Curator Dashboard

Sequencing facility offers to perform a full range of genomic applications, such as Whole Genome Sequencing (WGS), RNA sequencing (including options for poly(A) selection, ribosomal depletion, and degraded/FFPE RNA), library preparation of ChIP samples, de novo sequencing, metagenomics sequencing, single-cell sequencing and PacBio long read sequencing applications.All next generation sequencing applications are performed on the Illumina platform with the NextSeq and NovaSeq instruments. Long-read sequencing applications are performed on the PacBio Revio using Single-Molecule, Real-Time (SMRT) Sequencing. The Revio is ideal for high-quality de novo whole genome assemblies, full-length transcriptomes, cell-type specific isoforms, and targeted long-read amplicon sequencing. Provides 10X genomics instrument for sample partitioning and molecular barcoding prior to sequencing. For metagenomics sequencing, 16S, 18S, or ITS regions can be isolated and sequenced as relevant and are sequenced on the NextSeq instrument, allowing researchers to characterize and study microbial communities from various environments such as soils, freshwater, seawater, wastewater, and host-microbe associations.Offers expertise of facility staff is available for researchers at any point in the experimental process.

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• SciCrunch
• 3 months ago - submitted by Edyta Vieth

Core is dedicated to advancing biomedical discovery through modern and highly advanced imaging technologies. Provides access to high-resolution, non- and minimally invasive imaging tools that enable visualization of biological processes in vivo. Core offers imaging services including MR Solutions Multi-Field MRI systems (3T, 7T, and 9.4T) for detailed anatomical and functional imaging, the IVIS Lumina S5 platform for sensitive bioluminescence and fluorescence imaging, and the TriTom Photoacoustic Imager for high-contrast 3D photoacoustic visualization and multi-spectral imaging of molecular and vascular dynamics.Facility supports a wide range of preclinical applications. These include longitudinal animal studies, drug development, biomarker discovery, and validation of novel imaging agents.

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• SciCrunch
• 3 months ago - submitted by Edyta Vieth

Facility provides comprehensive electronics fabrication and packaging capabilities bridging the high risk, resource-intensive gap between innovation and product development in an information-secure environment. AEP offers backplane electronics design, device fabrication, fanout wafer level packaging, electrical device test and integration capabilities, and operates dedicated pilot line toolsets for technology development. Assists with thin film processing, thin film characterization, device packaging and characterization, photolithography, etching, and flexible electronics. AEP is capable of processing 2 wafers all the way up to 300 mm round wafers.Services include microelectronic device prototyping and packaging, wafer coating or cleaning, wafer metrology, and pilot scale product demonstration. AEP is equipped with the tools and expertise to help take your electronic device from prototype fabrication to final packaging.

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• SciCrunch
• 3 months ago - submitted by Edyta Vieth

Core includes two full-service microscopy facilities available to researchers, clinical partners and industry members with the instruments and resources for a range of bioimaging services as well as analysis of non-biological materials. The ALMC has two locations; one within Biodesign (Biodesign Imaging Facility: BIF) and the other located in the School of Life Sciences (Regenerative Medicine Imaging Facility: RMIF). Both locations offer the technology, instrumentation and expertise to meet critical research needs in optical microscopy. These tools enable the observation of subcellular structures, track signaling pathways, and measure molecular interactions in live or fixed biological samples. Both locations are configured to accommodate live cell imaging and are BSL-2 certified with available cell culture facilities to maintain and prep samples. In both locations there is a dedicated image analysis workstation with software that includes deconvolution, particle tracking, colocalization, 3D measurements, extended depth of field and other analytic and image processing modules.

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• SciCrunch
• 3 months ago - submitted by Edyta Vieth

Fixed-specification binocular biological microscope ideal for teaching, routine clinical applications, and general laboratory use. It utilizes Universal Infinity System UIS2 infinity optics and features a compact, ergonomic design that minimizes fatigue during long observation sessions. Discontinued by Evident (formerly Olympus) and replaced by the upgraded CX33.

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• RRID
• 3 months ago - submitted by rong xiong

Software service for finding CURIEs from lexical strings. Dictionary based named entity recognition service built on top of Babel cliques.

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• RRID
• 3 months ago - submitted by Gaurav Vaidya

Software application for high-speed identifier normalization API service using Babel cliques and using in-memory Redis databases.

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• RRID
• 3 months ago - submitted by Gaurav Vaidya

Software tool to create cliques of equivalent identifiers across many biomedical vocabularies.

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• RRID
• 3 months ago - submitted by Gaurav Vaidya

Core provides access to instrumentation in flow cytometry including the Cytek Aurora Evo analyzer and the Cytek Aurora CS. Services provided include guidance in flow cytometry sample preparation, panel design, instrument usage, cell sorting, troubleshooting, data analysis including proteomics, metabolomics, bulk RNA sequencing, single cell RNA sequencing, and spatial transcriptomics. Provides consultation in experimental design, training and guidance in data analysis, and assistance with troubleshooting.

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• RRID
• 3 months ago - by Anonymous

Software R package designed to make text mining and natural language processing (NLP) easier by applying the principles of tidy data to unstructured text.

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• RRID
• 3 months ago - by Anonymous

Software code for the scib package used in benchmarking study for data integration tools. In our study, we benchmark 16 methods (see Tools) with 4 combinations of preprocessing steps leading to 68 methods combinations on 85 batches of gene expression and chromatin accessibility data.

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• RRID
• 3 months ago - by Anonymous

Software package installer for Python. You can use pip to install packages from the Python Package Index and other indexes.

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• RRID
• 3 months ago - by Anonymous

Software open-source Python library that makes it easy to work with geospatial data. It extends the popular data analysis library, Pandas, by allowing you to perform spatial operations on geometric shapes like points, lines, and polygons.

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• RRID
• 3 months ago - by Anonymous

Software application developed by Illumina that translates the raw, binary output files from Illumina sequencing systems into usable, standard text-based files known as FASTQ files. Conversion software that both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

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• RRID
• 3 months ago - submitted by Jacques Deguine

Public research university in Uruguay. Based in Montevideo, it is the most important higher education institution in the country. One of the largest public universities in South America in terms of enrollment.

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• RRID
• 3 months ago - submitted by Edyta Vieth

The Institut Pasteur de Montevideo (IP Montevideo) is one of the most recent affiliates of the Institut Pasteur International Network (RIIP in French), composed of 33 independent centres located in five continents and united by the same values. Dedicated to scientific research in biomedicine, IP Montevideo is composed by high-tech scientific platforms in areas such as genomics, proteomics, bioinformatics, molecular and cellular biology; laboratories are open to young scientists’ research projects; it has become an international education centre with courses on the latest biological knowledge and state-of-the-art technologies; and promotes start-ups for the development of biotechnological applications.

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• RRID
• 3 months ago - submitted by Edyta Vieth

Core was established as a joint unit between the University of the Republic and the Pasteur Institute of Montevideo, with the aim of supporting national and regional scientific and technological development. Our team of highly qualified imaging scientists is committed to technological development and the delivery of services of the highest quality, organized around four fundamental pillars: Services, Training and dissemination, Technology development and innovation (hardware, software, and methods), and Biological research projects.

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• RRID
• 3 months ago - by Anonymous

Software pipeline for automated identification of targeted cell types from multiple heterogeneous single-cell transcriptomic datasets (formats supported: .h5ad). It is designed to simplify and accelerate integrative large-scale single-cell analyses.

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• RRID
• 3 months ago - submitted by Guillaume Lemaire

Core provides specialized expertise, instrumentation, and technical support for assessment of mitochondrial function in cells, tissues, and isolated mitochondria. Provides standardized mitochondrial isolation, experimental design consultation, assay optimization, data analysis, and interpretation. Services include high-resolution respirometry using the Oroboros O2k-FluoRespirometer, simultaneous measurement of oxygen consumption and reactive oxygen species production, mitochondrial respiratory control and coupling analyses, electron transport system complex activity assays, citrate synthase activity, mitochondrial calcium handling, and assessment of mitochondrial content and oxidative stress. Studies can be performed using isolated mitochondria, permeabilized tissue fibers, tissue homogenates, and intact cells, depending on the scientific question and sample availability. Core also assists with protocol development, selection of normalization strategies, troubleshooting, training, and preparation of methods and data for grants, presentations, and publications.

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• RRID
• 3 months ago - by Anonymous

Core provides services including preparation of research tissue specimens for microscopic investigation with imaging capabilities for brighfield and fluorescent microscopy. Offers preparation tissue specimens for Histological sectioning utilizing both frozen and paraffin embedding techniques, preparation of mounted sections on glass slides. Facility maintains microtomes and cryostats for the preparation of tissue sections and houses several high end fluorescent microscopy systems, including the Leica Stellaris 8 tau-STED Super Resolution Microscope, the Nikon A1R+ HD Confocal Microscope,and the Nikon Ti2 HCA Inverted Fluorescence Microscope. Core also provides access to the Spatial Biology Platforms: Akoya PhenoCycler Fusion 2.0, 10x Genomics Visium and 10x Genomics Xenium.

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• RRID
• 3 months ago - submitted by Luke Fritzky