Curator Dashboard

Software program for interactive processing of LC-MS-based metabolomics data. Open source cross platform metabolomics data analyser. Used to reduce complexity of metabolomics analysis by developing highly intitute interface for exploring and validating metabolomics data. Program features multi-file chromatographic aligner, peak-feature detector, isotope and adduct calculator, formula predictor, pathway visualizer, and isotopic flux animator. Data from both triple quadropole and full spectrum instruments is supported.

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• RRID
• 4 years ago - by Anonymous

Reference database of human transcriptional regulatory interactions. Manually curated database of human and mouse transcriptional regulatory networks.

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• RRID
• 4 years ago - submitted by yuan zhuang

Software Python library for mixed effects meta regression including meta analysis.

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• SciCrunch
• 4 years ago - submitted by Taylor Salo

Clinical Imaging Core Service Center includes RADCORE, Tumor Response Assessment (TRAC) and Research imaging guided biopsies cores. Supports cancer clinical trials. RADCORE staff include clinical research professionals with range of expertise in imaging based clinical research protocols and offers services in consultation, management of research protocols and Radiology IND/IDE support office. Tumor Response Assessment Core (TRAC) team of Radiologist is skilled in evaluating tumor response imaging assessments for patients enrolled in cancer clinical trials being conducted at UPHS. Research imaging guided biopsies Interventional Radiology and technical staff provides consultation to define biopsy protocol and pathology tissue collection.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Provides project based bioinformatics support for ITMAT translational researchers. Provides computational infrastructure and programming support needed to conduct high-throughput proteomics experiments. We also support other genomics high-throughput technologies to a lesser extent. The projects range from building Web applications for data analysis pipelines, scripting, clinical and basic science research support, and database and algorithm development. Recent efforts have focused on explorations of new models of computation, specifically cloud computing and GPUs, for use in genomic scale research.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides consultations and fee for service support in big data analyses using methods of data science in biomedical and health research related to digestive disease and liver research.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Flow cytometry analysis software for fast analysis, easy collaborative access to data, and tailored data visualization.

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• RRID
• 4 years ago - by Anonymous

Software package for liquid chromatography mass spectrometry retention time alignment.

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• SciCrunch
• 4 years ago - by Anonymous

Facility is focused on characterization of multifunctional soft materials. Includes four instrumentation suites based on soft matter centered research areas which will be unified by general theme of characterization of hierarchically structured multicomponent, multifunctional soft materials: Molecular Characterization, Processing and Mechanics, Thin Films and Interfacial Analysis, and Nanostructure Characterization.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Provides infrastructure for imaging based small animal research.Includes noninvasive anatomy, physiology, and biochemistry assessment for disease detection and therapeutic monitoring.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Operated by Institute of Marine Sciences with support from UCSC Division of Physical and Biological Sciences. Available to UCSC and University of California marine and coastal research community.Provides equipment including Shimadzu TOC-VCPH TC/TN analyzer,Dionex ICS-2000 Ion Chromatograph,UIC Carbon Coulometer Analyzer, Perkin-Elmer AAnalyst 100 Atomic Absorption Spectrophotometer, Thermo Genesys 10S UV-Visible Spectrophotometer, Turner Designs 10-AU Field Fluorometer, Turner Designs TD-700 Lab Fluorometer, Turner Designs TD-20/20 Luminometer,Lachat QuikChem 8000 Flow Injection Analyzer, Guildline 8410 PortaSal Salinometer, Labconco Freeze Dryer.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Provides advanced imaging technologies and image analysis tools including vital imaging of cellular processes within cells, tissue explants, and organoids.Supports services for transmission electron microscopy of biological samples.Imaging capabilities include fluorescence imaging of samples;Transmitted light imaging; Live cell imaging;FRAP, FLIP, Photoactivation/conversion;FRET, FLIM; Image processing, analysis, quantification; Transmission electron microscopy.Microscopes and Equipment include:Zeiss Axio Imager M2 Motorized Upright Microscope;Zeiss Cell Discoverer 7; Zeiss ELYRA S.1 Superresolution Microscope; Zeiss LSM 780 NLO Multiphoton Microscope;Zeiss TIRF3;Zeiss Stallion Digital Imaging Workstation;FEI Morgagni Transmission Electron Microscope;Leica UC6 Ultramicrotome;ImageXpress Pico & BioTek Cytation 7;Cryostar NX70 Cryostat.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides intravital imaging equipment to acquire advanced descriptive and quantitative data for imaging studies. Includes Olympus FVMPE-RS advanced multiphoton microscope, multichannel, multiphoton excitation system specifically tailored for intravital and deep tissue imaging.System is additionally equipped with 458 and 588 nm stimulation laser lines for photobleaching, light stimulation and/or photoactivation of various fluorescent or caged constructs. Uses Spectra-Physics InSight X3 dual-line, tunable multiphoton laser for ultrafast, multichannel imaging.Available Neurotar Mobile Home Cage allows researchers to integrate real-time imaging with behavioral/locomotion tracking. Offers training and access to imaging system, support in design of experimental procedures, acquisition of image data, and analysis of acquired images.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP.

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• RRID
• 4 years ago - submitted by Samantha White

Provides integration and analysis of publicly available resources as well as newly collected transcriptomic data following deubiquitinating enzyme (DUB) knockout or inhibition to facilitate exploration of DUB function in oncology.

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• RRID
• 4 years ago - submitted by Charles Hoyt

Standard for health care data exchange, published by HL7. Platform provides healthcare information exchange standard that makes use of HL7-defined set of “resources” to support information sharing by variety of means, including documents, messages, services and RESTful interfaces. FHIR defines resources for clinical and administrative content (e.g. Observation, Patient, etc.) as well as resources for “infrastructure” purposes. Some of these infrastructure resources are used to define standard itself – i.e. what the characteristics of resources are, what codes can be used in them, etc.

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• dkNET
• 4 years ago - submitted by Maryann Martone

Software tool for identification and classification of phage virion proteins using deep learning.

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• RRID
• 4 years ago - submitted by Zhencheng Fang

Provides research MRI capabilities for investigators at UNMC and across greater Omaha area. Housed in Hixson-Lied Center, CAMRI operates Siemens 3T Prisma MRI instrument that can collect high quality data of any MR modality using advanced gradients and research grade pulse sequences. Variety of head coils (20-, 32-, and 64-channel) are available to optimize data collection for needs of specific studies. Studies incorporating functional MRI can take advantage of CAMRI�s suite of MRI-compatible response devices, mirrored 32-inch LCD screen, and integrated stimulus display computer.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core of University of Ottawa and Ottawa Hospital Research Institute. Provides advice on bioinformatics research design, conduct bioinformatics analysis, and provide support for grant proposals that involve bioinformatics (including conducting pilot studies, support/collaboration letters and methodological text). Areas of expertise include:Analysis of high throughput sequencing data; single cell (Chromium 10x), RNA-seq (including small RNA), ChIP-seq, ATAC-seq, Hi-C.Large scale analysis integrating multiple data types.Helps to arrange for analysis of your biological samples with local core facilities such as StemCore, Proteomics Resource Center, or OHRI Mass Spectrometry Core Facility. Provides yearly training courses in RNA-seq analysis and Bioinformatics analysis using R as well as individual training and analysis support on request.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth