Curator Dashboard

Core offers services for researchers who want to apply advanced molecular genetic techniques in rodent models of physiology and disease. Provides expertise in generating novel mutant and transgenic mouse strains using genome engineering in mouse embryos and in embryonic stem cells (ESCs). Available technologies include:Generation of genome-edited mice by embryo pronuclear microinjection of DNA and genome editors (e.g., CRISPR/Cas9, site-specific recombinases) or traditional BAC transgenesis;Generation of genome-edited mice from mouse embryonic stem cells (mESCs) by chimeric blastocyst injection;Generation of genome-edited mice from mESCs by tetraploid blastocyst injection; Generation of mice from induced pluripotent stem cells;Assisted reproductive technologies; Sperm and embryo cryopreservation, storage and import/export;in vitro fertilization (IVF); Embryo rederivation technologies for animal import into barrier vivaria through quarantine.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

ABCF can provide MAbs from established hybridomas for RESEARCH PURPOSES ONLY, can assist in generating MAbs, offers a weekly mycoplasmal contamination screening service for tissue culture samples, distributes cell lines developed at Memorial Sloan Kettering Cancer Center and Rockefeller University.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

MTGTF is to support the investigators in using genetically modified mouse models in Brown University, affiliated hospitals and academic institutions in Rhode Island and other states. Provides services of molecular design and generation of transgenic and knock-out mouse models as well as general advice on use and management of such models. Conventional ES cell gene-targeting system is employed to serve as alternative or to fill the limitations of CRISPR/Cas9 system. Routine services include genotype analysis, sperm or embryo cryopreservation and storage, rederivation, in vitro fertilization (IVF). Other services, such as mouse vasectomy, embryo transfer, colony scale-up, intracytoplasmic sperm injection (ICSI) are also available. New services requiring MTGTF resources can be created through request.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core supports DNA Sequencing of PCR, Plasmid, BAC and Fosmid templates, Fragment Analysis of Microsatellites, AFLP, t-RFLP, SHAPE Experiments and Human Cell Line Authentication.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core for high resolution structural biology at the University of Vermont. X-ray crystallography allows biological and biomedical researchers to visualize proteins, RNA, DNA and their complexes at atomic resolution. The molecular details of specimens as small as DNA binding domains and as large as the ribosome have been elucidated via this powerful method. The CXX provides resources for all stages of macromolecular structure determination.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Advanced Genomic Technologies Cluster provides next-generation sequencing and Sanger sequencing. Next-generation sequencing services are provided using Illumina MiSeq and NextSeq sequencers. Services are available for amplicon re-sequencing, viral or microbial whole genome sequencing and 16S microbiome sequencing. Sanger DNA Sequencing can be performed on DNA templates such as PCR products and plasmids using ABI 3730xl and ABI3130xl instruments.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides expertise in biostatistics, microarray data analysis, proteome informatics, next generation sequencing data analysis, functional analysis, database development and information technology, including data storage infrastructure and high performance computing. Working closely with VGN Proteomics Facility, offers investigators experimental design consultations, comprehensive data analysis, data management and publishing, and manuscript and grant support. Core personnel also engage in teaching and training activities for data analysis and compute resources necessary for VGN network investigators. Our goal is to provide network researchers with bioinformatics expertise.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Open source software package for R programming language that is used to acquire chemical information from online data sources. Package contains functions that allow programmer to interact with webpages and APIs to retrieve chemical information.

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• RRID-Legacy
• 7 years ago - submitted by Tamás Stirling

Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.

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• RRID-Legacy
• 7 years ago - by Anonymous

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

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• SciCrunch
• 7 years ago - by Anonymous

Web tool as flexible cloud-based platform for cancer genomics research. Platform that serves as large-scale repository and provides computational infrastructure necessary to carry out cancer genomics research at unprecedented scales. ISB-CGC is providing access to TCGA data and computation on Google Cloud Platform.

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• SciCrunch
• 7 years ago - submitted by Ko-Wei Lin

Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data.

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• SciCrunch
• 7 years ago - submitted by Ekaterina Noskova

Spreadsheet program included as part of free, web-based software office suite offered by Google within its Google Drive service. Service also includes Google Docs and Google Slides, word processor and presentation program respectively.

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• RRID-Legacy
• 7 years ago - submitted by Joe Menke

Software tool for identifying hub objects and sub-networks from complex interactome. Predicts and explore nodes and subnetworks in given network by several topological algorithms. Provides interface to analyze topology of protein-protein interaction networks, such as human, yeast, rat, mouse, fly etc. Plugin works with Cytoscape 2.6 or above, which requires Java 1.5 or above.

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• RRID-Legacy
• 7 years ago - submitted by Yanming Liu

Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution.

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• SciCrunch
• 7 years ago - submitted by Haris Zafeiropoulos

Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more.

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• RRID-Legacy
• 7 years ago - submitted by Edyta Vieth

Software tool to dig out more robust and reliable differentially expressed genes between two groups. Samples from different groups will be re-sampled randomly associated with total number of samples.

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• RRID-Legacy
• 7 years ago - by Anonymous

Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program.

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• RRID-Legacy
• 7 years ago - submitted by Joe Menke

Software tool for dendritic spine analysis that enables to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo and in vitro imaging sessions, automatically aligns images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics such as length, thickness, and overall number, for accurate quantitative comparison.

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• RRID-Legacy
• 7 years ago - submitted by Maci Heal