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A not for profit organization to accelerate research into aging by sharing resources: providing access to cost and time effective, aged murine tissue through a biorepository and database of live ageing colonies, as well as promoting the networking of researchers and dissemination of knowledge through its online collaborative environment; MiCEPACE. ShARM will provide valuable resources for the scientific community while helping to reduce the number of animals used in vital research into aging. The biobank of tissue and networking facility will enable scientists to access shared research material and data. By making use of collective resources, the number of individual animals required in research experiments can be minimized. The project also has the added value of helping to reduce the costs of research by connecting scientists, pooling resource and combining knowledge. ShARM works in partnership with MRC Harwell and the Centre for Intergrated Research into Musculoskeletal Ageing (CIMA).

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• SciCrunch
• 13 years ago - by Anonymous

Software that generates container-based behavioral experiments for reproducible science. It offers a library of experiments, games, and surveys, support for multiple kinds of databases, and robust documentation for the provided tools.

• RRID-Legacy
• 9 years ago - submitted by Vanessa Sochat

Magnetic resonance imaging research facility located at University of Colorado Boulder.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

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• SciCrunch
• 17 years ago - by Anonymous

Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes.

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• RRID-Legacy
• 9 years ago - by Anonymous

Database containing detailed information about small molecules produced by human microbiome. Provides metabolite data including structure, names, descriptions, chemical taxonomy, chemical ontology, physico-chemical data, spectra and contains detailed information about microbes that produce these chemicals, enzymatic reactions responsible for their production, bioactivity of chemicals and anatomical location of these chemicals and microbes. Many data fields in the database are hyperlinked to other databases including FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, and GenBank. Database is FAIR compliant.The data in MiMeDB are released under the Creative Commons (CC) 4.0 License.

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• dkNET
• 2 years ago - submitted by Ko-Wei Lin

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. MMdb is being developed within the context of the MUGEN network of Excellence, a consortium of 21 leading research institutes and universities, and currently holds all mutant mouse models that were developed within the consortium. Its primary aim is to enable information exchange between participating institutions on mouse strain characteristics and availability. More importantly, it aims to create a mouse-centric international forum on modelling of immunological diseases and pave the way to systems biology of the mouse by correlating various genotypic and phenotypic characteristics. The basic categorization of models is based on three major research application categories: * Model of Human Disease * Model of Immune Processes * Transgenic Tool Mutant strains carry detailed information on affected gene(s), mutant alleles and genetic background (DNA origin, targeted, host and backcrossing background). Each gene/transgene index also includes IDs and direct links to Ensembl (EBI��s genome browser), ArrayExpress (providing expression profiles), Eurexpress II (for embryonic expression patterns) and NCBI��s Entrez Gene database. Phenotypic description is standardized and hierarchically structured, based on MGI��s mammalian phenotypic ontology terms, but also includes relevant images and references. Since version 2.1.0 MMdb is also utilizing PATO. Availability (in the form of live mice, cryopreserved embryos or sperm, as well as ES cells) is clearly indicated, along with handling and genotyping details (in the form of documents or hyperlinks) and all relevant contact information (including EMMA and JAX hyperlinks where available).

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• SciCrunch
• 17 years ago - by Anonymous

Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations.

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• RRID-Legacy
• 9 years ago - by Anonymous

Core for image based analysis, laser capture microdissection, and live cell fluorescence imaging. Provides range of consultation and laboratory services performed by core staff. Users training is available.Cell and Tissue imaging on confocal microscopes including Zeiss LSM 710, Leical Sp8 and Leica Stellaris.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns.

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• SciCrunch
• 12 years ago - by Anonymous

Software for analysis and simulation of gene sequences and structural variants. This software works with FASTA, FASTQ, BAM, VAR, META, and NEWICK file formats.

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• SciCrunch
• 9 years ago - submitted by Li Xia

Software customzable pipeline for biomedical information extraction. Deep learning and dictionary- based biomedical Named Entity Recognition pipeline to automatically extract domain specific information from medical text and in particular research articles. Pipeline contains NER models on cell lines, chemicals, disease, gene/protein and species.

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• RRID
• 2 years ago - submitted by Rafsan Ahmed

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies.

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• SciCrunch
• 17 years ago - by Anonymous

Web application for creating, collecting, testing, and sharing metadata. It provides templates for metadata models or structures, and is capable of testing those models quickly using real data.

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• SciCrunch
• 9 years ago - submitted by Jeffrey Grethe

Bioinformatics Core Facility at the John G. Rangos Sr. Research Center provides bioinformatics as well as biostatistics services across a wide range of disease domains. The next-generation sequencing data analysis includes, but is not limited to, whole genome-, whole exome-, bulk and single cell epigenome-, bulk and single cell transcriptome, spatial transcriptome, microbiome, metabolome, proteome and lipidome data analysis. The facility specializes in T-, and B- cell repertoire data analysis, multi-omics initiatives, and multimodal analysis. Shiny dashboard and other web application development is also supported.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways.

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• SciCrunch
• 17 years ago - by Anonymous

Software application for PhoxX® Diode Laser to support Omicron products. It is related to uManager open source microscopy software for control of microscopes.

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• RRID-Legacy
• 9 years ago - by Anonymous

Facility, couples cytometry with microscopy, genomics and proteomics using instrumentation, expertise and services. Utilizes advanced super resolution microscopy techniques to gain understanding of cell sorting, analysis and enable cutting-edge spatial and single cell and multi-omics services.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Data set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available.
Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.

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• SciCrunch
• 17 years ago - by Anonymous

Program based on convolutional neural networks for spike detection from calcium traces. It is written in Python and Keras.

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• RRID-Legacy
• 9 years ago - by Anonymous