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Database which contains the signal transduction proteins for complete and draft bacterial and archaeal genomes. The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes.
Proper citation: MiST - Microbial Signal Transduction database (RRID:SCR_003166) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. Search engine that integrates over 100 curated and publicly contributed data sources and provides integrated views on the genomic, proteomic, transcriptomic, genetic and functional information currently available. Information featured in the database includes gene function, orthologies, gene expression, pathways and protein-protein interactions, mutations and SNPs, disease relationships, related drugs and compounds.
Proper citation: IntegromeDB (RRID:SCR_004620) Copy
Database for identifying orthologous phenotypes (phenologs). Mapping between genotype and phenotype is often non-obvious, complicating prediction of genes underlying specific phenotypes. This problem can be addressed through comparative analyses of phenotypes. We define phenologs based upon overlapping sets of orthologous genes associated with each phenotype. Comparisons of >189,000 human, mouse, yeast, and worm gene-phenotype associations reveal many significant phenologs, including novel non-obvious human disease models. For example, phenologs suggest a yeast model for mammalian angiogenesis defects and an invertebrate model for vertebrate neural tube birth defects. Phenologs thus create a rich framework for comparing mutational phenotypes, identify adaptive reuse of gene systems, and suggest new disease genes. To search for phenologs, go to the basic search page and enter a list of genes in the box provided, using Entrez gene identifiers for mouse/human genes, locus ids for yeast (e.g., YHR200W), or sequence names for worm (e.g., B0205.3). It is expected that this list of genes will all be associated with a particular system, trait, mutational phenotype, or disease. The search will return all identified model organism/human mutational phenotypes that show any overlap with the input set of the genes, ranked according to their hypergeometric probability scores. Clicking on a particular phenolog will result in a list of genes associated with the phenotype, from which potential new candidate genes can identified. Currently known phenotypes in the database are available from the link labeled ''Find phenotypes'', where the associated gene can be submitted as queries, or alternately, can be searched directly from the link provided.
Proper citation: Phenologs (RRID:SCR_005529) Copy
https://www.cincinnatichildrens.org/research/support/clinical-translational-research
Clinical research support center for investigators and industry sponsors.Provides support services, research tools, experienced research personnel, and facilities to conduct or facilitate pediatric and adult clinical research from identification and development of research opportunities to phase I through phase IV clinical research trials.
Proper citation: Cincinnati Children's Hospital Office for Clinical and Translational Research Core Facility (RRID:SCR_022633) Copy
https://sbpdiscovery.org/research/shared-resources/flow-cytometry/
Facility that provides access to high-speed cell sorting, analytical flow cytometry, imaging flow cytometry, and validated immune profiling spectral antibody panels. Core staff provide technical expertise in experiment design, data analysis, hardware and software training, operate the facility cell sorters, and are available to assist with analysis experiments for those who prefer to have their samples run by an expert cytometrist.
Proper citation: Sanford Burnham Prebys Medical Discovery Institute Flow Cytometry Core Facility (RRID:SCR_014854) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/XTRACT
Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.
Proper citation: XTRACT (RRID:SCR_024933) Copy
https://aushsi.shinyapps.io/baseline/
Web tool to detect under- or over-dispersion in a baseline table from baseline table.
Proper citation: baseline (RRID:SCR_025128) Copy
Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles.
Proper citation: Natural Products Atlas (RRID:SCR_025107) Copy
Software platform to annotate cell types.
Proper citation: Cellarium (RRID:SCR_025438) Copy
https://www.unmc.edu/chvr/research/core-facilities/bioassay-core.html
Core provides equipment, personnel, and protocols for routine and advanced cellular and molecular assays for research.
Proper citation: University of Nebraska Medical Center Bioassay Core Facility (RRID:SCR_026270) Copy
https://www.ohsu.edu/custom/library/digital-collections/projectionmap
Data set of thalamo-centric mesoscopic projection maps to the cortex and striatum. The maps are established through two-color, viral (rAAV)-based tracing images and high throughout imaging.
Proper citation: Mouse Thalamic Projectome Dataset (RRID:SCR_015702) Copy
https://nationalmaglab.org/user-facilities/high-b-t-facility
Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory.
Proper citation: National High Magnetic Field Laboratory High B/T Core Facility (RRID:SCR_017360) Copy
https://www.danforthcenter.org/our-work/core-facilities/advanced-bioimaging-laboratory/
Core provides instruments for live cell imaging including Leica SP8-X confocal microscope and other fluorescence microscopes. Facility provides workstation for confocal image processing, ancillary equipment required for transmission electron microscopy. Services are provided as self services after user training by IMF staff or as full services done by core facility staff.
Proper citation: Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility (RRID:SCR_018951) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, it has been replaced by Monarch Initiative. LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal model for their research. LAMDHI is a free, Web-based, resource to help researchers bridge the gap between bench testing and human trials. It provides a free, unbiased resource that enables scientists to quickly find the best animal models for their research studies. LAMHDI includes mouse data from MGI, the Mouse Genome Informatics website; zebrafish data from ZFIN, the Zebrafish Model Organism Database; rat data from RGD, the Rat Genome Database; yeast data from SGD, the Saccharomyces Genome Database; and fly data from FlyBase. LAMHDI.org is operational today, and data is added regularly. Enhancements are planned to let researchers contribute their knowledge of the animal models available through LAMHDI. The LAMHDI goal is to allow researchers to share information about and access to animal models so they can refine research and testing, and reduce or replace the use of animal models where possible. LAMHDI Database Search: LAMHDI brings together scientifically validated information from various sources to create a composite multi-species database of animal models of human disease. To do this, the LAMHDI database is prepared from a variety of sources. The LAMHDI team takes publicly available data from OMIM, NCBI''s Entrez Gene database, Homologene, and WikiPathways, and builds a mathematical graph (think of it as a map or a web) that links these data together. OMIM is used to link human diseases with specific human genes, and Entrez provides universal identifiers for each of those genes. Human genes are linked to their counterpart genes in other species with Homologene, and those genes are linked to other genes tentatively or authoritatively using the data in WikiPathways. This preparatory work gives LAMHDI a web of human diseases linked to specific human genes, orthologous human genes, homologous genes in other species, and both human and non-human genes involved in specific metabolic pathways associated with those diseases. LAMHDI includes model data that partners provide directly from their data structures. For instance, MGI provides information about mouse models, including a disease for each model, as well as some genetic information (the ID of the model, in fact, identifies one or more genes). ZFIN provides genetic information for each zebrafish model, but no diseases, so zebrafish models are integrated by using the genes as the glue. For instance, a zebrafish model built to feature the zebrafish PKD2 gene would plug into the larger disease-gene map at the node representing the zebrafish PKD2 gene, which is connected to the node representing the human PKD2 gene, which in turn is connected to the node representing the human disease known as polycystic kidney disease. (Some of the partner data LAMHDI receives can even extend the base map. MGI provides a disease for every model, and in some cases this allows the creation of a disease-to-gene relationship in the LAMHDI database that might not already be documented in the OMIM dataset.) With curatorial and model information in hand, LAMHDI runs a lengthy automated process that exhaustively searches for every possible path between each model and each disease in the data, up to a set number of hops, producing for each disease-to-model pair a set of links from the disease to the model. The algorithm avoids circular paths and paths that include more than one disease anywhere in the middle of the path. At the end of this phase, LAMHDI has a comprehensive set of paths representing all the disease-to-model relationships in the data, varying in length from one hop to many hops. Each disease-to-model path is essentially a string of nodes in the data, where each node represents a disease, a gene, a linkage between genes (an orthologue, a homologue, or a pathway connection, referred to as a gene cluster or association), or a model. Each node has a human-friendly label, a set of terms and keywords, and - in most cases - a URL linking the node to the data source where it originated. When a researcher submits a search on the LAMHDI website, LAMHDI searches for the user''s search terms in its precomputed list of all known disease-to-model paths. It looks for the terms not only in the disease and model nodes, but also in every node along each path. The complete set of hits may include multiple paths between any given disease-to-model pair of endpoints. Each of these disease-to-model pair sets is ordered by the number of hops it involves, and the one involving the fewest hops is chosen to represent its respective disease-to-model pair in the search results presented to the user. Results are sorted by scores that represent their matches. The number of hops is one barometer of the strength of the evidence linking the model and the disease; fewer hops indicates the relationship is stronger, more hops indicates it may be weaker. This indicator works best for comparing models from a single partner dataset: MGI explicitly identifies a disease for each mouse model, so there can be disease-to-model hits for mice that involve just one hop. Because ZFIN does not explicitly identify a disease for each model, no zebrafish model will involve fewer than four hops to the nearest disease, from the zebrafish model to a zebrafish gene to a gene cluster to a human gene to a human disease.
Proper citation: LAMHDI: The Initiative to Link Animal Models to Human DIsease (RRID:SCR_008643) Copy
Database to advance the availability and use of public health data for science and policy making that includes data from all weekly notifiable disease reports for the United States dating back to 1888. Additional U.S. and international data will be released twice yearly.
Proper citation: Project Tycho (RRID:SCR_010489) Copy
http://dunham.gs.washington.edu/protocols.shtml
A portal for Maitreya Dunham's lab, which works on the genomic analysis of experimental evolution in yeast using microarrays and the chemostat. Research interests of the lab include experimental evolution of genetic networks in yeast, aneuploidy and copy number variation, comparative genomics, technology development and human genetics in yeast.
Proper citation: Maitreya Dunham's Lab (RRID:SCR_000784) Copy
A biorepository and biomaterial supply resource which establishes, verifies, maintains, and distributes cells, cultures and DNA derived from cell cultures to the scientific community around the world. Scientists can browse the sample catalog and request specific cell lines for their research studies. An inventory of the remaining stock of each cell line and DNA preparation is presented in real time. Coriell's significant cell biobank collections include: NIGMS Human Genetic Cell Repository, NINDS Human Genetics DNA and Cell Line Repository, NIA Aging Cell Repository, NHGRI Sample Repository for Human Genetic Research, NEI Age-Related Eye Disease Study (AREDS) Genetic Repository, HD Community BioRepository, American Diabetes Association, GENNID Study, and Autism Research Resource. The repositories are ISO 9000-2001 compliant.
Proper citation: Coriell Cell Repositories (RRID:SCR_003244) Copy
Project to adapt model of open source software distributions to address technical limitations of data sharing and develop all components of data distribution. Builds on top of git-annex and extends it with intuitive command line interface. Enables users to operate on data using familiar concepts, such as files and directories, while transparently managing data access and authorization with underlying hosting providers. Can create DataLad datasets using any data files published on the web.
Proper citation: DataLad (RRID:SCR_003931) Copy
http://tulane.edu/som/regenmed/services/index.cfm
The Stem Cell Research and Regenerative Medicine''s Tissue Culture Core provides cells for research use within the department, as well as for distribution to other facilities. The core obtains hMSCs from bone marrow donor samples and expands these cells for research use. The hMSC''s are also characterized for bone, fat and cartilage differentiation, and are stored on site for use. The Tissue Culture Core also handles the expansion and characterization of mouse and rat MSC''s. The animal cells are cultured in a separate area, and never interact with human derived cells. We also have a supply of hMSC''s marked with GFP+, Mito Red and Mito Blue available.
Proper citation: Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core (RRID:SCR_007342) Copy
Center that facilitates the optimal use of nonhuman primate models in biomedical research by identifying, developing, characterizing and producing reagents for monitoring or modulating immune responses. They distribute non-human primate-specific antibodies for in vitro diagnostics, as well as develop and produce primate recombinant antibodies for in vivo cell depletion or modulating immune responses.
Proper citation: Nonhuman Primate Reagent Resource (RRID:SCR_012986) Copy
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