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http://hcv.lanl.gov/content/immuno/immuno-main.html
The HCV Immunology Database contains a curated inventory of immunological epitopes in HCV and their interaction with the immune system, with associated retrieval and analysis tools. The funding for the HCV database project has stopped, and this website and the HCV immunology database are no longer maintained. The site will stay up, but problems will not be fixed. The database was last updated in September 2007. The HIV immunology website contains the same tools, and may be usable for non-HCV-specific analyses. For new epitope information, users of this database can try the Immuno Epitope Database (http://www.immuneepitope.org).
Proper citation: HCV Immunology Database (RRID:SCR_007086) Copy
Composed of many projects, including the Minnesota Twin Family Study (MTFS) and The Sibling Interaction and Behavior Study (SIBS), this research center seeks to identify genetic and environmental influences on development and psychological traits. Both projects are longitudinal research studies including twins, siblings, and parents. Over 9800 individuals have contributed to these exciting projects! By studying twins and siblings and their families, we can estimate how genes and environment interact to influence character, strengths, vulnerabilities and values. Participants in the MTFS include families with same-sex identical or fraternal twins who were born in Minnesota. The SIBS study is comprised of adoptive and biological siblings and their parents. Most participants partake in day-long visits to the MCTFR, and due to the longitudinal nature of our projects, they return every 3-4 years for follow-up visits.
Proper citation: Minnesota Center for Twin and Family Research (RRID:SCR_006948) Copy
https://github.com/jstjohn/SimSeq
An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries .
Proper citation: SimSeq (RRID:SCR_006947) Copy
https://www.nitrc.org/projects/fmridatacenter/
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community.
Proper citation: fMRI Data Center (RRID:SCR_007278) Copy
National genetics data repository facilitating access to genotypic and phenotypic data for Alzheimer's disease (AD). Data include GWAS, whole genome (WGS) and whole exome (WES), expression, RNA Seq, and CHIP Seq analyses. Data for the Alzheimer’s Disease Sequencing Project (ADSP) are available through a partnership with dbGaP (ADSP at dbGaP). Repository for many types of data generated from NIA supported grants and/or NIA funded biological samples. Data are deposited at NIAGADS or NIA-approved sites. Genetic Data and associated Phenotypic Data are available to qualified investigators in scientific community for secondary analysis.
Proper citation: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) (RRID:SCR_007314) Copy
http://www.ikaros-project.org/
Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models.
Proper citation: Ikaros Project (RRID:SCR_007391) Copy
http://ngs.ym.edu.tw/ym500/index.php
An Integrative small RNA Sequencing database for miRNA research and provides an integrative web interface for miRNA quantification, isomiR identification, arm switching discovery, and, most of all, novel miRNA predictions.
Proper citation: YM500 (RRID:SCR_007429) Copy
http://www.mcell.cnl.salk.edu/
Software modeling tool for realistic simulation of cellular signaling in complex 3-D subcellular microenvironment in and around living cells. Program that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate movements and reactions of molecules within and between cells.
Proper citation: MCell (RRID:SCR_007307) Copy
A computer-readable format for representing models of biochemical reaction networks in software. It''s applicable to models of metabolism, cell-signaling, and many others. This website is the portal for the global SBML development effort; you can find information about all aspects of SBML.
Proper citation: SBML (RRID:SCR_007422) Copy
Software platform, general technologies and theoretical supports for computational biology with the grand aim to make precise whole cell simulation at the molecular level possible.Technologies include formalisms and techniques, including technologies to predict, obtain or estimate parameters such as reaction rates and concentrations of molecules in the cell. The E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale system like the cell. The E-Cell Project is open to anyone who shares the view with u that development of cell simulation technology, and, even if such ultimate goal might not be within ten years of reach yet, solving various conceptual, computational and experimental problems that will continue to arise in the course of pursuing it, may have a multitude of eminent scientific, medical and engineering impacts on our society.
Proper citation: Electronic Cell Project (RRID:SCR_007381) Copy
Portal covering the broad field of primatology, providing original content and links to resources about nonhuman primates in research, education and conservation. Through email lists and other resources, PIN also supports an informal primate information network comprised of thousands of individuals around the world working with nonhuman primates in a variety of roles. Services Provided: - Primate Info Net (PIN): A comprehensive Web site with links to research, conservation, and education resources related to nonhuman primates. - PrimateLit Database (1940 to date): PrimateLite is a free, bibliographic database of more than 200,000 citations to the nonhuman primate literature. Indexing for PrimateLit is provided by the Primate Information Center, Washington NPRC, Seattle. - International Directory of Primatology: The International Directory of Primatology is a searchable directory of the field of primatology with detailed information about organizations, field studies, population management groups, and contact information for more than 3,000 primatologists. - Primate-Science: Primate-Science is a professionally oriented, e-mail-based electronic discussion forum for people engaged in research with nonhuman primates. - Primate-News: Primate-News is an e-mailed-based news clipping service open to anyone interested in nonhuman primates. - Primate Enrichment Forum: Primate Enrichment Forum is a professionally oriented, e-mail-based electronic discussion forum for individuals interested in environmental enrichment for nonhuman primates. - AskPrimate: AskPrimate is a cooperative e-mail reference service available to the research community and the general public. - Primate-Jobs: Primate-Jobs is a job listing service that includes paid and volunteer positions, wanted and available. - Careers in Primatology: Careers in Primatology is a resource for people considering careers in primate research, education, conservation, or veterinary medicine. - Audiovisual Resources: Audiovisual Resources is a collection of primate-related videotapes, slides, and audiotapes available for research and educational uses. - The Callicam: The Callicam is a Webcam feature of the Wisconsin NPRC''s common marmoset site that allows students in the classroom to observe marmoset behavior and learn about their natural history, care, and management.
Proper citation: Primate Info Net (RRID:SCR_007380) Copy
The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). :The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, t he system provides computationally derived data such as multiple sequence alignments, homology models, and a series of query and visualization tools. :The GPCRDB is designed to be a data storage medium, as well as a tool to aid biomedical scientists with answering questions by offering a single point of access to many types of data that are integrated and visualized in a user-friendly way. Although most parts of the GPCRDB are self-explanatory, if you have not used this resource before it is adviced that you to take a look at the usage page. Sponsors: This resource is supported by Organon and Unilever, and the NIH. Keywords: G protein, Coupled, receptor, Molecular, Heterogenous, Data, Sequence, Ligand, Mutation, Computational, Software, Alignment, Homology, Model, Visualization, Tool, Biomedical, Scientist, Integration,
Proper citation: G Protein-Coupled Receptor Data Base (RRID:SCR_007419) Copy
https://www.kent.edu/neuroscience
Neuroscience is dedicated to understanding how the brain and nervous system function in health, disease and repair. Neuroscience research at Kent State University is supported by over 50 faculty members from numerous departments and disciplines. Our researchers have a wide range of expertise including behavioral neuroscience, sensory neuroscience, developmental neuroscience and neurodegenerative diseases.
Proper citation: Kent State University Department of Neuroscience (RRID:SCR_007458) Copy
Next generation sequencing and genotyping services provided to investigators working to discover genes that contribute to disease. On-site statistical geneticists provide insight into analysis issues as they relate to study design, data production and quality control. In addition, CIDR has a consulting agreement with the University of Washington Genetics Coordinating Center (GCC) to provide statistical and analytical support, most predominantly in the areas of GWAS data cleaning and methods development. Completed studies encompass over 175 phenotypes across 530 projects and 620,000 samples. The impact is evidenced by over 380 peer-reviewed papers published in 100 journals. Three pathways exist to access the CIDR genotyping facility: * NIH CIDR Program: The CIDR contract is funded by 14 NIH Institutes and provides genotyping and statistical genetic services to investigators approved for access through competitive peer review. An application is required for projects supported by the NIH CIDR Program. * The HTS Facility: The High Throughput Sequencing Facility, part of the Johns Hopkins Genetic Resources Core Facility, provides next generation sequencing services to internal JHU investigators and external scientists on a fee-for-service basis. * The JHU SNP Center: The SNP Center, part of the Johns Hopkins Genetic Resources Core Facility, provides genotyping to internal JHU investigators and external scientists on a fee-for-service basis. Data computation service is included to cover the statistical genetics services provided for investigators seeking to identify genes that contribute to human disease. Human Genotyping Services include SNP Genome Wide Association Studies, SNP Linkage Scans, Custom SNP Studies, Cancer Panel, MHC Panels, and Methylation Profiling. Mouse Genotyping Services include SNP Scans and Custom SNP Studies.
Proper citation: Center for Inherited Disease Research (RRID:SCR_007339) Copy
The Neuroscience Training Program at The Johns Hopkins University School of Medicine addresses the broad areas encompassed by modern neuroscience. The purpose of the Program is to train doctoral students for independent research and teaching in neuroscience. It is the goal of the Program to ensure that candidates for the Ph.D. and M.D./Ph.D. degrees obtain a background covering molecular/cellular and systems/cognitive approaches to neuroscience, as well as receive training that brings them to the forefront of research in their particular area of interest. A series of core courses in neuroscience, along with advanced electives, seminar series, laboratory rotations and original independent dissertation research form the Neuroscience Graduate Training Program. The Neuroscience Training Program and the Neuroscience Department are among the oldest in the United States and date back to 1980. The faculty of the Neuroscience Training Program have trained about 250 Ph.D. and M.D./Ph.D. students and 500 postdoctoral fellows over the past ten years. All doctoral candidates receive full tuition remission and a stipend. Research within the department ranges from investigating the development of the nervous system, synaptic plasticity and the molecular and cellular mechanisms of learning and memory to the neural basis of higher brain function such as perception and decision-making. Our faculty are also at the forefront of research into the molecular mechanisms of neurological and psychiatric diseases, including Parkinson''s, Alzheimer''s'' disease, amyotrophic lateral sclerosis (ALS), schizophrenia, depression, drug addiction, mental retardation and autism.
Proper citation: Johns Hopkins University Neuroscience (RRID:SCR_007455) Copy
http://healthsciences.howard.edu/education/colleges/medicine/departments/pharmacology/Overview
The Department of Pharmacology offers programs leading to the Master of Science and Doctor of Philosophy degrees. The primary objective of these programs is to prepare candidates for research and teaching careers. The first few semesters are devoted primarily to core course work designed to give the student a broad background in the fundamental theories and techniques of pharmacology.During this time, the student gains exposure to methods for the solution of research problems by working in the laboratories of various faculty members culminating in a selection of a thesis advisor. The department has spacious laboratories equipped with modern instruments that are used by both faculty and students in such research areas as biochemical, molecular, cardiovascular, autonomic, clinical, and neuropharmacology, drug metabolism, cancer research and toxicology.
Proper citation: Howard University Washington D.C Department of Pharmacology (RRID:SCR_007454) Copy
http://ki.se/ki/jsp/polopoly.jsp?l=en&d=4329
Department of Clinical Neuroscience at Karolinska Institutet conducts research and teaching regarding the function of the brain - from a molecular level to the effect on society. This activity is closely integrated with medical clinics within Stockholm.
Proper citation: Karolinska Institute Department of Clinical Neuroscience (RRID:SCR_007456) Copy
http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook/tissue-arrays
Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers
Proper citation: Aged Rodent Tissue Arrays (RRID:SCR_007332) Copy
http://library.med.utah.edu/kw/brain_atlas/
Brain atlas in sagittal, coronal, and axial planes some from myelin stained sections, others from MRI. The structures are outlined and labeled on the zoomable images in the coronal series. The labels can also be used in quiz mode. Designed as part of of program for second year medical students studying neuroanatomy.
Proper citation: Atlases of the Brain (RRID:SCR_007293) Copy
The establishment of the Neuroscience Center at Dartmouth (NCD) in 2002 has produced a new and unique interdisciplinary group whose mission is to foster collaborative and interactive research and education in the neurosciences. Training opportunities in neuroscience include undergraduate minor/major in Neuroscience, graduate training toward a Ph.D., and postdoctoral training. The NCD draws from the strengths in three key areas: Clinical, Cognitive & Behavioral, and Molecular/Cellular/Systems Neuroscience. It is the vision of its researchers to produce and disseminate new knowledge, and in doing so train and educate the next generation of neuroscientists. Interactions among members of the neuroscience community are enhanced and foster a highly interactive atmosphere through the development of this integrated Center. By promoting multidisciplinary efforts in both basic and applied research, the Center''s scientists will contribute to human health and well being by increasing our understanding of the mechanisms underlying nervous system function, both in health and disease. This will lead to valuable discoveries that translate into novel pharmaceutical agents and therapeutic approaches for the treatment of a variety of central nervous system diseases and disorders. The research facilities are located in Hanover, NH, Lebanon, NH (Dartmouth-Hitchcock Medical Center) and the Veteran Affairs Medical Center in White River Junction, Vt. Research interests comprise a broad range of studies within the neurosciences and provide a wide range of research opportunities for students. In addition, the NCD augments the education of residents and fellow at the clinical level who have academic neuroscience interests.
Proper citation: Dartmouth Medical School Neuroscience (RRID:SCR_007449) Copy
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