Curator Dashboard

Software R package for detection, characterization and visualization of localized hypermutated regions, often referred to as kataegis. Aims to identify putative kataegis loci from common data formats housing genomic variants.

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• RRID
• 3 years ago - submitted by Daan Hazelaar

Open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. Core unit of Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form network of biological interactions and are grouped into pathways including classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. External domain expert provides expertise, curator formalizes it into database structure, and external domain expert reviews representation. System of evidence tracking ensures that all assertions are backed up by primary literature. Website is designed to give the user graphical map of known biological processes and pathways that is also an interface. Database and website enable to find, organize, and utilize biological information to support data visualization, integration and analysis.

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• RRID
• 3 years ago - submitted by Edyta Vieth

Software tool for prediction of RNA–RNA, RNA–DNA, and DNA–DNA interactions. Both RIsearch1 and RIsearch2 enable quick localisation of potential near complementary interactions between given query and target sequences. RIsearch1 performs computation with whole sequences. RIsearch2 focuses on perfect complementary seed regions and extends them on both ends. User defined seed and extension constraints makes RIsearch2 applicable to all kinds of interaction predictions (e.g., siRNA and Cas9–gRNA off-target predictions).

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• 3 years ago - by Anonymous

Software Python framework for interactive multiobjective optimization methods.

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• RRID
• 3 years ago - by Anonymous

Commercial organization provides software tools for video and data analysis used in healthare and education.Provides performance analysis solutions for team sports and individual athletes at every level.

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• RRID
• 3 years ago - by Anonymous

Ontology for describing key metadata elements of spatial reference atlases. Ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures. Identifies and defines relationships between four common atlases and characterizes their properties and organization. This model can serve as suggestion for minimum requiremens for atlases and will accelerate neuroscience data integration.

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• dkNET
• 3 years ago - submitted by Maryann Martone

One of the metadata models of openMINDS metadata framework. Composed of modular metadata schemas for spatial anchoring of neuroscience data structures, including brain atlas definitions.

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• dkNET
• 3 years ago - submitted by Maryann Martone

Core uses technologies to create and produce variety of high quality viral vectors.Provides investigators with the most suitable and efficient gene transfer vectors.Vectors produced include AD, AAV, and Lenti/retro. VVC staff can assist investigators with selection of gene transfer vector, its design and potential applications. Services include AdV vector creation and production, AAV vector production, Lentiviral vector production,AAV neutralizing antibody screening and titration.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Core offers services, training and provides access to optical microscopes and imaging.Offers collaboration for complex projects.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Provides access to cutting edge technologies in mass spectrometry, methodology, and instrumentation. Provided expertise include the fields of Chemical Biology,Pharmaceutical Biology,Cancer Biology,Microbial Biology,Infectious Disease,Metabolic Disease,Chronic Pain Research,Quantitative Biosciences, Drug Discovery and Drug Development,Translational and Regulatory Sciences,Nanotechnology,.Bioinformatics and Technology Development

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Provides access to conventional transmission electron microscope and associated sample processing services.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Provides access to ultra high field NMR instrumentation including probes for solution and solid state NMR, and resonators and high power gradients for diffusion and magnetic resonance microimaging. Supports research programs including structure determination of small molecules, proteins, carbohydrates, nucleic acids, and macromolecular complexes at atomic resolution, quantitative analysis of complex mixtures, metabolomics applications, diffusion analysis, characterization of materials, and MR microimaging.Expert training and assistance is available in experiment design and/or pulse sequence customization, sample preparation, data acquisition, processing, analysis, and reporting of results e.g. manuscript and/or grant preparation, in addition to comprehensive support.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Core of COBRE Center at department of Pathology located on sixth floor of Aldrich building at Rhode Island Hospital.Provides services, instrumentation, training and support. Equipment includes ArcturusXT laser capture microdissector, Stratagene MX3005p realtime PCR instrument, BioRad iCycler, Agilent Bioanalyzer, Olympus fluorescence-capable microscope with image analysis software, Ventana Discovery immunohistochemistry processor, microtome, cryostat, Beecher tissue arrayer and Aperio ScanScope.Tissue bank has 40 cu ft of ultra-low freezer space and provides human tumor tissue samples to all interested investigators who have received IRB approval for academic testing and research.Services include Tissue Sample Processing,Histology,Immunohistochemistry,Digital slide scanning by Aperio ScanScope,Tissue Microarrays,DNA/RNA extraction, Microdissection,Macrodissection verification by pathologist,Digital image analysis,Visium Spatial Gene Expression Assay,RNAscope Assay,Enzyme Linked Immunosorbent Assays (ELISAs),Technical assistance,Pathologist consultation,Technical assistance, Equipment use and training.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin.

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• RRID
• 3 years ago - by Anonymous

Software package for genome wide annotation for mouse, primarily based on mapping using Entrez Gene identifiers.

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• RRID
• 3 years ago - by Anonymous

Software tool to implement interface for querying SQLite-based annotation data packages. Used for manipulation of SQLite-based annotations in Bioconductor.

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• RRID
• 3 years ago - by Anonymous

Software R package for adaptive shrinkage. Implements Empirical Bayes approach for large scale hypothesis testing and false discovery rate estimation.

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• RRID
• 3 years ago - by Anonymous

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

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• RRID
• 3 years ago - by Anonymous

Software package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events. Mapping alternative splicing events to proteins.

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• RRID
• 3 years ago - by Anonymous