Curator Dashboard

Database of the results of the ADNI study. ADNI is an initiative to develop biomarker-based methods to detect and track the progression of Alzheimer's disease (AD) that provides access to qualified scientists to their database of imaging, clinical, genomic, and biomarker data.

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• SciCrunch
• 17 years ago - by Anonymous

Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).

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• SciCrunch
• 9 years ago - by Anonymous

Software R package for simultaneous exploration of multiple datasets. Compositional omics model based visual integration.Used to integrate omics data for visualization, with special focus on compositionality.

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• RRID
• 3 years ago - by Anonymous

Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation).

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• SciCrunch
• 12 years ago - by Anonymous

ReproNim seeks to implement a shift in the way neuroimaging research is performed and reported. Through the development and implementation of technology that supports a comprehensive set of data management, analysis and utilization frameworks in support of both basic research and clinical activities, our overarching goal is to improve the reproducibility of neuroimaging science and extend the value of our national investment in neuroimaging research. Reproducibility is critical because the current literature is fraught with published results that are due to mistakes; or turn out to be false positive (contributed to by the lack of statistical power). More importantly, given the current publication system, it is exceedingly difficult to discern between false positive and true positive finding as data is hard to aggregate, and exact methods are hard to replicate.

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• NIF
• 9 years ago - submitted by Matt Travers

SDI is composite measure of area level deprivation based on seven demographic characteristics collected in the American Community Survey and used to quantify the socio-economic variation in health outcomes.

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• RRID
• 2 years ago - by Anonymous

Integrated Grants is a virtual database currently indexing funded research resources including NIH Research Portfolio Online Reporting Tool (RePORT) (current grants, updated monthly) and ResearchCrossroads (1970-2008, defunct as of 2009).

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• SciCrunch
• 13 years ago - by Anonymous

Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Facility provides imaging instrumentation and analysis software along with training and expertise.Instrumentation and technologies available to users include Zeiss LSM800 AIRYSCAN confocal microscope integrated with Zen software; PerkinElmer / Akoya Vectra 3.0 Automated Quantitative Pathology Imaging System;Agilent/BioTek Cytation 5 with BioSpa8 live-cell microscopy system for fluorescence and phase contrast microscopy; Olympus IX-83 ZDC2 microscope equipped with PRIMO UV light-based bioengineering device for micropatterning and microfabrication; Olympus IX73 Inverted Fluorescence Microscope.Image analysis software hosted on appropriately powered workstations with cloud connectivity for high capacity storage: HALO3, Inform, Volocity, AutoDeblur, Image-J / Fiji.Transmission and scanning electron microscopy including FEI Talos F200i (200kV TEM and STEM electron microscope (TEM), equipped for micro-analysis, and cryo-EM;FEI Helios CX5 dual beam FIB-SEM system with X-ray microanalysis detectors; instruments for specimen preparation for transmission and scanning electron microscopy including ultramicrotomes Leica Ultracut UC6 and UC7, critical point dryer Samdri-970, Leica ACE 600 coater and ThermoFisher Vitrobot.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

A software application for such tasks as photo retouching, image composition and image authoring. It has many capabilities such as it can be used as a simple paint program, an expert quality photo retouching program, an online batch processing system, a mass production image renderer, an image format converter, etc. GIMP is expandable and extensible and designed to be augmented with plug-ins and extensions. The advanced scripting interface allows everything from the simplest task to the most complex image manipulation procedures to be easily scripted.

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• SciCrunch
• 17 years ago - by Anonymous

Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information.

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• SciCrunch
• 9 years ago - submitted by Christoph Ziegenhain

Web application that is embedded in GNPS, which is community service. Web enabled mass spectrometry search engine for searches of all small molecule Mass Spectrometry data. Used to search single MS/MS spectrum against public GNPS spectral libraries and all public MS/MS datasets.

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

Non-profit organization to increase the openness, integrity, and reproducibility of scientific research. COS priorities are to (1) make the entire scientific workflow accessible, (2) increase scientists' accountability, (3) facilitate good practices by scientists, (4) increase reward for good practices, and (5) promote reproducibility of scientific findings. COS has three primary activities: * Infrastructure development to support the scientific workflow and to connect technologies that support scientific research and communication, such as the Open Science Framework * Community building on open practices among open-source developers, open science researchers, and the broader scientific community, such as the Open Science Collaboration * Metascience, research on scientific practices, such as Reproducibility Project: Psychology and our partnership with Science Exchange, Reproducibility Project: Cancer Biology.

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• SciCrunch
• 13 years ago - by Anonymous

IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application.

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• RRID-Legacy
• 9 years ago - by Anonymous

Core to capture mass spectral data obtained through time-of-flight measurements that can be used for 3D nanoscale compositional analysis to identify light mass and heavy mass species with equivalent sensitivity.

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• RRID
• 3 years ago - submitted by Anne Steputis

A non-profit research and public policy organization devoted to improving the worlds diet, preventing obesity, and reducing weight stigma.

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• SciCrunch
• 17 years ago - by Anonymous

Project that is a translation of the BraVa arterial vasculature database into the NIFTI MRI file format that can be applied to stroke studies, fMRI resting state imaging studies and other clinical neuroscience studies. Group artery region labels and arterial density maps are provided as well. Human Brain Major Artery Atlas 10.7490/f1000research.1114378.1

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• RRID-Legacy
• 9 years ago - by Anonymous

Core provides expertise and high frequency ultrasound instrumentation suitable for image acquisition and analysis applicable to your research studies. Provides Fuji/Visualsonics Vevo 3100 ultrasound imaging machine to perform ultrasounds on small animals. The scanner has high temporal and spatial resolution; current imaging probes utilize frequencies from 13-55 MHz.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

An application ontology established by a collaborative group of influenza researchers that includes consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)

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• SciCrunch
• 13 years ago - by Anonymous

Virtual resource for neuroscience.

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• NIF
• 9 years ago - submitted by Matt Travers