Curator Dashboard

System designed to facilitate behavioral observations in home cage environment. Instrumented observation cage to measure and test behavior of laboratory rodents. Device comes with PhenoTyper top unit which included lighting and camera, both powered by EthoVision XT, and range of optional sensors and stimuli.

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• RRID
• 3 years ago - by Anonymous

System consists of hardware and software for assessment of motor performance and motor learning in mice. Hardware includes two goal boxes with horizontal ladder in between. Touch sensitive rungs of the ladder make it possible to measure step durations and step types. ErasmusLadder software controls experiments by sending protocol and start command to apparatus. Sessions are performed automatically, and afterwards, data is sent back to software for storage and analysis.

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• 3 years ago - by Anonymous

Software package for digital image analysis. Used to search for optimal methods for image classification and segmentation. Computes shape, color and texture descriptors of arbitrary regions of interest. Color analysis includes RGB, CMY, HSY, YIQ, YUV, CIELab and CIEXYZ models. Texture feature extraction algorithms include co-occurrence matrix, run-length matrix, autoregression model, brightness distribution statistics, local binary patterns, histogram of oriented gradients, Haar and Gabor transforms. Enables calculation of morphological features such as moments of inertia, Feret diameters, ratios of Danielson, Blair-Bliss or Malinowska, and many others. Implements algorithms of discriminant analysis and data classification such as linear discriminant analysis, mutual information, convex decision boundary and support vector machines.

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• 3 years ago - by Anonymous

Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms.

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• 3 years ago - submitted by Anita Bandrowski

Database to establish comprehnsive gene resource for epithelial-mesenchymal transition.

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• 3 years ago - by Anonymous

Web application to find and extract open reading frames (ORFs). Used to find and output sequences of open reading frames in one or more nucleotide sequences.

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• 3 years ago - by Anonymous

Software application for predicting protein functions from protein sequences using deep neural networks combined with sequence similarity based predictions.

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• 3 years ago - by Anonymous

Portal provides everything needed to start using Planet services. Planet Application Program Interface to retrieve Planet Labs PBC's satellite images and products.

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• 3 years ago - by Anonymous

Software Python package to predict metabolite mediated cell-cell communications by single-cell RNA-seq data. Used for inferring metabolite, such as lipid, mediated cell-cell communication events using single-cell RNA-seq data.

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• dkNET
• 3 years ago - submitted by Ko-Wei Lin

Website describing International Classification of Diseases-Oncology codes that corresponds to different cancer sites in the Surveillance, Epidemiology, and End Results (SEER) registry.

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• 3 years ago - by Anonymous

Website describing International Classification of Diseases codes that corresponds to lymphomas in the Surveillance, Epidemiology, and End Results (SEER) registry.

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• 3 years ago - by Anonymous

Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States.

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• 3 years ago - by Anonymous

Web application that tracks the status of the BICAN consortium tissue samples and related data.NIMP is developed under NIH BRAIN Initiative's BICAN U24MH130988 award as a part of the coordinating unit for biostatistics, informatics, and engagement (CUBIE) for the BRAIN Initiative Cell Atlas Network (BICAN) program.NIMP consists of two portals for BICAN collaborative data generation: the Specimen Portal and the Sequence Library (SeqLib) Portal. The Specimen Portal focuses on tissue management from donors to brain slabs and annotated brain samples. The SeqLib Portal manages the workflow starting from tissue, all the way downstream to track data deposition to assay-dependent, data-modality-specific archives. Both portals work in tandem to generate multimodal genomic data that can be traced back to their anatomical origins using the Allen Brain Atlas. The portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting. All of the underlying functionalities are achieved through a robust agile development strategy using NHash resource identifiers, metadata standardization, active combinatorial dashboarding, resource provenance linkage and rendering (e.g. Sankey diagrams), and dedicated interfaces with NIH Neuro Biobank, sequencing centers, NeMO, and the larger BICAN data ecosystem.

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• 3 years ago - submitted by Anita Bandrowski

Software R package as visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.Used for graphical display of correlation matrix, confidence interval. Contains some algorithms to do matrix reordering. Good at details, including choosing color, text labels, color labels, layout, etc.

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• 3 years ago - by Anonymous

Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering.

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• 3 years ago - by Anonymous

Software Python based app for analyzing polarization resolved microscopy data to measure molecular orientation and order in biological samples.

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• 3 years ago - submitted by Cristel Chandre

Vector Borne Infectious Disease core produces tick vectors for research on Lyme disease and other tick borne diseases. Diagnostic Parasitology component provides diagnostic services to clinical veterinarians and core and affiliate investigators when parasitic diseases are suspected in resident nonhuman primates. Services for affiliate investigators include blood parasite detection via microscopic examination of prepared blood smears and quantitative buffy-coat analysis, and intestinal parasite detection via microscopic examination of direct wet mounts, zinc sulfate flotation prepared slides, or parasite specific assays.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER AVAILABLE. SAME SERVICES ARE AVAILABLE IN Molecular Virology and Sequencing Core. Documented on January 28, 2025. Core is divided into virus characterization, isolation, and production part and next generation sequencing part. Virus Characterization, Isolation and Production component provides virus expansion and characterization, viral titer by plaque and TCID50 assays, live virus neutralization and inhibition assays at both BSL-2 and -3 level including SARS-CoV-2. Next Generation Sequencing component provides expertise in next generation sequencing and genomic services including whole genome, epigenetics, targeted amplicons, and 16S metagenomics.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Shared instrument facility that has a Bruker Skyscan 1272 ex-vivo microCT that is capable of X-ray imaging at sub-micron resolution. The instrument can optionally be equipped with a 16-sample sample changer to automate the scanning queue. Core provides visualization and image analysis support for researchers, using open-source 3D Slicer biomedical imaging suite.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Core offers micro-imaging and micro-analysis solutions by providing access to several photon-, scanned probe-, ion beam-, and electron beam-based imaging and analytical instruments, services, and technical expertise for characterization of materials including nano-engineered materials, microelectronics, photonics, biomaterials, and others with applications in life sciences, drug discovery, environmental and energy research. Consultative services are also available.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth