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https://dpcpsi.nih.gov/onr/nrcc

Coordinates nutritional sciences-related research and research training across the National Institutes of Health (NIH) and among Federal Agencies by providing mechanisms to communicate research, research training, policy, and education initiatives. The DNRC facilitates the exchange of information, coordinates workshops and seminars on critical issues, encourages national and international research collaborations, and serves as the NIH primary point of contact for the Department of Health and Human Services (DHHS) and other agencies, departments, and organizations in matters pertaining to nutritional sciences and physical activity. Through its dedicated efforts to promote scientific policy reviews, innovative research, interagency collaboration, and technical advancements, the DNRC strives to define the increasing roles of nutritional sciences and physical activity in health promotion and disease prevention and treatment.

Proper citation: NIH Division of Nutrition Research Coordination (RRID:SCR_001469) Copy   

•   Source: SciCrunch Registry

http://nashua.case.edu/PathwaysWeb/Web/

An integrated software system for storing, managing, analyzing, and querying biological pathways at different levels of genetic, molecular, biochemical and organismal detail. The system contains a pathways database and associated tools to store, compare, query, and visualize metabolic pathways. The aim is to develop an integrated database and the associated tools to support computational analysis and visualization of biochemical pathways. At the computational level, PathCase allows users to visualize pathways in multiple abstraction levels, and to pose predetermined and ad hoc queries using a graphical user interface. Pathways are represented as graphs, and implemented as a relational database. The available functional annotations include the identity of the substrate(s), product(s), cofactors, activators, inhibitors, enzymes or other processing molecules, GO-categories of enzymes (as well as GO hierarchy visualizations two-way-linked to PathCase enzymes), EC number information and the associated links, and synonyms and encoding genes of gene products.

Proper citation: PathCase Pathways Database System (RRID:SCR_001835) Copy   

•   Source: SciCrunch Registry

http://videocast.nih.gov/

VideoCasting of special NIH events, seminars, conferences, meetings and lectures available to viewers on the NIH network and the Internet from the VideoCast web site. VideoCasting is the method of electronically streaming digitally encoded video and audio data from a server to a client. VideoCast is often referred to as streaming video. Streaming files are not downloaded, but rather are broadcast in a manner similar to television broadcasts. The videos are processed by a compression program into a streaming format and delivered in a staggered fashion to minimize impact upon the network and maximize the experience of the content for the viewer. When users request a streaming file they will receive an initial burst of data after a short delay (file latency). While content is being viewed, the streaming server machine and software continues to stream data in such a manner that the viewer experiences no break in the content. CIT can broadcast your seminar, conference or meeting live to a world-wide audience over the Internet as a real-time streaming video. The event can be recorded and made available for viewers to watch at their convenience as an on-demand video or a downloadable podcast. CIT can also broadcast NIH-only or HHS-only content.

Proper citation: NIH VideoCasting (RRID:SCR_001885) Copy   

•   Source: SciCrunch Registry

http://www.jobs.nih.gov/

A listing of all current openings across the NIH. You may search for NIH Jobs, browse job descriptions, view all descriptions or use the quick links.

Proper citation: Jobs(at)NIH (RRID:SCR_006471) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/searches/AMA_form.shtml

Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display.

Proper citation: Adult Mouse Anatomy Ontology (RRID:SCR_006568) Copy   

•   Source: SciCrunch Registry

https://cgc.umn.edu

Center that acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available.

Proper citation: Caenorhabditis Genetics Center (RRID:SCR_007341) Copy   

•   Source: SciCrunch Registry

https://datajoint.org/

MATLAB and Python 3 high-level programming interface for MySQL databases to support data processing chains in science labs. Specifically designed to provide robust and intuitive data model for scientific data processing chains.Used for scientific data pipelines and workflow management.

Proper citation: DataJoint (RRID:SCR_014543) Copy   

•   Source: SciCrunch Registry

http://i2b2.cchmc.org/

A data warehouse that integrates information on patients from multiple sources and consists of patient information from all the visits to Cincinnati Children''''s between 2003 and 2007. This information includes demographics (age, gender, race), diagnoses (ICD-9), procedures, medications and lab results. They have included extracts from Epic, DocSite, and the new Cerner laboratory system and will eventually load public data sources, data from the different divisions or research cores (such as images or genetic data), as well as the research databases from individual groups or investigators. This information is aggregated, cleaned and de-identified. Once this process is complete, it is presented to the user, who will then be able to query the data. The warehouse is best suited for tasks like cohort identification, hypothesis generation and retrospective data analysis. Automated software tools will facilitate some of these functions, while others will require more of a manual process. The initial software tools will be focused around cohort identification. They have developed a set of web-based tools that allow the user to query the warehouse after logging in. The only people able to see your data are those to whom you grant authorization. If the information can be provided to the general research community, they will add it to the warehouse. If it cannot, they will mark it so that only you (or others in your group with proper approval) can access it.

Proper citation: i2b2 Research Data Warehouse (RRID:SCR_013276) Copy   

•   Source: SciCrunch Registry

https://www.immport.org/home

Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.

Proper citation: The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) Copy   

•   Source: SciCrunch Registry

http://www.metabolomicsworkbench.org

Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops.

Proper citation: Metabolomics Workbench (RRID:SCR_013794) Copy   

•   Source: SciCrunch Registry

http://www.geworkbench.org

geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include: * loading data from local or remote data sources. * visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways. * providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory networks reconstruction, BLAST searches, pattern/motif discovery, etc. * validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks (one of the 7 National Centers for Biomedial Computing funded through the NIH Roadmap). Additionally, geWorkbench is supported by caBIG, NCI''s cancer Biomedical Informatics Grid initiative.

Proper citation: genomics Workbench (RRID:SCR_013599) Copy   

•   Source: SciCrunch Registry

http://chavi-id.org

A consortium whose goal is to further HIV research and accelerate the development of a preventative HIV vaccine. Its main research target is to define immunogens and immunization regimens that induce sustained HIV cross-protective B cell and CD4+ T cell responses.

Proper citation: CHAVI-ID (RRID:SCR_014047) Copy   

•   Source: SciCrunch Registry

http://www.webarraydb.org/webarray/index.html

An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.

Proper citation: WebArrayDB (RRID:SCR_005577) Copy   

•   Source: SciCrunch Registry

http://www.chori.org/

CHORI is the internationally renowned biomedical research institute of Children''s Hospital and Research Center at Oakland. With world-class scientists and research centers known both nationally and internationally in multiple fields, CHORI is 5th in the nation for National Institutes of Health pediatric research funding. Bridging basic science and clinical research in the treatment and prevention of human disease, CHORI is a leader in translational research, providing cures for blood diseases, developing new vaccines for infectious diseases, and discovering new treatment protocols for previously fatal or debilitating conditions. Striving to provide the highest standard of excellence and innovation, CHORI brings together a multidisciplinary collaborative of distinguished investigators in six different Centers of Research: The Center for Cancer Research, The Center for Genetics, The Center for Immunobiology & Vaccine Development, The Center for Nutrition & Metabolism, The Center for Prevention of Obesity, Cardiovascular Disease & Diabetes, and The Center for Sickle Cell Disease & Thalassemia. Within these major areas of focus, CHORI pushes the frontiers of science and of excellence beyond their borders. Among the leading biotech enterprises in the Bay Area, CHORI produced 25 patents in the last 5 years alone. In addition to providing world-class research, CHORI is also a teaching institute, offering unique educational opportunities to high school, college, doctoral and post-doctoral students.

Proper citation: Childrens Hospital Oakland Research Institute (RRID:SCR_005582) Copy   

•   Source: SciCrunch Registry

http://cs.nyu.edu/~bingsun/

NYU Bioinformatics group applies algorithmic, statistical, and mathematical techniques to solve problems of interest to biology, biotechnology and biomedicine. The group focuses on bioinformatics, computational biology and systems biology with many active projects in areas ranging from single molecules to entire populations: Analysis of Single-Molecule/Single-Cell Data, SPM-based Transcriptomic Profiling, Whole-Genome Haplotype Sequencing using SMASH (Single Molecule Approaches to Haplotype Sequencing), SUTTA (Scoring and Unfolding Trimmed Tree Assembler) assembly algorithm, Analysis of Spatio-Temporal Data, Model Checking and Model Building for Systems Biology, GOALIE-based Phenomenological Models and their Verification, Causality Analysis, Causal Models and their Verification, Analysis of EHR (Electronic Health Record Data) and Disease Models (e.g., Chronic Fatigue Syndrome, Congestive Heart Failure, Deep Vein Thrombosis, etc.), Models of Cancer, Applications to Pancreatic Cancer, Polymorphisms and Biomarkers, Strategies for Group Testing, Epidemiological and Bio-Warfare Models, Planning with Large Agent Networks against Catastrophes (PLAN C), Population Genomics, and Genome Wide Association Studies (GWAS). The group has received its funding from Air Force, Army, CCPR, DARPA, NIH, NIST, NSF, NYSTAR, etc. and various other governmental and commercial entities. Currently, the group is part of an NSF funded Expedition in Computing project (CMACS: Center for Modeling and Analysis of Complex Systems at CMU) and collaborates widely, both nationally and internationally. The group is highly multi-disciplinary, attracting researchers and students from mathematics, statistics, computer science, and biology who team up with physicians, physicists, and chemists as well as professionals in their own disciplines. This group is led by Prof. Bud Mishra, a professor of computer science and mathematics at NYU''s Courant Institute of Mathematical Sciences.

Proper citation: NYU Bioinformatics Group (RRID:SCR_005697) Copy   

•   Source: SciCrunch Registry

http://www.mouseimaging.ca/

A unique resource and comprehensive imaging facility combining the latest state-of-the-art digital medical imaging technologies for the characterization of mouse functional genomics. The goals of the Mouse Imaging Centre are: * To provide a variety of medical imaging technologies adapted to studying genetically modified mice. These technologies include magnetic resonance (MR) imaging, micro computed tomography (micro-CT), ultrasound biomicroscopy (UBM), and optical projection tomography (OPT). * To screen large numbers of mice for models of human diseases. * To image an individual mouse over time to observe development, disease progression and responses to experimental treatment. * To develop an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. * To work by collaboration with researchers throughout the world. When we look for human diseases in the human population, we make extensive use of medical imaging. Therefore, it makes sense to have available the same imaging capabilities as we investigate mice for models of human disease. The Mouse Imaging Centre (MICe) has developed high field magnetic resonance imaging microscopy, ultrasound biomicroscopy, micro computed tomography, and optical techniques. With these imaging tools, MICe is screening randomly mutagenized mice to look for phenotypes that represent human diseases and is taking established human disease models in mice and using imaging to follow the progression of disease and response to treatment over time. It is clear that imaging has a major contribution to make to phenotyping genetic variants and to characterizing mouse models. MICe is staffed by an exciting new team of about 30 investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. The Mouse Imaging Centre (MICe) is not a fee-for-service facility but works through collaborations. Services include: * Projects involving MicroCT are available as a fee for service. * We will eventually move to the same model above with MRI. * Ultrasound Biomicroscopy is used for cardiac, embryo and cancer studies and is available as fee for service at $100 per study or in some cases on a collaborative basis. * Optical Projection Tomography has only limited availability on a collaborative basis. Mouse Atlas As our images are inherently three-dimensional, we will be able to make quantitative measures of size and volume. With this in mind, we are developing a mouse atlas showing the normal deviation of organ sizes. This atlas is an important resource for biologists as it has the potential to eliminate the need to sacrifice as many controls when making comparisons with mutants. Mouse Atlas Examples: * Variational Mouse Brain Atlas * Cerebral Vascular Atlas of the CBA Mouse * Neuroanatomy Atlas of the C57Bl/6j Mouse * Vascular Atlas of the Developing Mouse Embryo * Micro-CT E15.5 Mouse Embryo Atlas

Proper citation: MICe - Mouse Imaging Centre (RRID:SCR_006145) Copy   

•   Source: SciCrunch Registry

https://www.researchmatch.org/

Free and secure registry to bring together two groups of people who are looking for one another: (1) people who are trying to find research studies, and (2) researchers who are looking for people to participate in their studies. It has been developed by major academic institutions across the country who want to involve you in the mission of helping today''''s studies make a real difference for everyone''''s health in the future. Anyone can join ResearchMatch. Many studies are looking for healthy people of all ages, while some are looking for people with specific health conditions. ResearchMatch can help ''''match'''' you with any type of research study, ranging from surveys to clinical trials, always giving you the choice to decide what studies may interest you.

Proper citation: ResearchMatch (RRID:SCR_006387) 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://amoebadb.org/amoeba/

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   

•   Source: SciCrunch Registry

https://dandiarchive.org

DANDI is a platform for publishing, sharing, and processing neurophysiology data funded by the BRAIN Initiative. The archive is not just an endpoint to dump data, it is intended as a living repository that enables collaboration within and across labs, and for others, the entry point for research.

Proper citation: Distributed Archives for Neurophysiology Data Integration (RRID:SCR_017571) Copy   

•   Source: SciCrunch Registry