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https://bioconductor.org/packages/release/bioc/html/MAST.html
Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Proper citation: MAST (RRID:SCR_016340) Copy
http://www.ohsu.edu/xd/health/services/brain/
A clinical care and research center for neurological conditions such as Alzheimer's, dementia and seizure disorders. It provides a dynamic setting for training healthcare professionals and neuroscience researchers to develop and implement evidence-based treatment.
Proper citation: OHSU Brain Institute (RRID:SCR_008932) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017.
A web based central repository for individual and group analysis of Arterial Spin Labeling (ASL) data sets and ASL pulse sequences developed at CMFRI UCSD for MRI researchers. This resource currently hosts more 1300 ASL data sets from 22 projects and consists of mainly two main tools 1) The Cerebral Blood Flow Database and Analysis Pipeline (CBFDAP) is a web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner. 2) Pulse Sequence Distribution System (PSDS) for managing dissamination of ASL pulse sequences developed at the UCSD CFMRI. This resource also includes web and video tutorials for end users.
Proper citation: CBFBIRN (RRID:SCR_009543) Copy
http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing.
Proper citation: MAxEntScan (RRID:SCR_016707) Copy
National Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases.
Proper citation: NIAID (RRID:SCR_016598) Copy
https://niaid.github.io/spice/
Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.
Proper citation: SPICE (RRID:SCR_016603) Copy
https://sleepdata.org/datasets/cfs
Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore.
Proper citation: Cleveland Family Study (RRID:SCR_016585) 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://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
https://www.jax.org/news-and-insights/2004/june/app-mouse-models-for-alzheimers-disease-research
An information resource about several models for mice to develop Alzheimer's-related characteristics as they age.
Proper citation: Mouse Models For Alzheimer's Disease Research (RRID:SCR_000708) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of human nutrition research and research training activities supported by the federal government. Information regarding trends in nutrition research, specific institutions and investigators involved in this research, or areas of agency emphases can be obtained from database searches or from published summary reports. Data for the system is prepared and submitted by participating agencies, and is updated annually. The database contains several thousand projects for each of fiscal years 1985present. Participating agencies include the Department of Health and Human Services, the U.S. Department of Agriculture, the Department of Veteran Affairs, the Agency for International Development, the Department of Defense, Department of Commerce, National Science Foundation, and the National Aeronautics and Space Administration.
Proper citation: Human Nutrition Research Information Management (RRID:SCR_001471) Copy
Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included.
Proper citation: MPIDB (RRID:SCR_001898) Copy
Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries.
Proper citation: EcoGene (RRID:SCR_002437) Copy
http://dejavu.vbi.vt.edu/dejavu/
Deja vu is a database of extremely similar Medline citations. Many, but not all, of which contain instances of duplicate publication and potential plagiarism. Deja vu is a dynamic resource for the community, with manual curation ongoing continuously, and we welcome input and comments. In the scientific research community plagiarism and multiple publications of the same data are considered unacceptable practices and can result in tremendous misunderstanding and waste of time and energy. Our peers and the public have high expectations for the performance and behavior of scientists during the execution and reporting of research. With little chance for discovery and decreasing budgets, yet sustained pressure to publish, or without a clear understanding of acceptable publication practices, the unethical practices of duplicate publication and plagiarism can be enticing to some. Until now, discovery has been through serendipity alone, so these practices have largely gone unchecked.
Proper citation: Deja Vu: a Database of Highly Similar and Duplicate Citations (RRID:SCR_002292) 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
Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.
Proper citation: Mash (RRID:SCR_019135) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
