Curator Dashboard

Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response.

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• SciCrunch
• 14 years ago - by Anonymous

Research center for translation research on diabetes within the health care delivery systems affiliated with the HMO Research Network, University of California San Francisco, and the State of California. Their aims include improving health care disparities, diabetes and obesity prevention, and health information technology interventions.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Sartorius Cell Culture Facility delivers hands-on training in cell culture to students, faculty, staff, and external personnel, while providing researchers across numerous Penn State disciplines access to the lab environment.

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• SciCrunch
• 3 years ago - submitted by Craig Praul

Database of protein-ligand crystal structures that is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. The resolved protein crystal structures with clearly identified biologically relevant ligands are annotated with experimentally determined binding data extracted from literature. A viewer is provided to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. The binding-affinity data ranges 13 orders of magnitude. The issue of redundancy in the data has also been addressed. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 best complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This collection of protein-ligand complexes will be useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques.

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• SciCrunch
• 13 years ago - by Anonymous

Core facility whose services include histology, immunohistochemistry, RNA in situ hybridization, mRNA probe generation, frozen sections for enzyme histochemistry, immunofluorescent antibody studies, live and fixed cell confocal, deconvolution microscopy and super resolution microscopy (SIM and STORM), and transmission electron microscopy, quantitative morphometric analysis, high throughput microscopy and high content analysis, laser capture microdissection for molecular genetic analyses, and digital images for internet communication and publication.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

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• SciCrunch
• 17 years ago - by Anonymous

Core facility which investigates the connections between chronic kidney disease, cardiovascular disease, and hypertension. It focuses specifically on investigating the pathophysiology, epidemiology, and therapeutic response in on-going studies or existing datasets of one of the three diseases with the aim of relating data from individual diseases to each other.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Provides space and equipment for collaborative pilot projects between engineers and neuroscientists, workshops, training classes and product demonstrations as requested by members of Wu Tsai Neuro. Facility provides tissue culture suite with two biosafety cabinets, CO2 incubators, centrifuge and fluorescent microscope, in vivo procedure suite to allow animal surgeries, four curtained electrophysiological rig/microscope areas, two microscope rooms, -20C and -80C freezers and 4C cabinets for temporary sample storage.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

A software toolkit that performs multiple imputation for group level, single sample t-tests. Whole brain group level statistic maps from fMRI rarely cover the entire brain as a result of missing data. Missingness between subjects in fMRI datasets can result from susceptibility artifacts, bounding box (acquisition parameters), and small differences in post-normalized morphology. The toolkit consists of several interactive command line scripts that guide the user to map the spatial distribution of missing data across contrast images, calculate spatial neighborhood averages that help impute values, perform conventional and multiple imputed t-statistics, save the results to brain maps, and create result tables. The toolkit contains an instruction manual (pdf), two Matlab scripts and one R-Statistics script, which depend on functions defined in the popular SPM toolbox and functions defined in the MICE package for (R).

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2022. Core facility which provides various histology, histochemistry, immunochemistry, and pathology services. They also provide technical training for histopathological methods and tools.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Offers analytical services, technical and scientific consulting and training, as well as pay-per-use research equipment.Provides scientific expertise and support for standard and customized assays, from initial study design to final interpretation and statistical analysis of experimental data. Services also include clinical sample acquisition, processing and archival for conducting inter-disciplinary translational research applications.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches.

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• SciCrunch
• 14 years ago - by Anonymous

Core which provides a complete range of microvascular phenotyping of murine models of diabetes, obesity and metabolic disease, including validated, reproducible and standardized phenotyping of the three major microvascular complications: diabetic polyneuropathy, nephropathy and retinopathy.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Provides support and services to clinical investigators including consulting, technology transfer, process and analytical development, clinical manufacturing and regulatory affairs.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open-source utilities that are C++ based command line applications that allow image analysis and processing using ITK or VTK libraries. Specifically the following utilities are contained thus far: * ImageMath - the swiss army knife image modification * ImageStat - compute stats on images * IntensityRescaler - rescale/normalize intensities using a prior brain tissue segmentation * convertITKformats - convert 3D images in all ITK formats (NRRD, NIFTI, GIPL, Meta etc) * DWI_NiftiNrrdConversion - convert DWI and DTI from/to NRRD and NIFTI, works with UNC DTI tools and FSL * CropTools - crops 3D and 4D images * PolydataMerge - Merges VTK polydata files * PolydataTransform - Transforms polydata files * TransformDeformationField - concatenates or average deformation fields (H-fields or displacement fields) * DTIAtlasBuilder - Creates a DTI average from multiple DTI images

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• SciCrunch
• 14 years ago - by Anonymous

Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present.

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• SciCrunch
• 10 years ago - submitted by Yueling Li

CRBS is a UCSD organized research unit (ORU) that exists to provide human resources, high technology equipment, and administrative services to researchers engaged in fundamental research on cell structure and function relationships in central nervous system processes, cardiovascular networking, and muscular contraction through multiple scales and modalities. CRBS scientists investigate these processes through invention, refinement, and deployment of sophisticated technologies, especially: - High-powered electron microscopes that reveal three-dimensional cell structures - State-of-the-art X-ray crystallography and magnetic resonance analysis that provide detail on protein structures at high-resolution - Laser-scanning and confocal light microscopes that reveal molecules tagged with fluorescent markers as they traffic within cells and pass transfer signals within and between cells - High performance computing and grid-based integration of distributed data CRBS facilitates an interdisciplinary infrastructure in which people from biology, medicine, chemistry, and physics can work with those from computer science and information technologies in collaborative research. Researchers share interests in the study of complex biological systems at many scales, from the structures of enzymes, proteins, and the body's chemical communications network at atomic and molecular levels, to an organism's physiology, strength, and support at cellular and tissue levels. The CRBS infrastructure integrates resources for high-performance computing, visualization, and database technologies, and the grid-integration of large amounts of archival storage data. The California Institute for Telecommunications and Information Technology (Cal-IT2) and the San Diego Supercomputer Center (SDSC) are collaborators in simulating the activity of biological systems, analyzing the results, and organizing the growing storehouse of biological information. CRBS is an entity evolving as research evolves. It forges interactions with biotechnology and biocomputing companies for technology transfer. Interaction, collaboration, and multiscale research produce new perspectives, reveal fruitful research topics, lead to the development of new technologies and drugs, and train a new generation of researchers in biological systems. Sponsors: CRBS is supported by the University of California at San Diego.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Computationally oriented experimental laboratory interested in the encoding of auditory information in the cerebral cortex and brainstem, and in the mechanisms of tinnitus and the effect of various drugs (Lidocaine, steroids, anti-oxidants) in relieving noise trauma induced tinnitus. The ferret (Mustela putorius) and the rat serve as their system model. Through chronic implants, they obtain electrophysiological data from awake behaving animals in order to investigate the response properties and functional organization of the auditory system, both in health and after noise trauma that induces tinnitus in rats. Projects: * Response Modulation to Ongoing Broadband Sounds in Primary Auditory Cortex * Neuronal Response Characteristics in the Inferior Colliculus of the Awake Ferret and Rat * Spectro-Temporal Representation of Feature Onsets in Primary Auditory Cortex * Targeting the changes in inferior colliculus induced by tinnitus

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• SciCrunch
• 15 years ago - by Anonymous

Collection of software tools for the computational analysis of brain anatomy with MRI data. It includes automated software tools from surface reconstruction to their mapping via metric optimization in the Laplace-Beltrami embedding space. It is general and can be applied to a wide range of anatomical structures including cortical, sub-cortical, and fiber bundle surfaces.

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• NIF
• 10 years ago - submitted by Matt Travers