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http://psb.kobic.re.kr/STAP/refinement/

STAP refinement of NMR Database is based the Statistical Torsion Angles Potentials to refine the NMR structure. It stored original solution NMR structures from the Protein Data Banks and our refined structures. Currently we carried out 2,405 refined NMR structure (until Sept 20, 2011). According to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. STAP of NMR Refinement Database is a public database of 2405 refined NMR solution structures from the Protein Data Bank (PDB). A simulated annealing protocol was employed to obtain refined structures with target potentials, including the newly developed STAP. The refined database was extensively analyzed using various quality indicators from several assessment programs to determine the nuclear Overhauser effect (NOE) completeness, Ramachandran appearance, (1)-(2) rotamer normality, various parameters for protein stability and other indicators. Most quality indicators are improved in our protocol mainly due to the inclusion of the newly developed knowledge-based potentials. This database can be used by the NMR structure community for further development of research and validation tools, structure-related studies and modelling in many fields of research.

Proper citation: Statistical Torsional Angles Potentials of NMR Refinement Database (RRID:SCR_008917) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.com/?page_id=23

Collection of neuroanatomically labeled MRI brain scans, created by neuroanatomical experts. Regions of interest include the sub-cortical structures (thalamus, caudate, putamen, hippocampus, etc), along with ventricles, brain stem, cerebellum, and gray and white matter and sub-divided cortex into parcellation units that are defined by gyral and sulcal landmarks.

Proper citation: Manually Labeled MRI Brain Scan Database (RRID:SCR_009604) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-3/search?q=*

A virtual database currently indexing available cell lines from: Coriell Cell Repositories, International Mouse Strain Resource (IMSR), ATCC, NIH Human Pluripotent Stem Cell Registry, NIGMS Human Genetic Cell Repository, and Developmental Therapeutics Program.

Proper citation: Integrated Cell Lines (RRID:SCR_008994) Copy   

•   Source: SciCrunch Registry

https://www.ohsu.edu/transgenic-mouse-models-core

Core assists investigators with developing genetically engineered rodent models of human diseases for studying mutant genes and investigating molecular mechanisms underlying pathological processes.

Proper citation: OHSU Animal Model Support Core Facility (RRID:SCR_009994) Copy   

•   Source: SciCrunch Registry

http://wren.bcf.ku.edu/

The Autism Genetic Database currently contains the full list of autism susceptibility genes as well as all Copy Number Variations (CNVs) found to have a relationship to autism. Additionally, all noncoding RNA molecules (snoRNA, miRNA, and piRNA) and chemically induced fragile sites are stored as well. This information is currently accessible via an in-house human genome browser focusing specifically on the chromosomal features associated with autism, and in a tabular format broken down by chromosome. Genome Browser:A genome browser that displays the genes, CNVs, ncRNAs and fragile sites in an easily accessible graphical visualization tool Tabular Data Display:A tabular data display that allows the user to observe the chromosomal spatial relationship between the genes, CNVs, ncRNAs and fragile sites. This also provides links to Entrez and pubmed for each gene, as well as miRBase for miRNAs, snoRNA-LBME-db for snoRNAs, and piRNABank for piRNAs.

Proper citation: Autism Genetic Database (RRID:SCR_010545) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/genomic_control/genomic_control.htm

Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software)

Proper citation: GC/GCF (RRID:SCR_009075) Copy   

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http://www.intlbiobank.com/

Not yet vetted by NIF curator

Proper citation: International Biobank, Inc. (RRID:SCR_010549) Copy   

•   Source: SciCrunch Registry

http://www.demogr.mpg.de/databases/ktdb/

A database that includes data on death counts and population counts classified by sex, age, year of birth, and calendar year for more than 30 countries. This database was established for estimating the death rates at the highest ages (above age 80). The core set of data in the database was assembled, tested for quality, and converted into cohort mortality histories by V��in�� Kannisto, the former United Nations advisor on demographic and social statistics. Comparable materials on England and Wales, was made available by A. Roger Thatcher, the former Director of the Office of Population Censuses and Surveys and Registrar-General of England and Wales (Kannisto, 1994). The Kannisto-Thatcher database was computerized under the supervision of James W. Vaupel at the Aging Research Unit of the Centre for Health and Social Policy at Odense University Medical School in 1993. Currently, the database is maintained by the Max Planck Institute for Demographic Research, Germany.

Proper citation: Kannisto-Thatcher Database on Old Age Mortality (RRID:SCR_008936) Copy   

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http://www.brc.riken.go.jp/lab/cell/english/

Not yet vetted by NIF curator

Proper citation: Riken BRC Cell Bank (RRID:SCR_010553) Copy   

•   Source: SciCrunch Registry

https://www.twbiobank.org.tw/new_web_en/index.php

Taiwan Biobank intends to conduct large-scale cohort studies and case-control studies on local diseases. The cohort study will call for 200,000 volunteers, while the case-control study will invite 100,000 patients with the 10 to 15 most common diseases. These studies will enable Taiwan Biobank to identify the disease-causing factors and mechanisms of common diseases to facilitate the development of better treatment and prevention, reduce the cost of medical treatment and make it possible to achieve the goal of improving the island nation’s health.

Proper citation: Taiwan Biobank (RRID:SCR_010557) Copy   

•   Source: SciCrunch Registry

http://virginiahughes.com/

Virginia Hughes'' Research Blog

Proper citation: http://virginiahughes.com/ (RRID:SCR_010558) Copy   

•   Source: SciCrunch Registry

http://func.mshri.on.ca/yeast/

YeastFunc is a public database for browsing of quantitative S. cerevisiae gene function predictions, gene function linkage predictions, and the evidence behind the predictions, overlayed upon the experimentally verified annotations as taken from the SGD, MGI and Ensembl Gene databases, respectively. Three aspects of gene function predictions are displayed: * First, for a particular gene, users can view all functions ranked by certainty that the corresponding gene-function pair is a true annotation. * Second, for a particular function, users can view all genes ranked by certainty. * The third aspect is functional linkage predictions, displayed alongside the first two aspects as gene-centered and function-centered images, respectively, and editable via Cytoscape. These functional linkage graphs are independently informative, though they are also used as a step in one of the gene function prediction techniques whose certainty scores are displaying on this site, so they can be treated as evidence. Evidence leading to all gene function predictions in the first two aspects as well as all experimentally verified gene function annotation is displayed alongside each of the first two aspects, allowing the user to understand the basis for the certainty score. To get started type a Gene Ontology ID, an SGD ID, an ORF ID, an Ensembl gene id, an Entrez gene id, a Uniprot id, a standard gene name, or a general search term in the text box. The results of your search will appear below the search box. These results are solely Gene Ontology terms and genes for the species that you selected. Click the result that you would like to investigate further. Note the paging toolbar at the bottom of the results list. If you are interested in performing your own analyses upon all prediction scores displayed on this site you may download the file. Of the 15,633,440 scored yeast gene-function pairs, 6,368 genes have scores and 4,877 genes have at least one experimentally verified function.

Proper citation: YeastFunc (RRID:SCR_010561) Copy   

•   Source: SciCrunch Registry

http://bis.zju.edu.cn/DaTo/

A biological database and software tool catalog based on text mined and human annotated url mentions in PubMed abstracts. Data are annotated as to the author''''s country of origin and url status is checked.

Proper citation: DaTo (RRID:SCR_010280) Copy   

•   Source: SciCrunch Registry

http://www.nordgen.org/index.php/en/content/view/full/467

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023.

Proper citation: Nordic Genetic Resource Centre (Plants) (RRID:SCR_010529) Copy   

•   Source: SciCrunch Registry

http://www.citeab.com/

Citation-ranked antibody search engine that provides a simple way to find antibodies that work. They use the number of citations as a transparent method to rank antibodies. Nobody can pay to be ranked higher. They are always looking for more commercial and academic antibodies to make CiteAb better. There is no charge to list.

Proper citation: CiteAb (RRID:SCR_009653) Copy   

•   Source: SciCrunch Registry

https://www.tycho.pitt.edu/

Database to advance the availability and use of public health data for science and policy making that includes data from all weekly notifiable disease reports for the United States dating back to 1888. Additional U.S. and international data will be released twice yearly.

Proper citation: Project Tycho (RRID:SCR_010489) Copy   

•   Source: SciCrunch Registry

http://pingstudy.ucsd.edu/

A large multi-site pediatric MRI and genetics data resource to facilitate studies of the genomic landscape of the developing human brain. It includes information about the developing mental and emotional functions of the children to understand the genetic basis of individual differences in brain structure and connectivity, cognition, and personality. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined. Investigators interested in the effects of a particular gene will be able to search the database for any brain areas or connections between areas that differ as a function of variation in a particular gene, and also to determine if the genes appear to affect the course of brain development at some point during childhood. A data exploration tool has been created for mapping and analyzing MRI data sets collected for PING and related developmental studies. Approved investigators will be able to view raw image sets and derived 3D brain maps of MRI and DTI data, conduct hypothesis testing, and graph brain area measures as they change across the time course of development. PING Cores * Coordinating Core: Functions include project management, screening of participants and maintaining the database * Neuroimaging Core: applying a standardized high-resolution structural MRI protocol involving 3-D T1-weighted scans, a T2-weighted volume, and a set of diffusion-weighted scans with multiple b values and diffusion directions, scans to estimate MRI relaxation rates, and gradient echo EPI scans for resting state fMRI. Importantly, adaptive motion compensation, using ����??PROMO����??, a novel real-time motion correction algorithm will be used. Specific PING protocols for each scanner manufacturer: ** PING MRI Protocol - GE ** PING MRI Protocol - Philips ** PING MRI Protocol - Siemens * Assessment Core: Cognitive assessments for the PING project are conducted using the NIH Toolbox for Cognition. * Genomics Core: functions as a central repository for receipt of saliva samples collected for each study participant. Once received, samples are catalogued, maintained, and DNA is extracted using state-of-the-field laboratory techniques. Ultimately, genome-wide genotyping is performed on the extracted DNA using the Illumina Human660W-Quad BeadChip. PING involves 10 sites throughout the country including UCSD, University of Hawaii, Scripps Genomics, UCLA, UC Davis, Kennedy Krieger Institute/Johns Hopkins, Sacker Institute/Cornell University, University of Massachusetts, Massachusetts General Hospital/Harvard, and Yale. Families who may want to participate in the study, or others who want to know more about it, may email questions to ping (at) ucsd.edu.

Proper citation: Pediatric Imaging Neurocognition and Genetics (RRID:SCR_008953) Copy   

•   Source: SciCrunch Registry

http://www.accessdata.fda.gov/scripts/opdlisting/oopd/index.cfm

Database of Orphan Drug Product designations. Searches may be run by entering the product name, orphan designation, and dates. Results can be displayed as a condensed list, detailed list, or an Excel spreadsheet.

Proper citation: Search Orphan Drug Designations and Approvals (RRID:SCR_010256) Copy   

•   Source: SciCrunch Registry

http://wiki.wholebraincatalog.org/wiki/Dangerous_Ideas

THIS RESOURCE IS NO LONGER IN SERVICE This is the website for a weekly social event called Dangerous Ideas, to promote more cross talk and cross pollination of ideas. There is a list of links to interesting new tools and technologies in the realm of computation and science. We'll be experimenting with webcasting this so others who can't physically join us can share in seeing what we think is cool. Its a completely open event-- anyone is welcome to join in, but should be prepared to present!

Proper citation: Dangerous Ideas (RRID:SCR_010531) Copy   

•   Source: SciCrunch Registry

http://www.accessdata.fda.gov/scripts/animaldrugsatfda/index.cfm?gb=1

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of approved veterinary drugs run by the FDA.

Proper citation: AnimalDrugsatFDA (RRID:SCR_010257) Copy   

•   Source: SciCrunch Registry