Curator Dashboard

UMass Metabolic Disease Research Center (MDRC), formerly the National Mouse Metabolic Phenotyping Center, is a core facility that performs standardized experiments using state-of-the-art equipment for the purpose of investigating transgenic mouse models of diabetes, obesity, and metabolic liver disease. Provides metabolic and functional characterization of mouse models of human diseases that are developed by academic and industry researchers in joint efforts to understand metabolic diseases and to identify new therapies.

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth

NMR Laboratory maintains two high field NMR spectrometers in support of structural and dynamics studies of biomolecules. Its capabilities include determining high resolution structures, biological macromolecules, elucidation and structural mapping of protein-protein, protein-nucleic acid, protein-peptide, protein-drug interactions, and studies of dynamics of proteins and their complexes in solution. Laboratory staff provide advice,consultation, training,assistance and complete structure elucidation services.Staff is responsible for maintenance, upgrades, implementation of new NMR pulse sequences, and assisting local and remote users with technical problems.Equipped with Bruker Avance 800 MHz NMR instrument fitted with TCI cryoprobe and Bruker Avance III 600 MHz with variety of probes.

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth

Designed to enhance multi-disciplinary research initiatives catalyzing key clinical and basic immunology research in vaccines, HIV/AIDS, autoimmunity, allergy/asthma, transplantation as well as cancer immunology.Provides expertise in multichromatic flow cytometry (immunophenotyping, antigen-specific intracellular cytokine staining and cell sorting), T and B cell Elispot, Fluorispot, T regulatory cell assays, magnetic bead selection of cell populations, and Luminex multiplexed bead array assays.Provides specialized clinical specimen analysis services for clinical studies or contracts.

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth

Established to produce immortalized cell lines from human blood (EBV transformations). Offers genomics applications for single cells, including RNA-seq, gene expression profiling by qPCR and DNA amplification for whole-genome or targeted (exome or PCR-based analysis) through 10x Genomics Chromium platform (similar to Drop Seq). Offers custom genotyping to analyze short tandem repeats, variable number tandem repeats and single nucleotide polymorphisms.

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth

Offers instrumentation and technical capabilities and plays significant consultative role in application of these technologies to basic science projects.Genomic Services include Oligo Synthesis,Gene Expression,Real-Time PCR,PyroSequencing,Next-Generation Sequencing (NGS),DNA Sequencing (Sanger)/Fragment AnalysisSingle Cell Genomics,RNA-DNA QC - Bioanalyzer and Fragment Analyzer QC.Protein Services include Peptide Synthesis,Mass Spectrometry,Protein Analytics - Mass Mapping/Edman Sequencing,Surface Plasmon Resonance (Biacore).

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth

Provides central resource of mass spectrometry based proteomics technologies to identify, characterize and quantify target proteins in various biological and biomedical samples. Provides mass spectrometry expertise for analyzing proteins and peptides for proteomics studies, support for data analysis from proteomics measurements, training in proteomics methods, and experimental design.

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth

Protein sets from fully sequenced genomes. Proteomes portal offers protein sequence sets obtained from translation of completely sequenced genomes. Published genomes from NCBI Genome are brought into UniProt if genome is annotated and set of coding sequences is available. Number of predicted coding sequences falls within statistically significant range of published proteomes from neighbouring species.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users.

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• SciCrunch
• 6 years ago - by Anonymous

Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections.

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• RRID-Legacy
• 6 years ago - submitted by Anita Bandrowski

Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.

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• RRID-Legacy
• 6 years ago - by Anonymous

Web service for querying or retrieving gene annotation data.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software package includes tests for trends and change points detection. Used in analysis of environmental data.

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• RRID-Legacy
• 6 years ago - by Anonymous

Web based application for visualization and presentation of HXMS data. Comprises tools helping in preparation of H/D experiments as well as tools for turning simple tables with data on H/D exchange into different ways of representation.

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• RRID-Legacy
• 6 years ago - by Anonymous

Cell viability counter. Touchscreen fluorescent automated cell counter for primary samples by Nexcelom Bioscience.

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• RRID-Legacy
• 6 years ago - submitted by Daniel Jin

BD LSRFortessa system can be configured with up to 7 lasers, blue, red, violet, UV and yellow-green. The instrument can accommodate the detection of up to 18 colors simultaneously with defined set of optical filters that meet or exceed the majority of today's assay requirements. BD FACSDiva software controls the efficient setup, acquisition, and analysis of flow cytometry data from the BD LSRFortessa workstation. The software is common across BD FACS instrument families, including the BD FACSCanto cell analyzer and BD FACSAria cell sorter systems.

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• RRID-Legacy
• 6 years ago - submitted by Daniel Jin

Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models.

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• SciCrunch
• 6 years ago - submitted by Jonathan Karr

Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.

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• SciCrunch
• 6 years ago - submitted by Jonathan Karr