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http://dkcoin.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO).

Proper citation: dkCOIN (RRID:SCR_004438) Copy   

•   Source: SciCrunch Registry

http://studyforrest.org

An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data.

Proper citation: studyforrest.org (RRID:SCR_003112) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/

Community portal for researchers and content management system for data and databases. Intended to provide common source of data to research community and data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. Central service where RRIDs can be searched and created. Designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas. Adds value to existing scientific resources by increasing their discoverability, accessibility, visibility, utility and interoperability, regardless of their current design or capabilities and without need for extensive redesign of their components or information models. Resources can be searched and discovered at multiple levels of integration, from superficial discovery based on limited description of resource at SciCrunch Registry, to deep content query at SciCrunch Data Federation.

Proper citation: SciCrunch (RRID:SCR_003115) Copy   

•   Source: SciCrunch Registry

http://braininfo.rprc.washington.edu

Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.

Proper citation: BrainInfo (RRID:SCR_003142) Copy   

•   Source: SciCrunch Registry

http://phenome.jax.org/

Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility.

Proper citation: Mouse Phenome Database (MPD) (RRID:SCR_003212) Copy   

•   Source: SciCrunch Registry

http://www.cellimagelibrary.org/

Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.

Proper citation: Cell Image Library (CIL) (RRID:SCR_003510) Copy   

•   Source: SciCrunch Registry

http://www.reactome.org

Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

Proper citation: Reactome (RRID:SCR_003485) Copy   

•   Source: SciCrunch Registry

http://scienceblogs.com/channel/brain-and-behavior/

ScienceBlogs posts about Brain & Behavior.

Proper citation: ScienceBlogs: Brain and Behavior (RRID:SCR_005159) Copy   

•   Source: SciCrunch Registry

http://www.labspaces.net/DNA

Hi. I''m genegeek (aka Catherine Anderson). I realized during my PostDoc that I preferred learning and explaining new results to doing science so I started a non-traditional career of teaching and outreach. I''ll be using this space to explore public perception of genetics and other cool molecular biology stuff. I hope to add to the great discussions re: new science discoveries and general understanding of genetics. I''ve been running an outreach program and enjoy talking to non-experts about their opinions and understanding. I hope my enthusiasm for the topics can come through the screen. My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

Proper citation: Daring Nucleic Adventures - genegeek (RRID:SCR_005215) Copy   

•   Source: SciCrunch Registry

http://scienceblogs.com/channel/medicine/

ScienceBlogs posts about Medicine & Health.

Proper citation: ScienceBlogs: Medicine and Health (RRID:SCR_005176) Copy   

•   Source: SciCrunch Registry

http://www.guardian.co.uk/science

Latest science news, comment, analysis and features from guardian.co.uk, the world''s leading liberal voice.

Proper citation: The Guardian: Science (RRID:SCR_005166) Copy   

•   Source: SciCrunch Registry

http://blogs.nejm.org/now/

A blog produced by the NEJM publishing communications team about new and innovative content in the New England Journal of Medicine (NEJM.org). Our goal is to inform you about what''s new and provide some additional context to complement the content published in NEJM. Each week we post a piece under Insights about one of the latest research papers in NEJM, discussing its clinical significance, where it may lead us in practice and research, and often giving an editor''s thoughts about why it was important to publish. We pose questions to stimulate your thinking and discussion. The idea is to make it easy for you to give us your views on a particular topic and make the conversation accessible to other doctors and physicians-in-training. Posts contain links to the full article, which will be free to all visitors for a limited time. We also feature two posts from the Resident e-Bulletin each week, with an article summary, Clinical Pearls, and Morning Report Questions teaching points that many of you find so useful in your roles as teachers or trainees. The blog gives us a new way to distribute and store this educational information on the social web, again, inviting comment and discussion. You''ll also hear about new products and applications as we bring them out, such as new Interactive Medical Cases, or iPhone applications, like NEJM This Week and the Image Challenge. We link to videos on the NEJMvideo channel on YouTube, share our Twitter feed, and links to NEJM in the News, too. We''d like this to be an open forum, complementary to the core content of NEJM, engaging you in a new experience beyond the journal page in a more interactive community.

Proper citation: Now at NEJM (RRID:SCR_005239) Copy   

•   Source: SciCrunch Registry

http://blogs.scientificamerican.com/observations/

From the editors and reporters of Scientific American, this blog delivers commentary, opinion and analysis on the latest developments in science and technology and their influence on society and policy. From reasoned arguments and cultural critiques to personal and skeptical takes on interesting science news, you''ll find a wide range of scientifically relevant insights here.

Proper citation: Scientific American Observations (RRID:SCR_005195) Copy   

•   Source: SciCrunch Registry

http://ogremk5.wordpress.com/

Science, Technology, Education, Government, and anti-woo. Cassandra had the gift of seeing the future, but the curse of having no one believe her.

Proper citation: Cassandras Tears (RRID:SCR_005229) Copy   

•   Source: SciCrunch Registry

http://www.genomeweb.com/newsletter/daily-scan

A roundup of the most interesting mainstream media articles, blog posts, and peer-reviewed literature relevant to genomic and proteomic scientists. Published daily online and by e-mail bulletin.

Proper citation: Daily Scan (RRID:SCR_004656) Copy   

•   Source: SciCrunch Registry

http://sciblogs.co.nz/

Sciblogs brings together the best science bloggers in the country (New Zealand) on one website, creating a hub for scientific analysis and discussion and facilitating reader interaction. The website is for scientists who want to reach out to a general audience to explain their science and how it relates to society. Some Sciblog contributors spend most of their time in the lab or buried in research. Others are authors or entrepreneurs. All of them know what they are talking about and have an interest in engaging in discussion on the big science-related issues facing society. Over time more bloggers will be added to the Sciblogs roster. If you would like to inquire about hosting a blog on Sciblogs contact us. You can easily keep an eye on new Sciblogs posts by subscribing via RSS or email or by following our Twitter feed. Alternatively, there is a Facebook page as well as a Facebook group feel free to join in! Categories: * Science * Agriculture * Technology * Health and Medicine * Environment and Ecology * Science and Society

Proper citation: Sciblogs (RRID:SCR_005219) Copy   

•   Source: SciCrunch Registry

http://neuroinformatics.kiv.zcu.cz/articles/read/eegerp-portal-eegbase-_2014-12-19

EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two possibilities: * Mapping from the persistence layer (relational database) * Mapping from the application layer (object oriented code) The mapping from the application layer to an ontology includes the precedent object relational mapping provided by Hibernate framework.

Proper citation: EEGbase (RRID:SCR_001452) Copy   

•   Source: SciCrunch Registry

http://iscc.coh.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Consortium to advance the understanding of intestinal epithelial stem cell biology during development, homeostasis, regeneration and disease. Its immediate goals are to isolate, characterize, culture and validate populations of intestinal stem cells; answer major questions in stem cell biology of the intestinal epithelium; and accelerate research by making information and resources available to the research community. Resources include data sets, protocols, and a resource catalog. Long-term goals include: 1) laying the ground work for therapeutic manipulation of the intestinal epithelium 2) contributing to the greater understanding of stem cell biology through knowledge of the intestine as a model stem cell-driven system. Research Projects are housed at 8 institutions across the nation: Oregon Health & Science University, Stanford University, Stowers Institute for Medical Research, University of California, Los Angeles School of Medicine (UCLA) (partnered with the VA Greater Los Angeles), University of North Carolina, Chapel Hill (UNC), University of Oklahoma, University of Pennsylvania, and University of Pittsburgh.

Proper citation: Intestinal Stem Cell Consortium (RRID:SCR_001555) Copy   

•   Source: SciCrunch Registry

http://www.findmice.org/index.jsp

Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known.

Proper citation: International Mouse Strain Resource (RRID:SCR_001526) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-1/search?q=*&l=

Integrated Animals is a virtual database currently indexing available animal strains and mutants from: AGSC (Ambystoma), BCBC (mice), BDSC (flies), CWRU Cystic Fibrosis Mouse Models (mice), DGGR (flies), FlyBase (flies), IMSR (mice), MGI (mice), MMRRC (mice), NSRRC (pig), NXR (Xenopus), RGD (rats), Sperm Stem Cell Libraries for Biological Research (rats), Tetrahymena Stock Center (Tetrahymena), WormBase (worms), XGSC (Xiphophorus), ZFIN (zebrafish), and ZIRC (zebrafish).

Proper citation: Integrated Animals (RRID:SCR_001421) Copy   

•   Source: SciCrunch Registry