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http://xoonips.sourceforge.jp/
Neuroinformatics (NI) is a new discipline that challenges the understanding of the structure and mechanism of the brain by combining neuroscience and information technology. The global collaborations in this field have been actively started with the support of the International Neuroinformatics Coordinating Facility (INCF) launched in November 2005. The Laboratory for Neuroinformatics at RIKEN Brain Science Institute (BSI) is involved in developing various cutting-edge technologies related to NI such as XooNIps. XooNIps succeeded the concept and basic feature of the vision science platform; Visiome, constructed by the NRV (i.e., Neuroinformatics Research in Vision) Project and has been developed based on a content management system (CMS); XOOPS, as infrastructure for NI databases to share different types of data on the Internet. :XooNIps has three features: :The first is the flexibility of developing databases. CMS-based XooNIps makes it easy to change the design or to extend the functions of databases by combining the different modules available on XOOPS. Therefore, even those who are not expert in computer system can develop their database on XooNIps. :The second is the diversity and extensibility of the data which can be handled by XooNIps. In order to handle different types of actual data, it provides not only the various data forms per se, but also the extension method to handle a new data form, which enables to deal easily with even a non-standardized data form. :The third is the facility to distribute metadata. XooNIps implements OAI-PMH (i.e., Open Archive Initiative-Protocol for Metadata Harvesting) which is one of the standard protocols to distribute metadata. This enables to collect information on other databases which are developed on XooNIps or to coordinate databases by exchanging metadata with other databases which implement OAI-PMH than those on XooNIps. :Since April 2007, Neuroinformatics Japan Center (NIJC) at RIKEN BSI takes charge of extending and maintaining XooNIps, and is committed to manage the documentation hereafter. :NIJC, as a national node of INCF, is developing and operating various NI platforms in neuroscience based on XooNIps to establish and facilitate NI research in Japan. XooNIps is also being applied to databases or organizational repositories in several institutions and universities, and laboratory groupware in various fields. We hope XooNIps will be of universal use in and out of Japan. :database; binary executable; software development tool; metadata; data set; :
Proper citation: XooNIps - Neuroinformatics Base Platform System (RRID:SCR_013590) Copy
Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis.
Proper citation: University of Chicago Digestive Diseases Research Core Center (RRID:SCR_015601) Copy
https://www.distillersr.com/products/distillersr-systematic-review-software
Literature review software by DistillerSR Inc. Automates management of literature collection, screening, and assessment using AI and intelligent workflows. From systematic literature review to rapid review to living review, makes any project simpler to manage and configure to produce transparent, audit-ready, and compliant results.
Proper citation: DistillerSR (RRID:SCR_023078) Copy
Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data.
Proper citation: Musculoskeletal Knowledge Portal (RRID:SCR_023171) Copy
Research and education program in Harvard Program in Therapeutic Science at Harvard Medical School to advance science and to develop technology needed to accelerate invention of new medicines and personalization of patient care. Used to study molecular causes of disease, ways drugs exert their therapeutic and adverse effects, design and interpretation of clinical trials.
Proper citation: Laboratory of Systems Pharmacology program (RRID:SCR_022873) Copy
http://naturalscenesdataset.org/
Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry.
Proper citation: Natural Scenes Dataset (RRID:SCR_023648) Copy
Open access integrated research platform, which links scientists, shared data, and analysis tools to accelerate Alzheimer’s disease research, disease preventions, treatments and cure. Unites diverse and geographically distributed network of data partners to foster cohort discovery, collaboration and sharing. Researchers can discover clinical, genetic, imaging and other data collected across many independent studies.
Proper citation: Global Alzheimers Association Interaction Network (RRID:SCR_023699) Copy
Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets.
Proper citation: TIGER Data Portal (RRID:SCR_023626) Copy
Clinical research platform and longitudinal observational study for Huntington’s Disease families intended to accelerate progress towards therapeutics. Collaboration between Huntington’s disease families, clinicians, and researchers to accelerate progress toward effective treatments.
Proper citation: Enroll-HD (RRID:SCR_023300) Copy
https://rostlab.org/owiki/index.php/PROFisis
Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures.
Proper citation: PROFisis (RRID:SCR_024179) Copy
http://contra.stanford.edu/contrafold/
Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.
Proper citation: CONTRAfold (RRID:SCR_023994) Copy
https://rostlab.org/owiki/index.php/Metastudent
Software tool to predict gene ontology terms for protein sequences through homology.
Proper citation: Metastudent (RRID:SCR_024110) Copy
Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions.
Proper citation: CTSim (RRID:SCR_024004) Copy
http://www.sph.umich.edu/csg/abecasis/QTDT/
How is association mapping going to help me find genes? During the past decade, the genes for a large number of rare mendelian traits have been identified. However, traditional linkage analyses lack power and precision when applied to complex disease. Association mapping, which compares the effects of different chromosomal variants, may be more successful at identifying genes of small effect. How does QTDT help association mapping? Association mapping can produce misleading results when the study population is not homogeneous, but includes individuals with different genetic backgrounds. Family based association tests, commonly referred to as TDTs (Transmission Disequilibrium Tests), do not produce misleading results in these circumstances. QTDT can use all the information in a pedigree to construct powerful tests of association that are robust in the presence of stratification. What does the Q stant for ? Q stands for Quantitative. Quantitative traits provide effective descriptions of many complex diseases, including asthma. For many of these conditions, all or nothing definitions of disease are arbitrary and unsatisfactory. QTDT incorporates variance components methodology in the analysis of family data and includes exact estimation of p-values for analysis of small samples and non-normal data. The QTDT abbreviation (for Quantitative Transmission Disequilibrium Tests) was first used by David Allison in his 1997 paper. This research was supported in part by the intramural program of the National Eye Institute and by National Institutes of Health Grants EY016862, EY007758, EY09859, EY012118, P30-EY014801, EY-014458, EY014467, HL084729, and HG002651, by the Foundation Fighting Blindness, the Macula Vision Research Foundation, the American Health Assistance Foundation, Research to Prevent Blindness, the Pew Charitable Trusts, the Mayo Clinic Foundation, the Casey Macular Degeneration Center Fund, the Marion W. and Edward F. Knight AMD Fund, the Harold and Pauline Price Foundation, National Genotyping Centre of Spain, and the Elmer and Sylvia Sramek Foundation. The Center for Inherited Disease Research, fully funded through a federal contract (HHSN268200782096C) from National Institutes of Health to
Proper citation: Linkage Disequilibrium Analyses for Quantitative and Discrete Traits (RRID:SCR_013365) Copy
http://www.scienceexchange.com/facilities/barts-and-the-london-school-of-medicine-and-dentistry
Barts and The London offers international levels of excellence in research and teaching while serving a population of unrivalled diversity. Through partnership with our linked trusts, notably Barts and The London NHS Trust, and our associated University Hospital Trusts _������������_ Homerton, Newham, Whipps Cross and Queen''''s (Romford) the School''''s research and teaching is informed by an exceptionally wide ranging and stimulating clinical environment.
Proper citation: Barts and The London School of Medicine and Dentistry Labs and Facilities (RRID:SCR_012710) Copy
http://www.scienceexchange.com/facilities/michigan-state-university
An Portal, Core facility
Proper citation: Michigan State University Labs and Facilities (RRID:SCR_012252) Copy
http://phaffcollection.ucdavis.edu/
Collection of wild yeast in the world. Academic and industrial resarchers utilize this collection for a variety of research and applications, including pigments, enzymes, food ingredients, and hosts for protein expression. Provides contract screening and strain selection services.
Proper citation: Phaff Yeast Culture Collection (RRID:SCR_016781) Copy
http://cmmt.ubc.ca/facilities-services/mouse-animal-production/
Supplier of mice for research purposes. The service is run by Dr. Elizabeth M. Simpson, Ph.D. and is affiliated with her lab.
Proper citation: CMMT Mouse Animal Production Service (RRID:SCR_016403) Copy
https://commons.cri.uchicago.edu/pcdc/
PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors.
Proper citation: Pediatric Cancer Data Commons (RRID:SCR_022369) Copy
http://www.jcvi.org/cgi-bin/tigrfams/index.cgi
Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site.
Proper citation: TIGRFAMS (RRID:SCR_005493) Copy
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