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http://livercenter.ucsf.edu

Center whose goal is to integrate bench science with clinical investigation, in support of its vision to understand and cure human liver diseases.

Proper citation: UCSF Liver Center (RRID:SCR_015595) Copy   

•   Source: SciCrunch Registry

https://www.4dnucleome.org

Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes.

Proper citation: 4D Nucleome (RRID:SCR_016925) Copy   

•   Source: SciCrunch Registry

http://livercenter.ucsf.edu/cell-biology-core

Core whose purpose is providing primary and immortalized liver cells for experimental use as well as other material such as human liver cells, primary hepatocytes, and immortalized cell lines.

Proper citation: UCSF Liver Center Cell Biology Core (RRID:SCR_015600) Copy   

•   Source: SciCrunch Registry

http://www.uchicagoddrcc.org/research-cores/integrated-translational-research-core

Core that serves as both a central repository for all the samples and data shared by the other cores and a catalyst for interdisciplinary research.

Proper citation: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core (RRID:SCR_015606) Copy   

•   Source: SciCrunch Registry

http://secrepedia.org

Encyclopedia of white and brown adipocyte secretome in mouse models and humans as key prerequisite to elucidating role of these mediators in normal physiology and disease.

Proper citation: Secrepedia (RRID:SCR_022590) Copy   

•   Source: SciCrunch Registry

http://www.childrennetwork.org/

Database of clinical information and serum and tissue samples from children across the United States and Canada with Biliary Atresia, Idiopathic Neonatal Hepatitis, Cystic Fibrosis Liver Disease, Alagille Syndrome, Alpha-1 Antitrypsin Deficiency, Bile Acid Synthesis Defects, Mitochondrial Hepatopathies, and Progressive Familial Intrahepatic Cholestasis in order to facilitate research and to perform clinical, epidemiological, and therapeutic trials in these important pediatric liver diseases. Three NIDDK-funded consortia, Biliary Atresia Research Consortium (BARC), Cholestatic Liver Disease Consortium (CLiC), and the Cystic Fibrosis Liver Disease (CFLD) Network were consolidated to form ChiLDREN. Most of the ChiLDREN studies are natural history studies aimed at acquiring information and data that will provide a better understanding of these rare conditions. Participants will be asked to allow study personnel to obtain information from medical records and an interview, and to collect blood, urine, and tissue samples when clinically indicated, in order to understand the causes of these diseases and to improve the diagnosis and treatment of children with these diseases. All of the information obtained in these studies is confidential and no names or identifying information are used in the study.

Proper citation: Childhood Liver Disease Research and Education Network (RRID:SCR_001497) Copy   

•   Source: SciCrunch Registry

https://kimosys.org

Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community.

Proper citation: Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) Copy   

•   Source: SciCrunch Registry

https://icsd.products.fiz-karlsruhe.de/

Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research.

Proper citation: Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) Copy   

•   Source: SciCrunch Registry

https://nih.figshare.com/

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   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/metagenomics/

Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.

Proper citation: MGnify (RRID:SCR_016429) Copy   

•   Source: SciCrunch Registry

http://sleepdisordergenetics.org

Software platform for accelerating genetic discoveries for sleep disturbance and circadian traits.

Proper citation: Sleep Disorder Knowledge Portal (RRID:SCR_016611) Copy   

•   Source: SciCrunch Registry

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

Software interactive tool for visualizing and analyzing network data in the spatial context of the chromosome. Used to discover the role of gene organization in functional regulatory networks. Plugin enables users of Cytoscape to overlay networks onto a circular chromosomal map.

Proper citation: NetCirChro (RRID:SCR_016616) Copy   

•   Source: SciCrunch Registry

https://joinsolver.niaid.nih.gov

Software tool to analyze human immunoglobulin V(D)J recombination and performing Ig nucleotide and amino acid alignment, as well as extensive mutation and Complementarity Determining Region 3 (CDR3H) analysis.

Proper citation: JOINSOLVER (RRID:SCR_016619) Copy   

•   Source: SciCrunch Registry

https://www.niaid.nih.gov/research/simmune-project

Software package to define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator.

Proper citation: Simmune (RRID:SCR_016618) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://motrpac-data.org/

National research consortium designed to discover and perform preliminary characterization of range of molecular transducers that underlie effects of physical activity in humans. Used to study molecular changes that occur during and after exercise and to advance understanding of how physical activity improves and preserves health. Six year program into mechanisms of how physical activity improves health and prevents disease led by NIH Office of Strategic Coordination, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute on Aging, and National Institute of Biomedical Imaging and Bioengineering.

Proper citation: MoTrPAC Data Hub (RRID:SCR_017611) Copy   

•   Source: SciCrunch Registry

http://antibodyregistry.org/

Public registry of antibodies with unique identifiers for commercial and non-commercial antibody reagents to give researchers a way to universally identify antibodies used in publications. The registry contains antibody product information organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones). Data is provided in many formats so that authors of biological papers, text mining tools and funding agencies can quickly and accurately identify the antibody reagents they and their colleagues used. The Antibody Registry allows any user to submit a new antibody or set of antibodies to the registry via a web form, or via a spreadsheet upload.

Proper citation: Antibody Registry (RRID:SCR_006397) Copy   

•   Source: SciCrunch Registry

http://www.lipidmaps.org/

Multi-institutional supported website and database that provides access to large number of globally used lipidomics resources. Internationally led the field of lipid curation, classification, and nomenclature since 2003. Produces new open-access databases, informatics tools and lipidomics-focused training activities will be generated and made publicly available for researchers studying lipids in health and disease.

Proper citation: LIPID Metabolites And Pathways Strategy (RRID:SCR_006579) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/ena/

Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.

Proper citation: European Nucleotide Archive (ENA) (RRID:SCR_006515) Copy   

•   Source: SciCrunch Registry

http://nkdep.nih.gov/

Educational resource to increase awareness of kidney disease and its risk factors, improve early detection of chronic kidney disease (CKD), reduce the burden of CKD, facilitate identification of patients at greatest risk for progression to kidney failure, stress the importance of testing those at risk, promote evidence-based interventions to slow progression of CKD, and support the coordination of Federal responses to CKD. Target audiences include individuals at risk, particularly those with diabetes, high blood pressure, and a family history of kidney disease, and primary care providers.

Proper citation: National Kidney Disease Education Program (RRID:SCR_006527) Copy   

•   Source: SciCrunch Registry