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http://adrc.ucsd.edu/

The UCSD ADRC conducts a wide variety of research studies dedicated to understanding the causes, clinical features, and treatments for Alzheimer's disease and related memory disorders. The goal of the center is to discover ways to prevent and eradicate the disease. The Center aims to maintain research subjects, clinical resources, and clinical data to support ongoing and proposed research and to assist in the development of new clinical and interdisciplinary research. An Alzheimer's brain bank with well characterized cases, including Mild Cognitive Impairment and Lewy Body disease, is maintained at the Center.

Proper citation: Shiley-Marcos Alzheimer's Disease Research Center (RRID:SCR_001928) Copy   

•   Source: SciCrunch Registry

http://www.doe-mbi.ucla.edu/

The UCLA-DOE Institute for Genomics and Proteomics carries out research in bioenergy, structural biology, genomics and proteomics, consistent with the research mission of the United States Department of Energy. Major interests of the 12 Principal Investigators and 9 Associate Members include systems approaches to organisms, structural biology, bioinformatics, and bioenergetic systems. The Institute sponsors 5 Core Technology Centers, for X-ray and NMR structural determination, bioinformatics and computation, protein expression and purification, and biochemical instrumentation. Services offered by this Institute: - Databases: * DIP (The Database of Interacting Proteins): The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. * ProLinks Database of Functional Linkages: The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage. - Data-to-Structure Servers: * SAVEs Structure Verification Server * Merohedral Twinning Test Server * SER Surface Entropy Reduction Server * VERIFY3D Structure Verification Server * ERRAT Structure Verification Server - Structure-to-Function Servers: * ProKnow Protein Functionator * Hot Patch Functional Site Locator

Proper citation: University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics (RRID:SCR_001921) Copy   

•   Source: SciCrunch Registry

http://www.mevislab.de/index.php?id=6

Modular framework for the development of image processing algorithms and visualization and interaction methods, with a special focus on medical imaging. It includes advanced medical imaging modules for segmentation, registration, volumetry, and quantitative morphological and functional analysis. The platform allows fast integration and testing of new algorithms and the development of application prototypes that can be used in clinical environments. In MeVisLab, individual image processing, visualization and interaction modules can be combined to complex image processing networks using a graphical programming approach. The algorithms can easily be integrated using a modular, platform-independent C++ class library. An abstract, hierarchical definition language allows the design of efficient graphical user interfaces, hiding the complexity of the underlying module network to the end user. JavaScript components can be added to implement dynamic functionality on both the network and the user interface level. MeVisLab is based on the Qt application framework, the OpenInventor 3D visualization toolkit and OpenGL. Several clinical prototypes have been realized on the basis of MeVisLab, including software assistants for neuro-imaging, dynamic image analysis, surgery planning, and vessel analysis. Feature Overview: :- Basic image processing algorithms and advanced medical imaging modules :- Full featured, flexible 2D/3D visualization and interaction tools :- High performance for large datasets :- Modular, expandable C++ image processing library :- Graphical programming of complex, hierarchical module networks :- Object-oriented GUI definition and scripting :- Full scripting functionality using Python and JavaScript :- DICOM support and PACS integration :- Intuitive user interface :- Integrated movie and screenshot generation for demonstration purposes :- Generic integration of the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) :- Cross-platform support for Windows, Linux, and MacOS X :- Available for 64-bit operating systems

Proper citation: Medical Image Processing and Visualization (RRID:SCR_002055) Copy   

•   Source: SciCrunch Registry

https://netbio.bgu.ac.il/tissuenet3/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/15/13. The Nation's one-stop resource for information about substance abuse prevention and addiction treatment offering more than 500 items to the public, many of which are free of charge. They distribute the latest studies and surveys, guides, videocassettes, and other types of information and materials on substance abuse from various agencies, such as the U.S. Departments of Education and Labor, the Center for Substance Abuse Prevention, the Center for Substance Abuse Treatment, the National Institute on Alcohol Abuse and Alcoholism, and the National Institute on Drug Abuse. They staff both English- and Spanish-speaking information specialists who are skilled at recommending appropriate publications, posters, and videocassettes; conducting customized searches; providing grant and funding information; and referring people to appropriate organizations. They are available 24 hours a day, 7 days a week to take your calls at 1-800-729-6686. NCADI services include: * an information services staff (English, Spanish, TDD capability) equipped to respond to the public's alcohol, tobacco, and drug (ATD) inquiries; * the distribution of free or low-cost ATD materials, including fact sheets, brochures, pamphlets, monographs, posters, and video tapes from an inventory of over 1,000 items; * a repertoire of culturally-diverse prevention, intervention, and treatment resources tailored for use by parents, teachers, youth, communities and prevention/treatment professionals; * customized searches in the form of annotated bibliographies from alcohol and drug data bases; * access to the Prevention Materials database (PMD) including over 8,000 prevention-related materials and the Treatment Resources Database, available to the public in electronic form; * rapid dissemination of Federal grant announcements for ATD prevention, treatment, and research funding opportunities.

Proper citation: SAMHSAs National Clearinghouse for Alcohol and Drug Information (RRID:SCR_002053) Copy   

•   Source: SciCrunch Registry

https://med.stanford.edu/sfgf.html

Stanford Genomics formerly Stanford Functional Genomics Facility provides services for high throughput sequencing, single cell assays, gene expression and genotyping studies utilizing microarray and real time PCR, and related services. High throughput sequencing (Illumina HiSeq 4000, NextSeq 500, MiSeq and MiniSeq), microarray gene expression and genotyping services (Affymetrix, Agilent and Illumina). Provides 24/7 access to instruments, equipment and software utilized within genomics field.

Proper citation: Stanford Genomics Service Center Core Facility (RRID:SCR_002050) Copy   

•   Source: SciCrunch Registry

https://dataverse.org/

Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization.

Proper citation: Dataverse Network Project (RRID:SCR_001997) Copy   

•   Source: SciCrunch Registry

http://microarrays.curie.fr/publications/U900-RPPA_PLT/Normacurve/

Analysis methodology that allows simultaneous quantification and normalization of reverse phase protein array (RPPA) data.

Proper citation: NormaCurve (RRID:SCR_001995) Copy   

•   Source: SciCrunch Registry

http://gara.bio.uci.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2017. Database of images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli. A number of different display and comparison tools are provided allowing patterns to be viewed from different perspectives, and descriptions of the methods and interpretations of these data are provided. Some of the more advanced tools require you to download software.

Proper citation: Glomerular Activity Response Archive (RRID:SCR_002089) Copy   

•   Source: SciCrunch Registry

http://www.cellsignal.com/

Privately held company that develops and produces antibodies, ELISA kits, ChIP kits, proteomic kits, and other related reagents used to study cell signaling pathways that impact human health.

Proper citation: Cell Signaling Technology (RRID:SCR_002071) Copy   

•   Source: SciCrunch Registry

http://ncmir.ucsd.edu/downloads/jinx.shtm

Jinx was developed to aid in the 3D reconstruction of tomographic datasets acquired with one of the various electron microscopes available at the resource. Tomographic datasets consist of a series of 2D images from which objects of interest are segmented out for the 3D reconstruction. Jinx offers the user a graphical interface to step through each image of the series and facilities to manually trace out objects of interest. It relies on JadeDisplay to support the display of large images with graphical overlays and the JAI libraries for histogram functionality and other types of image manipulations. Jinx is currently under active development and future releases will offer semi-automated segmentation algorithms based on fuzzy logic, level set, and watershed algorithm. This software is free; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version. See the GNU General Public License for more details. For a copy of the GNU General Public License, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA. Sponsors: Jinx presented here was produced at the National Center for Microscopy and Imaging Research at San Diego, which is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant P41 RR04050. open source license, GNU general public license

Proper citation: National Center for Microscopy and Imaging Research: Jinx (RRID:SCR_001939) Copy   

•   Source: SciCrunch Registry

https://neurograd.ucsd.edu/handbook/prog-requirement/comp-neuro/index.html

The Computational Neuroscience specialization is a new facet of the broader Neuroscience graduate program at UCSD. The goal of the specialization is to train the next generation of neuroscientists with the broad range of computational and analytical skills that are essential to understand the organization and function of complex neural systems. The specialization is intended for students with backgrounds in neuroscience, physics, chemistry, biology, psychology, computer science, engineering, and mathematics. This specialization allows Neuroscience students to concentrate on a focused program of rigorous course work in both the theoretical and experimental aspects of computational neuroscience. Students are encouraged to pursue thesis research that includes both an experimental and a computational component, often arranged by the student as a collaboration between two research groups. The program is focused on these major themes relevant for computational neuroscience research: - Neurobiology of Neural Systems - the anatomy, physiology, and behavior of systems of neurons, with emphasis on basic phenomenology. - Advanced Measurement Tools in Neuroscience - Advanced imaging and recording techniques reflecting the impact of experimental physics on neuroscience. - Algorithms for the Analysis of Neural Data - New algorithms and techniques for analyzing data obtained from physiological recording - Theoretical Basis for Collective Neural Dynamics - A synthesis of approaches from mathematics and physical sciences as well as biology will be used to explore the collective properties and nonlinear dynamics of neuronal systems. Sponsors: This program is supported by the University of California at San Diego.

Proper citation: University of California at San Diego Computational Neuroscience (RRID:SCR_001930) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ONTODT

Ontology that contains entities such as: datatype, datatype generator, datatype quality and others giving the possibility to represent arbitrary complex datatypes. This is an important fact for a general data mining ontology that wants to represent and query over modelling algorithms for mining structured data. The ontology was first developed under the OntoDM (Ontology of Data Mining, http://kt.ijs.si/panovp/OntoDM) ontology, but for generality and reuse purpose it was decided to export it as a separate ontology. Additionaly, the OntoDT ontology is based on and ISO/IEC 11404 (http://www.iso.org/iso/catalogue_detail.htm?csnumber=39479) standard and can be reused used independently by any domain ontology that requires representation and reasoning about general purpose datatypes.

Proper citation: Ontology of General Purpose Datatypes (RRID:SCR_010397) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ONTOMA

Ontology for common concepts for communication between traditional medicine and western medicine. (In French)

Proper citation: Ontology of Alternative Medicine French (RRID:SCR_010390) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/OGMD

Ontology including the disease names, phenotypes and their classifications involved in Glucose Metabolism Disorder, Diabetes. (OBO and OWL format are available in sourceforge.)

Proper citation: Ontology of Glucose Metabolism Disorder (RRID:SCR_010399) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/TADS

Anatomy Ontology of the Tick, Families: Ixodidae, Argassidae

Proper citation: Tick Gross Anatomy Ontology (RRID:SCR_010433) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/TM-CONST

Ontology of the value set for the constitution property of the International Classification of Traditional Medicine (ICTM).

Proper citation: Traditional Medicine Constitution Value Set (RRID:SCR_010435) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/TM-SIGNS-AND-SYMPTS

Ontology of the value set for the Signs and Symptoms property of the International Classification of Traditional Medicine (ICTM).

Proper citation: Traditional Medicine Signs and Symptoms Value Set (RRID:SCR_010438) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/UNITSONT

A small ontology for the units of measurement developed during the development of the Sleep Domain Ontology (SDO). It supports the use of SDO within the PhysioMIMI application.

Proper citation: Units Ontology (RRID:SCR_010441) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/UO

Metrical units ontology for use in conjunction with PATO

Proper citation: Units of Measurement Ontology (RRID:SCR_010442) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NIFSUBCELL

Ontology that contains cell parts and subcellular structures from SAO-CORE and Gene Ontology Cellular Component (GO-CC). http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl

Proper citation: NIF Subcellular Ontology (RRID:SCR_010366) Copy   

•   Source: SciCrunch Registry