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A web portal that provides access to data, tools and materials that will aid in craniofacial research. Included is access to genomic and imaging based data sets from a variety of species, including zebrafish, human and mouse.
Proper citation: FaceBase (RRID:SCR_005998) Copy
http://www.ncbi.nlm.nih.gov/pubmedcommons/
A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments.
Proper citation: Pubmed Commons (RRID:SCR_014021) Copy
https://metagenote.niaid.nih.gov/
Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository.
Proper citation: METAGENOTE (RRID:SCR_018494) Copy
Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
Proper citation: LocusZoom.org (RRID:SCR_021374) Copy
https://guolab.shinyapps.io/app-mimivirus-publication/
Web interactive and searchable genome wide comparison tool for browsing human and mimivirus homologous proteins. User friendly Shinny app helps users browse protein sequence homology between humans and mimivirus at genome wide level for querying new homologs and generating new hypotheses.
Proper citation: App for searching human and mimivirus homologous proteins (RRID:SCR_022140) Copy
https://github.com/immunogenomics/harmony
Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data.
Proper citation: Harmony (RRID:SCR_022206) Copy
Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
Proper citation: ImageJ (RRID:SCR_003070) Copy
http://www.type2diabetesgenetics.org/
Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.
Proper citation: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) Copy
https://github.com/gelles-brandeis/CoSMoS_Analysis
Software tools for analyzing co-localization single-molecule spectroscopy image data.
Proper citation: CoSMoS_Analysis (RRID:SCR_016896) Copy
http://www.bx.psu.edu/~giardine/vision/
International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.
Proper citation: ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) Copy
https://panoramaweb.org/project/home/begin.view?
Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents.
Proper citation: PanoramaWeb (RRID:SCR_017136) Copy
Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com.
Proper citation: NIH Figshare Archive (RRID:SCR_017580) Copy
Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers.
Proper citation: AmoebaDB (RRID:SCR_017592) Copy
Free, cloud-based platform for publishing, sharing, and processing standardized neurophysiology data, primarily using the Neurodata Without Borders (NWB) format. Supported by the BRAIN Initiative, it enables researchers to collaborate, reuse datasets, and adhere to FAIR data principles.
Proper citation: Distributed Archives for Neurophysiology Data Integration (RRID:SCR_017571) Copy
https://bioinformaticshome.com/tools/rna-seq/descriptions/LIGER.html
Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets.
Proper citation: LIGER (RRID:SCR_018100) Copy
http://www.ncbi.nlm.nih.gov/proteinclusters
Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP
Proper citation: Protein Clusters (RRID:SCR_003459) Copy
http://senselab.med.yale.edu/brainpharm/
A database to support research on drugs for the treatment of different neurological disorders. It contains agents that act on neuronal receptors and signal transduction pathways in the normal brain and in nervous disorders. It enables searches for drug actions at the level of key molecular constituents, cell compartments and individual cells, with links to models of these actions.
Proper citation: Brain Pharmacological Database (RRID:SCR_003042) Copy
http://www.ncbi.nlm.nih.gov/gene/about-generif
A database and annotation tool that provides a simple mechanism to allow scientists to add to the functional annotation of genes described in Gene. To be processed, a valid Gene ID must exist for the specific gene, or the Gene staff must have assigned an overall Gene ID to the species. The latter case is implemented via records in Gene with the symbol NEWENTRY.
Proper citation: Gene Reference into Function (RRID:SCR_003436) Copy
https://www.pathology.umn.edu/research/liver-tissue-cell-distribution-system
Tissue bank that provides human liver tissue from regional centers for distribution to scientific investigators throughout the United States. These USA regional centers have active liver transplant programs with human subjects approval to provide portions of the resected pathologic liver for which the transplant is performed.
Proper citation: Minnesota Liver Tissue Cell Distribution System (RRID:SCR_004840) Copy
http://udn.nichd.nih.gov/brainatlas_home.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 1, 2019. The first brain atlas for the common marmoset to be made available since a printed atlas by Stephan, Baron and Schwerdtfeger published in 1980. It is a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. For the present atlas, an adult female was perfused through the heart with PBS followed by 10% formalin. The brain was then sent to Neuroscience Associates of Knoxville, TN, who prepared the brain for histological analysis. The brain was cut in the coronal (frontal) plane at 40 microns, every sixth section stained for Nissl granules with thionine and every seventh section stained for myelinated fibers with the Weil technique. The mounted sections were photographed at the NIH (Medical Arts and Photography Branch). The equipment used was a Nikon Multiphot optical bench with Zeiss Luminar 100 mm lens, and scanned with a Better Light 6100 scan back driven by Better Light Viewfinder 5.3 software. The final images were saved as arrays of 6000x8000 pixels in Adobe Photoshop 6.0. A scale in mm provided with these images permitted construction of the final Nissl atlas files with a horizontal and vertical scale. Some additional re-touching (brightness and contrast) was done with Adobe Photoshop Elements 2.0. The schematic (labeled) atlas plates were created from the Nissl images. The nomenclature came almost exclusively from brainmaps.org, where a rhesus monkey brain with structures labeled can be found. The labels for the MRI images were placed by M. R. Zametkin, under supervision from Dr. Newman.
Proper citation: Brain atlas of the common marmoset (RRID:SCR_005135) Copy
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