complex polygenic disorder, Multifactorial birth defect, Unaffected first-degree relatives of individuals with genetic disease, Heritable disease, Genetic disease, ControlNIGMS, NIH Blueprint for Neuroscience Researchrelated to: Integrated Cell Lines, used by: NIF Data Federation, listed by: One Mind Biospecimen Bank ListingLast checked upnlx_143798
Ascidian Stock Center (ASC)Resource, biomaterial supply resource, material resource, organism supplierSupplier of Ciona (C. robusta and C. savignyi) adults and stable transgenic animals expressing tissue-specific fluorescent proteins for research laboratories. This ascidian culturing facility is located at the marine laboratory of the University of California at Santa Barbara (UCSB).ascidian, model organism, ciona, embryology, marine organism, culturing facilitySCR_014949(Ascidian Stock Center (ASC), RRID:SCR_014949)NIGMShosted by: University of California at Santa Barbara, California, USALast checked down
Caenorhabditis elegans Natural Diversity Resource (CeNDR)Resource, biomaterial supply resource, material resource, organism supplier, portal, data or information resourceSupplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery.c. elegans, caenorhabditis elegans, strains, n2, roundworm, nematode, gene analysis, organism supplier, portalSCR_014958(Caenorhabditis elegans Natural Diversity Resource (CeNDR), RRID:SCR_014958)Northwestern University; Illinois; USA Amazon Web Services Research Grant, American Cancer Society Research Scholar Award, NIGMS, Northwestern University Start-up Funds, NSF, Weinberg College of Arts and Sciences starter innovation awardPMID:27701074Last checked up
Laboratory for Fluorescence DynamicsResource, biomedical technology research center, service resource, access service resource, training resourceBiomedical technology research center and training resource that develops novel fluorescence technologies, including instrumentation, methods and software applicable to cellular imaging and the elucidation of dynamic processes in cells. The LFD's main activities are: * Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists. * Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications. * Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community.fluorescence, measurement, microscopy, spectroscopy, biochemistry, cell culture, data analysis, biomolecule, membrane, in-vitro, optical spectroscopy, biological process, tissue culture, fluorescence microscopy, optical and laser technology centerSCR_001437(Laboratory for Fluorescence Dynamics, RRID:SCR_001437)University of California at Irvine; California; USA NCRR, NIGMSLast checked downnlx_152663
BioCARSResource, biomedical technology research center, service resource, access service resource, training resourceBiomedical technology research center and training resource that is a state-of-the art, national user facility for synchrotron-based studies of dynamic and static properties of macromolecules by X-ray scattering techniques such as crystallography (specializing in time-resolved), small- and wide-angle X-ray scattering and fiber diffraction. BioCARS operates two X-ray beamlines, embedded in a Biosafety Level 3 (BSL-3) facility unique in the U.S. that permits safe studies of biohazardous materials such as human pathogens.synchrotron, macromolecule, x-ray, crystallography, x-ray scattering, fiber diffraction, biological process, time-resolved crystallography, structural biology technology centerSCR_001439(BioCARS, RRID:SCR_001439)University of Chicago; Illinois; USA NCRR, NIGMSPMID:21685684Last checked upnlx_152665
MacCHESSResource, biomedical technology research center, service resource, access service resource, training resourceBiomedical technology research center that is funded for two purposes: for core research as motivated by the important biomedical problems and support to all structural biologists making use of the Cornell High Energy Synchrotron Source (CHESS) facility for crystallographic and small-angle X-ray scattering experiments, as well as for novel experiments requiring special equipment and staff assistance not readily available at other synchrotron sources. MacCHESS provides a facility for developing new technology and for advancing the research goals of structural biologists as well as the broader biological research community. MacCHESS has a strong commitment to training future leaders, who will be able to translate advances in synchrotron science and structural biology into valuable biomedical applications. It operates three insertion-device beamlines (stations A-1, F-1 and F-2) devoted to macromolecular crystallography. The resource also supports additional bending magnet stations for part-time macromolecular X-ray experiments. The resource specializes in large unit-cell diffraction, ultra-high-resolution diffraction, multiple-wavelength anomalous dispersion (MAD) phasing, rapid-throughput crystallography (structure-based drug design and structural genomics), microdiffraction, high-pressure cryo-cooling, multiple-beam diffraction and software development.structure, macromolecule, crystallography, beamlne, x-ray, bending magnet, unit-cell diffraction, ultra-high-resolution diffraction, dispersion phasing, drug design, structural genomics, microdiffraction, cryo-cooling, high pressure cooling, diffraction, software, synchrotron, cryo-crystallography, small-angle x-ray solution scattering, microcrystallography, structural biology, structural biology technology centerSCR_001443(MacCHESS, RRID:SCR_001443)Cornell University; New York; USA NIGMSLast checked upnlx_152668
National Center for Macromolecular ImagingResource, biomedical technology research center, service resource, access service resource, training resourceBiomedical technology research center establishing the infrastructure for fast, routine, atomic structure determination of subcellular complexes by electron cryo-microscopy, computer reconstruction and modeling. Their emphasis is on specimens that cannot currently be studied by conventional structural techniques such as x-ray crystallography or NMR. The ultimate outcome of their research is a three-dimensional image of the complex that can be used for design of drugs and vaccines for a variety of diseases. The center is focused on extending the resolution, speed and flexibility of cryo-electron microscopy for the three-dimensional structure determination of biological macromolecular assemblies. Cryo-electron microscopy can visualize molecules under near-native conditions at resolutions ranging from 0.3 to 5 nm and can yield images of individual molecules in a range of different conformations as they exist in solution. Other cryo-electron mycroscopy techniques, such as cryo-electron tomography, are being developed to capture molecular structures in situ. The equipment, techniques and expertise developed are available to the research community through collaborative projects. The NCMI also provides training through workshops and other forms of dissemination via both traditional and modern Internet-based methods.cryo-electron microscopy, structure determination, structure, macromolecule, assembly, model, reconstruction, subcellular complex, electron cryo-microscopy, 3d spatial image, structural biology technology centerSCR_001445(National Center for Macromolecular Imaging, RRID:SCR_001445)Baylor University; Texas; USA NIGMSrelated to: EMDataBank.org: Unified Data Resource for Cryo Electron MicroscopyLast checked upnlx_152670
National Magnetic Resonance Facility at MadisonResource, biomedical technology research center, service resource, access service resource, training resourceBiomedical technology research center that develops NMR technologies for the high-throughput determination of the structures of small proteins and RNA; for elucidating the structure and dynamics of challenging systems such as complexes, membrane proteins and paramagnetic proteins; and for metabolomics and natural product analysis. NMRFAM equipment and resources are available to ALL scientists both within and outside of the university. Their experienced staff is available to train users as well as provide consultation and collaboration on experimental design, datPictures of NMRFAMa collection and analysis. Service and Collaborations # low-cost access to NMR instrumentation (400,500(2),600(4),750,800,900 MHz) mixture of 4 Agilent/Varian and 6 Bruker spectrometers (cryogenic probes on all but 400) # HPLC-SolidPhaseExtraction-liquid handling for 1.7 and 5mm NMR tubes with integrated MicrOTOF Mass spectrometer # Bruker AXS Nanostar SAXS (small angle X-ray scattering) # external access to processing and analysis servers, metabolomics database, software packages, and pulse program libraries # consultation with current and potential usersnmr spectrometer, structure, function, protein, rna, dynamics, complex, membrane protein, paramagnetic protein, metabolomics, analysis, spectroscopy, nucleic acid, automation, data analysis, macromolecule, small angle x-ray scattering, structural biology technology centerSCR_001449(National Magnetic Resonance Facility at Madison, RRID:SCR_001449)University of Wisconsin-Madison; Wisconsin; USA NCRR, NIGMSLast checked upnlx_152672
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