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https://commonfund.nih.gov/hmp/

NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016.

Proper citation: Human Microbiome Project (RRID:SCR_012956) Copy   

•   Source: SciCrunch Registry

https://github.com/YuanXue1993/SegAN

Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps.

Proper citation: SegAN (RRID:SCR_016215) Copy   

•   Source: SciCrunch Registry

http://nhprtr.org/

Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species.

Proper citation: Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) Copy   

•   Source: SciCrunch Registry

https://cic.ini.usc.edu/

Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks.

Proper citation: Mouse Connectome Project (RRID:SCR_017313) Copy   

•   Source: SciCrunch Registry

https://mibig.secondarymetabolites.org/

MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters.

Proper citation: Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) Copy   

•   Source: SciCrunch Registry

http://www.orbitproject.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 29, 2014. The orbit project was a registry of biomedical resources.

Proper citation: OrbitProject (RRID:SCR_010463) Copy   

•   Source: SciCrunch Registry

http://ods.od.nih.gov/Research/CARDS_Database.aspx

Database of federally funded research projects pertaining to dietary supplements. CARDS contains projects funded by the United States Department of Agriculture (USDA), the Department of Defense (DOD) and the Institutes and Centers (ICs) of the National Institutes of Health (NIH) beginning with fiscal year 1999, the first year that NIH ICs began reporting research related to dietary supplements. Projects funded by other Federal agencies will be added to CARDS as they become available. The Office of Dietary Supplements (ODS) will post notices on its website and listserv when CARDS updates are completed. Codes assigned to each research project allow the CARDS user to identify: * research related to specific dietary supplement ingredients; for example, vitamin E or St. John''''s wort * the type of study; for example, a Phase III study or an animal study * health outcomes or biological effects; for example, osteoporosis or antioxidant function * whether the research is directly related or indirectly related to dietary supplements. For example, a clinical trial comparing bone density in women given a daily calcium supplement versus a placebo would be classified as directly related to dietary supplements. A study examining the activation of steroid hormone receptors by supplemental vitamin D in cell culture would be classified as indirectly related to dietary supplements because the direct physiological or health effects of vitamin D supplementation are not being studied. A search of the CARDS database can be used to sort and tabulate information for a variety of purposes. For example, a researcher may want to know which ICs at the NIH fund research on herbal supplement ingredients. A consumer may want to know if the Federal government is supporting research on a popular dietary supplement ingredient such as vitamin C.

Proper citation: CARDS Database (RRID:SCR_009011) Copy   

•   Source: SciCrunch Registry

http://immport.org/immport-open/public/reference/cytokineRegistry

A registry of cytokines, chemokines, and receptors generated for the purpose of collecting, integrating, and mapping between entity names and synonyms from several resources. These resources include MeSH, the Protein Ontology, EntrezGene, HGNC, MGI, UniProt and others.

Proper citation: Cytokine Registry (RRID:SCR_014368) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.niaid.nih.gov/chemokinedb/

Resource of chemokines and receptors with detailed information including taxonomy, nomenclature, structure, physiological function, tissue information, and phenotype, collected from IUPHAR/BPS, UniGene, and UniProt public databases.

Proper citation: ChemokineDB (RRID:SCR_016593) Copy   

•   Source: SciCrunch Registry

http://software.broadinstitute.org/gsea/msigdb/index.jsp

Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.

Proper citation: Molecular Signatures Database (RRID:SCR_016863) Copy   

•   Source: SciCrunch Registry

https://github.com/VH-Lab/vhlab-microscopyimageanalysis-matlab

Software Matlab app for analysis of high density imaging data like that from Array Tomography.

Proper citation: vhlab-microscopyimageanalysis-matlab (RRID:SCR_024450) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://imagej.net/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://obofoundry.org/ontology/cl.html

Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.

Proper citation: Cell Type Ontology (RRID:SCR_004251) Copy   

•   Source: SciCrunch Registry

http://crcns.org

Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.

Proper citation: CRCNS (RRID:SCR_005608) Copy   

•   Source: SciCrunch Registry

https://www.facebase.org/

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   

•   Source: SciCrunch Registry

http://compbio.soe.ucsc.edu/yeast_introns.html

Database of information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Listed are known spliceosomal introns in the yeast genome and the splice sites actually used are documented. Through the use of microarrays designed to monitor splicing, they are beginning to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition. In version 3.0, expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors is included. These data are displayed on each intron page for browsing and can be downloaded for other types of analysis.

Proper citation: Yeast Intron Database (RRID:SCR_007144) Copy   

•   Source: SciCrunch Registry

http://crcview.hegroup.org/

Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.

Proper citation: CRCView (RRID:SCR_007092) Copy   

•   Source: SciCrunch Registry

http://www.cpc.unc.edu/projects/addhealth

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

Proper citation: Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Copy   

•   Source: SciCrunch Registry