Curator Dashboard

Database for residue-level membrane protein-lipid contact annotations derived from experimentally determined Protein Data Bank structures. Includes automated Python pipeline for identifying lipid-containing PDB structures, calculating all-atom heavy-atom residue-lipid contacts using a 4.0 Angstrom distance cutoff, generating cluster-aware train, validation, and test splits, and producing documented dataset files for machine learning and structural bioinformatics. The dataset is deposited on Zenodo under CC0, while the code is released on GitHub under the MIT license. Contains large-scale experimentally-validated dataset of residue-level protein-lipid contacts from membrane protein structures.

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• SciCrunch
• 2 months ago - by Anonymous

Programmable, automated laboratory instrument used for slide based FISH (Fluorescence In Situ Hybridization) and ISH procedures. It is specialized, microprocessor controlled hot plate designed specifically for the denaturation and hybridization of DNA on glass microscope slides.

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• RRID
• 2 months ago - by Anonymous

130-watt programmable sonicator manufactured by Sonics & Materials, Inc. It is commonly used in laboratory settings for processing small volumes of liquid from 150 microliters to 150 milliliters.

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• 2 months ago - by Anonymous

Ultra-high-resolution Field Emission Scanning Electron Microscope (FE-SEM). It is used to examine the micro and nano-scale surface structures of materials and is widely utilized in scientific research, electronics, and materials science.

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• 2 months ago - by Anonymous

Compact, low-pressure benchtop plasma system used primarily in laboratories and small-scale production for ultra-fine surface cleaning, activation, etching, and coating. It utilizes cold gas plasma to alter material surfaces without damaging the bulk part.

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• 2 months ago - by Anonymous

Core provides comprehensive infrastructure and expertise to support structural biology research. Instrumentation includes Titan Krios, Talos Arctica, and Helios Hydra Bio, alongside dedicated sample preparation equipment. Offers services, consultation, and user training covering grid preparation and screening, automated data collection for single particle analysis (SPA) and cryo-electron tomography (cryo-ET), focused ion beam scanning electron microscopy (FIB-SEM), microcrystal electron diffraction (MicroED), and data processing.

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• RRID
• 2 months ago - submitted by Edyta Vieth

HIPAA-compliant digital platform developed by the Sylvester Comprehensive Cancer Center at the University of Miami. It is used to manage clinical trials, monitor patient symptoms at home, and deliver personalized lifestyle medicine interventions. Used to conduct studies with improved protocol adherence and data collection practices, as well as participant outreach and communication. MWR enables real time, bidirectional calling and messaging, behavioral intervention delivery, remote monitoring, and electronic patient reported outcome (ePROs) data collection.

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• 2 months ago - by Anonymous

Software R package for constructing networks of samples (e.g., patients) for each available data type and then efficiently fuses these into one network that represents the full spectrum of underlying data. Used to taking multiple views of a network and merging them into a combined view.

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• 2 months ago - submitted by Massimiliano Romano

Confocal laser scanning microscope primarily used in biological and medical research. It is designed to capture extremely detailed, 3D and 4D images of living cells, tissues, and organisms by using advanced laser technology to scan samples layer by layer.

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• 2 months ago - by Anonymous

Software pipeline to measure strand specific centromeric RNA normalized with DCS control of nanopore sequencing. Analysis pipeline for transcript capturing and analysis through nanopore sequencing.

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• 2 months ago - submitted by Santosh Kumar

Program uses cancer surveillance infrastructure to provide researchers with access to tissue and data. SEER Program cancer registry provides researchers with de-identified, but linked, archival, formalin-fixed, paraffin-embedded (FFPE) tissue from clinical care and/or clinical data obtained from medical record abstraction for secondary use in cancer research. Researchers may also request de-identified demographic information, outcomes, pathology reports, custom clinical data collection, and/or digital whole slide images. Used for studying rare cancers, early onset cancers, multiple primary cancers, unusual cancer outcomes, and cancers in small populations.

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• RRID
• 2 months ago - submitted by Alison Van Dyke

Software automated pipeline for population genomic analyses, pathogen identification, variant detection, and biosurveillance. The pipeline accepts paths to raw reads for one or more organisms and creates reports in the form of an interactive HTML document. Significant features include the ability to analyze unidentified eukaryotic and prokaryotic samples, creation of reports for multiple user-defined groupings of samples, automated discovery and downloading of reference assemblies from NCBI RefSeq, and initial identification based on k-mer sketches followed by multi gene phylogeny and SNP-based phylogeny.

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• 2 months ago - by Anonymous

Core to improve access, efficiency, and support for research teams working with a wide range of data sources to study and address population health issues. Part of data ecosystem of research data hubs and related services at NYULH. Our goal is to help Population Health PIs and Analysts solve their administrative and analysis issues. This includes data acquisition, storage, cleaning, analysis, and dissemination.

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• SciCrunch
• 2 months ago - submitted by Edyta Vieth

Core provides advanced mass spectrometry-based proteomics to support basic, translational, and clinical cancer research. Delivers high quality, quantitative proteomic data using instrumentation, including Thermo Scientific Astral Zoom and Ascend Tribrid orbitrap mass spectrometers. Services include gel band protein identification, immunoprecipitation and pulldown proteomics, cleavable cross-linking mass spectrometry, and global quantitative proteomics and post‑translational modification analysis using tandem mass tag‑based multiplexing or label‑free data-independent acquisition and data-dependent acquisition approaches. The CPSR supports end-to-end proteomics pipelines—from whole cells and primary tumor organoids through quantitative analysis and data visualization—providing comprehensive “soup to nuts” analytical capability.

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• 2 months ago - by Anonymous

JEOL JEM-2100 is a versatile, 200 kV transmission electron microscope (TEM) designed for high-resolution imaging and structural analysis across materials, nanotechnology, and biological sciences. It allows researchers to visualize nanoscale structures, perform chemical composition mapping, and analyze atomic crystal lattices.

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• RRID
• 2 months ago - submitted by Edyta Vieth

Core for high resolution imaging and structural analysis of biological specimens, soft matter, and nanomaterials. Used to process samples from solution or powder, allowing researchers to visualize internal structures down to the subnanometer scale. It is critically important that the samples are non-magnetic.

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• 2 months ago - submitted by Edyta Vieth

Software statistical framework for comprehensive integration of multi-modal single-cell data. Used for integration of multi-omic data sets in unsupervised fashion.

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• 2 months ago - submitted by Massimiliano Romano

Software framework for the alignment of cancer cell lines and tumors across multiple molecular layers. Used for matching in vitro cancer models to patient tumors.

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• 2 months ago - submitted by Massimiliano Romano

Software automated and comprehensive pipeline for cancer genome mutational signature analysis. Provides one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution, doublet base substitution, small insertion and deletion and copy number alteration. It can auto-extract mutational signatures, fit mutation data to all/specified COSMIC reference signatures (SBS/DBS/INDEL) and run bootstrapping analysis for studying signature stability.

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• 2 months ago - submitted by Massimiliano Romano

Software R package to compress multi-omic data into a single matrix of reduced size. Used for fast and scalable identification of relevant multi-omics relationships between biological entities at the bulk and single-cells level.

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• RRID
• 2 months ago - submitted by Massimiliano Romano