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http://ophid.utoronto.ca/navigator/

A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches.

Proper citation: Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) Copy   

•   Source: SciCrunch Registry

http://cvs.anu.edu.au/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Vision Science is a large discipline at the ANU that is found in several teaching and research faculties and several large research institutes. About 85 research staff participate in all forms of vision science from machine vision, to neurophysiology, behaviour and cognition. The scale of analysis ranges from molecular to systems approaches and covers insect, vertebrate and human visual systems. Topics such as disease and development of the human visual system are also covered. CVS works to connect and sustain the component parts of the ANU vision science community.

Proper citation: Centre for Visual Sciences (RRID:SCR_008324) Copy   

•   Source: SciCrunch Registry

http://www.bitlifesciences.com

Information and human resource exchange services for academia and industries, professional and commercial societies from major industrial sectors and academic organizations. Events: Annual Drug Discovery Science & Technology (IDDST), World DNA and Genome Day celebrating the discovery of DNA double helix structure, Life science Forum, World AIDS Day, Pepcon Conference, iBio and World Cancer Congress.

Proper citation: BIT Life Sciences (RRID:SCR_008313) Copy   

•   Source: SciCrunch Registry

http://brainconnection.positscience.com/

An educational site providing accessible information about how the brain works and how people learn

Proper citation: Brain Connection (RRID:SCR_008315) Copy   

•   Source: SciCrunch Registry

http://degradome.uniovi.es/diseases.html

This resource has cataloged a total of 80 human hereditary diseases caused by mutations in protease-coding genes, which implies that more than 10% of the human protease genes are involved in human pathologies. They are classified in three groups: loss of function, gain of function, and an heterogeneous group including non-protease homologs (np), putative proteases, and hedgehog proteins with only autoprocessing activity. Type of inheritance is indicated by R (recessive) or D (dominant).

Proper citation: Human Hereditary Diseases of Proteolysis (RRID:SCR_008344) Copy   

•   Source: SciCrunch Registry

http://www.ohsu.edu/xd/research/centers-institutes/onprc/

Center that aims to develop biomedical technologies using nonhuman primate (NHP) models. Its goal is to uncover the root causes of various disease and disorders, unlock secrets of the brain, and unleash new methods of diagnostics and treatment.

Proper citation: Oregon National Primate Research Center (RRID:SCR_008291) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/mammals/dog

The genome of the domesticated dog, a close evolutionary relation to human, is a powerful new tool for understanding the human genome. Comparison of the dog with human and other mammals reveals key information about the structure and evolution of genes and genomes. The unique breeding history of dogs, with their extraordinary behavioral and physical diversity, offers the opportunity to find important genes underlying diseases shared between dogs and humans, such as cancer, diabetes, and epilepsy. The Canine Genome Sequencing Project produced a high-quality draft sequence of a female boxer named Tasha. By comparing Tasha with many other breeds, the project also compiled a comprehensive set of SNPs (single nucleotide polymorphisms) useful in all dog breeds. These closely spaced genomic landmarks are critical for disease mapping. By comparing the dog, rodent, and human lineages, researchers at the Broad Institute uncovered exciting new information about human genes, their evolution, and the regulatory mechanisms governing their expression. Using SNPs, researchers describe the strikingly different haplotype structure in dog breeds compared with the entire dog population. In addition, they show that by understanding the patterns of variation in dog breeds, scientists can design powerful gene mapping experiments for complex diseases that are difficult to map in human populations. Contribute Although the astounding generosity of Eli and Edythe L. Broad and several other venture philanthropists empowers our scientists to tackle many of the most important problems at the cutting edge of genomic medicine, there are many other critical challenges that they cannot yet pursue because of limited resources. We need additional visionary partners to join the Broads and the Broad Institute in transforming medicine with the power of genomics.

Proper citation: Dog Genome Project (RRID:SCR_008486) Copy   

•   Source: SciCrunch Registry

http://www.biobankcentral.org/resource/wwibb.php

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. Web-based portal to connect all the constituencies in the global biobank community. The project seeks to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum. Biobanks are the meeting point of two major information trends in biomedical research: the generation of huge amounts of genomic and other laboratory data, and the electronic capture and integration of patient clinical records. They are comprised of large numbers of human biospecimens supplemented with clinical data. Biobanks when implemented effectively can harness the power of both genomic and clinical data and serve as a critical bridge between basic and applied research, linking laboratory to patient and getting to cures faster. As science and technology leaders work to address the many challenges facing U.S. biobanks logistical, technical, ethical, financial, intellectual property, and IT BioBank Central will serve as an accurate and timely source of knowledge and news about biorepositories and their role in research and drug development. The Web site also provides a working group venue, patient and public education programs, and a forum for international collaboration and harmonization of best practices.

Proper citation: BioBank Central (RRID:SCR_008645) Copy   

•   Source: SciCrunch Registry

http://www.alzfdn.org/index.htm

Non profit organization and informational portal directed towards patients and families. AFA is an umbrella orgnization uniting over 1600 member organizations to collaborate on education, resources, best practices and advocacy. AFA provides several grant opportunities for AFA's nonprofit member organizations and to individuals in need.

Proper citation: Alzheimer's Foundation of America (RRID:SCR_008724) Copy   

•   Source: SciCrunch Registry

http://www.alzresearch.org/index.cfm

A Alzheimer's Disease Research Center (ADRC) whose goal is to conduct basic and clinical research aimed at understanding Alzheimer's disease. The Center enrolls a variety of individuals for clinical trials, evaluation and follow-up, including: normal control subjects, individuals with mild memory problems, and patients diagnosed with Alzheimer's Disease or related dementias. Researchers can request data and specimens obtained from ADRC subjects. These include blood or DNA, brain specimens, and cross-sectional or longitudinal clinical and cognitive data, all from ADRC subjects.

Proper citation: Johns Hopkins Alzheimer's Disease Research Center (RRID:SCR_008757) Copy   

•   Source: SciCrunch Registry

https://www.humanconnectome.org/software/connectome-workbench

Software brain visualization, analysis and discovery tool for fMRI and dMRI brain imaging data, including functional and structural connectivity data generated by the Human Connectome Project. Used to map brain imaging data. Allows for visualization of outputs from HCP pipelines from single subject, or average data from group of subjects and register that data onto standard brain atlas.

Proper citation: Connectome Workbench (RRID:SCR_008750) Copy   

•   Source: SciCrunch Registry

http://depts.washington.edu/adrcweb/

Research center investigating the basic mechanisms underlying the development of Alzheimer's disease and related disorders, directing particular attention to biomarkers and experimental new treatments. They also continue to search for genetic risk factors underlying Alzheimer's disease (AD). Their main priorities are to find causes, effective treatments, and prevention strategies. Their investigators also are partnering with other Alzheimer's Centers across the country to evaluate promising new medications and other treatments for AD. The ultimate goal of their basic and clinical studies is to improve patient care and function, and improve the quality of life for both the patient and the caregiver. ADRC Cores: * Administration * Clinical Core * Satellite Core * Data Management & Biostatistics * Neuropathology Core * Education & Information Transfer * Genetics

Proper citation: University of Washington Alzheimers Disease Research Center (RRID:SCR_008814) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/educational-resources/neuroscience-and-psychiatry/neuroscience-and-psychiatry-module-2-fear-safety-anxiety-and-anxiety-disorders.shtml

This is the second in a series of modules on neuroscience and psychiatry. This module describes neuroscience research on animal models of fear that informed human studies of fear/safety, anxiety and anxiety disorders. This model helps shed light on the symptoms of PTSD and lead to the development of a novel treatment that has been successful in research studies for several anxiety disorders.

Proper citation: Neuroscience and Psychiatry Module 2: Fear/Safety Anxiety and Anxiety Disorders (RRID:SCR_008843) Copy   

•   Source: SciCrunch Registry

http://www.linkrbrain.eu

An online tool for managing and viewing datasets. Data can be viewed in 2D or 3D with activation points as points clouds or projections on the cortex surface. Data can be imported as a NIfTI file or a list of activation peaks and results can be exported as a PDF file.

Proper citation: linkRbrain (RRID:SCR_014562) Copy   

•   Source: SciCrunch Registry

https://gemini.readthedocs.io/en/latest/

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

Proper citation: GEMINI (RRID:SCR_014819) Copy   

•   Source: SciCrunch Registry

http://humanconnectome.org/consortia/

Project to map the neural pathways that underlie human brain function for several modalities of neuroimaging data including fMRI. The purpose of the Project is to acquire and share data about the structural and functional connectivity of the human brain. It will greatly advance the capabilities for imaging and analyzing brain connections, resulting in improved sensitivity, resolution, and utility, thereby accelerating progress in the emerging field of human connectomics. Altogether, the Human Connectome Project will lead to major advances in the understanding of what makes us uniquely human and will set the stage for future studies of abnormal brain circuits in many neurological and psychiatric disorders. The sixteen institutes and centers of the NIH Blueprint for Neuroscience have funded two major grants that will take complementary approaches to deciphering the brain's amazingly complex wiring diagram. An 11-institution consortium led by Washington University in St. Louis and the University of Minnesota received a 5-year grant to enable development and utilization of advanced Magnetic Resonance Imaging (MRI) methods to chart brain circuitry. A consortium led by Massachusetts General Hospital and the University of California at Los Angeles received a grant to enable building and refining a next-generation 3T MR scanner that improves the quality and spatial resolution with which brain connectivity data can be acquired at this field strength.

Proper citation: NIH Human Connectome Project (RRID:SCR_006942) Copy   

•   Source: SciCrunch Registry

http://pga.mgh.harvard.edu/primerbank/

Database of human and mouse primer pairs for gene expression analysis by polymerase chain reaction (PCR) and quantitative PCR (qPCR). A total of 306,800 primers covering most known human and mouse genes can be accessed from the PrimerBank database, together with information on these primers such as T(m), location on the transcript and amplicon size. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. All primers in PrimerBank were carefully designed to ensure gene specificity. All experimental validation data for mouse primers are available from PrimerBank. You can submit your primers. They will be added to the database once they are properly QCd.

Proper citation: PrimerBank (RRID:SCR_006898) Copy   

•   Source: SciCrunch Registry

http://www.alttox.org/

A website dedicated to advancing non-animal methods of toxicity testing, both to better protect the health of humans, animals, and the environment and to reduce the numbers and suffering of animals used in current toxicology assessments. The website is designed to encourage the exchange of technical and policy information on in vitro and in silico methods for all types of toxicity tests. The AltTox Forum is a message board for the AltTox community to use for posting news, information, and perspectives as well as encouraging feedback and commentary. This online community is intended to foster progress internationally in the development, validation, and acceptance of in vitro methods, with the goal of decreasing our reliance on animal-based safety testing. The Forum is moderated by a group of internationally-recognized subject matter experts. The Way Forward invited commentaries, which are posted in the TTRC, are opinion pieces written by experts in each relevant subfield. These essays are meant to help chart the course for future developments by advancing opportunities to overcome challenges and barriers to progress. Stakeholders are invited to comment on these essays in The AltTox Forum. AltTox users are encouraged to contribute to the website and interact with other users in several ways, including: :- Participating in the online forum :- Providing invited expert commentaries :- Suggesting or submitting content, events, monthly features, data, and graphics :- Providing feedback through the Website Feedback surve To encourage objectivity, the website content is overseen by an editorial board of distinguished subject matter experts.

Proper citation: AltTox: Non-animal Methods for Toxicity Testing (RRID:SCR_007212) Copy   

•   Source: SciCrunch Registry

http://humancyc.org/

The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version.

Proper citation: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) Copy   

•   Source: SciCrunch Registry

http://hearingimpairment.jax.org/screening.html

The fairly common occurrence of hearing-loss or deafness in both humans and mice, and the anatomical and functional similarities of their inner ears, attest to the potential of mice as models to study hereditary hearing loss. Hundreds of standard inbred, recombinant inbred, and congenic strains are maintained at The Jackson Laboratory, as well as hundreds of inbred strains with spontaneous or induced mutations. To assess hearing impairment in inbred and mutant strains of mice we measure auditory-evoked brainstem response (ABR) thresholds.

Proper citation: The Jackson Laboratory Hearing Research Program (RRID:SCR_007196) Copy   

•   Source: SciCrunch Registry