Curator Dashboard

Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls.

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• RRID-Legacy
• 6 years ago - submitted by Lanying Wei

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
• 4 months ago - submitted by Edyta Vieth

An ontology in the domain of interaction network that aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It is aimed to represent general interactions (e.g., molecular interactions) and interaction networks (e.g., Bayesian network). INO was initiated by supporting literature mining related to interactions and interaction networks. INO aligns with BFO. INO is a community-based ontology, and its development follows the OBO Foundry principles.

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• SciCrunch
• 13 years ago - by Anonymous

Framework for creating brain cell type nomenclature, and include examples using published datasets. System allows designation of cell types with or without hierarchical organization. Nomenclature convention initially applied to brain cells and types, is intended to encompass existing naming strategies used in publications across diverse research teams. Allows tracking of many different taxonomies, including those from different organ systems or across diverse areas of bioscience.

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

Reference database of inferred immune receptor genes. Public repository used by immunologists and computational biologists to publish, review, and maintain adaptive immune receptor (antibody and T-cell receptor) genes. Curated database of Ig and TR receptor germline sequences. Provides sets for use in receptor repertoire annotation and analysis, in formats suitable for widely-used analysis tools. Enables reproducible, evidence-based analysis of immune receptor diversity across populations and species, supporting both fundamental immunology research and precision medicine applications.

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• RRID
• 4 months ago - submitted by William Lees

Ontology providing an RDF representation of the MIxS (Minimal Information about any Sequence) family of checklists.

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• SciCrunch
• 13 years ago - by Anonymous

Web application and standalone application to read, visualize and explore content of NWB:N 2 files.Used to share neurophysiological data in Neurodata Without Borders format.

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

Core provides support for data analysis, statistics, and software development. Offers advice on experimental design, statistical modelling, and hypothesis testing and runs training courses to assist research scientists in performing their own analyses.

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• RRID
• 4 months ago - by Anonymous

Ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI).

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• SciCrunch
• 13 years ago - by Anonymous

Provides either dynamic or static control of O2 condition for animal modeling when used in combination with A-Chamber Animal Chamber.

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• SciCrunch
• 5 years ago - submitted by Ray Gould

Core provides expertise in radiochemistry, PET tracer development, preclinical PET and MRI imaging, cancer modelling, and advanced image analysis. Supports translational imaging research, with strengths in molecular imaging, pharmacodynamic biomarker development, and AI-enabled image analytics. Provided instruments include a GE PETtrace 800 cyclotron, radiosynthesis platforms, and small-animal NanoScan PET/MRI system. Services include expertise in both PET and MRI acquisition and analysis, supporting studies in cancer biology, metabolism, and therapy response.

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• RRID
• 4 months ago - by Anonymous

Ontology to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (http://www.orpha.net) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated monthly and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14).

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• SciCrunch
• 13 years ago - by Anonymous

Open source identity and access management solution written in Java. Offers features such as Single-Sign-On, Identity Brokering and Social Login, User Federation, Client Adapters, Admin Console, and Account Management Console by WildFly, a division of Red Hat.

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• dkNET
• 5 years ago - submitted by Maryann Martone

Multidisciplinary public university with eight faculties located in the city of Turku in southwestern Finland. The university also has campuses in Rauma and Pori and research stations in Kevo and Själö.

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• RRID
• 3 months ago - submitted by Edyta Vieth

Ontology of a modified version of Medical Subjects Headings Thesaurus 2014, that is an OWL representation of MeSH so that it can be integrated with other ontologies represented in OWL. It contains all terms that are in MeSH and in the MeSH concept tree, including the pharmacological actions (represented as subclass relations). Concepts in the MeSH concept tree are merged with MeSH term ids. Note that, while this ontology is composed of MeSH terms, it does not correspond directly to UMLS MeSH. In particular, a single term in UMLS MeSH often results in multiple classes in this ontology. For example, in MeSH there is a single term with the label Heart. The internal code (unique identifier) for this term is A07.541. In this ontology there are two entirely different terms, both of which have the label Heart. The codes for these terms are A07.541 and D006321.

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• SciCrunch
• 13 years ago - by Anonymous

Core provides services related to manipulation and delivery of nucleic acids to biological systems. Services include Production and titering of recombinant viral vectors,including Lentiviruses, Adenoviruses, and Adeno associated viruses;Subcloning;Tagging of open reading frames;Development of plasmids and/or RNAs for CRISPR/Cas manipulation;piggyBac transposon delivery systems;Real-time PCR analysis;Recombineering;In vitro transcription; Core maintains stock of plasmids that provide components for building constructs envisioned by investigator and provides consultative services.Provides training opportunities in the technologies described above, either as a for-credit, one semester class or on a project-related, fee-based basis.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Private research university in Rochester, New York. University grants undergraduate and graduate degrees, including doctoral and professional degrees.

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• SciCrunch
• 17 years ago - submitted by Andrea Stagg

Ontology of the meridian value set used in the International Classification of Traditional Medicine.

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• SciCrunch
• 13 years ago - by Anonymous

Web tool used to batch edit Wikidata items, based on simple set of text commands. Can add and remove statements, labels, descriptions, and aliases.Can add statements with optional qualifiers and sources.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Core provides investigators with access to specialized expertise in primary cell isolation, ex vivo organ function assessment, histology, and advanced tissue imaging. The Core supports cardiovascular, pulmonary, and vascular research through customized experimental services, consultation, and rigorous functional and molecular analyses that accelerate mechanistic discovery and translational research.

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• RRID
• 3 months ago - submitted by Hongwei Yao