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Centre of Excellence in Vision Science that brings together major vision research programs at the The Australian National University with cognate programs at the Universities of Queensland, Sydney and Western Australia. The research is focused on unravelling the cellular basis of visual sensing and processing; on revealing the algorithms that underlie the visual control of behavior and perception; and on discovering the cellular mechanisms that make the eye and retina stable, and whose breakdown causes blindness.
Proper citation: ARC Centre of Excellence in Vision Science (RRID:SCR_003196) Copy
http://www.etsu.edu/com/pharmacology/default.aspx
Faculty members of our Department are actively engaged in delivering outstanding teaching to undergraduate students, graduate students, medical students, and residents. Our Doctor of Philosophy (graduate) students matriculate to Pharmacology through the Biomedical Sciences Graduate Program at the Quillen College of Medicine. Students pursuing Master of Science and Doctor of Philosophy degrees may pursue a focus in Toxicology. Our faculty members are trained in several medical disciplines and our research applies methodological approaches that span molecular biology, cellular biology, systems biology, and human biology and pathology. Through research, our department strives to understand human disease pathology and use this understanding to develop new therapeutic entities (e.g. drugs) for the treatment of major human diseases. The primary foci of department research efforts are cardiovascular and neuropsychiatric diseases, although other areas of interest and activity exist. Our laboratories are funded by the National Institutes of Health, American Heart Association, the American Foundation for Suicide Prevention and a variety of other agencies and sources.
Proper citation: East Tennessee State University, Department of Pharmacology (RRID:SCR_003350) Copy
A social writing platform, free for education, to easily create a classroom workspace where teacher and students can communicate and work on writing projects alone or in teams. Rich assessment tools give the power to measure student contribution and engagement in real-time. Wikispaces Classroom works great on modern browsers, tablets, and phones. For a fee it is also available to non-educators including companies, organizations, universities, groups, etc.
Proper citation: Wikispaces (RRID:SCR_003228) Copy
http://resexomedb.bioinf-dz.org/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. An online catalog for whole-exome sequencing (WES) results including mutations and gene-disease associations identified by WES. It is browsable and searchable by mutation, gene, study or publication. In addition, it centralizes all publications, software, platforms related to exome / whole genome sequencing.
Proper citation: resExomeDB (RRID:SCR_003224) Copy
The major and minor in Neuroscience at Duke University was approved by the Arts and Sciences Council of Trinity College of Arts and Sciences on April 9, 2009. The program offers three academic plans: Bachelor of Science (B.S.) degree in Neuroscience, Bachelor of Arts (A.B.) degree in Neuroscience, and a Minor in Neuroscience. Although Neuroscience is a new major/minor, there is a rich and long-standing tradition of excellence in undergraduate neuroscience research and education at Duke. Groups of faculty in the Department of Psychology and Neuroscience and the Department of Biology, as well as the Department of Neurobiology in the Duke University School of Medicine, have been especially engaged in teaching neuroscience in undergraduate classes and hosting independent study projects in their research laboratories. Building upon this broad foundation, the new Undergraduate Studies in Neuroscience program is a truly interdisciplinary experience reflecting the diverse sources of knowledge that advance our understanding of the brain sciences. Undergraduate Studies in Neuroscience is a unique collaboration among many Departments and Schools , with administrative support provided by Trinity College of Arts and Sciences and the Duke Institute for Brain Sciences.
Proper citation: Duke University Trinity College of Arts and Sciences Undergraduate Neuroscience (RRID:SCR_003345) Copy
A software application for such tasks as photo retouching, image composition and image authoring. It has many capabilities such as it can be used as a simple paint program, an expert quality photo retouching program, an online batch processing system, a mass production image renderer, an image format converter, etc. GIMP is expandable and extensible and designed to be augmented with plug-ins and extensions. The advanced scripting interface allows everything from the simplest task to the most complex image manipulation procedures to be easily scripted.
Proper citation: GNU Image Manipulation Program (RRID:SCR_003182) Copy
Interactive repository of mutations and other allelic variations of the genes involved in the DNA repair disorders, Xeroderma Pigmentosum (XP), Cockayne Syndrome (CS), Trichothiodystrophy (TTD), and other UV-sensitivity disorders. Any omitted data or new data may be submitted by using the on-line data submission form. There is a message board system to support discussions amongst those interested in XP and DNA Repair. RESOURCES * Educational module of the molecular biology of Nucleotide Excision Repair * Introduction to the DNA Repair disorders (XP, CS, TTD, UVs) * Background on each of the XP genes * A searchable database of mutations and sequence variations for the XP genes * Contact point for the submission of new mutation data * Discussion Forums and a Guest Book * Web Links to Additional Resources
Proper citation: Allelic Variations of The XP Genes (RRID:SCR_003376) Copy
https://github.com/arq5x/lumpy-sv/
Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed.
Proper citation: LUMPY (RRID:SCR_003253) Copy
http://sig.biostr.washington.edu/projects/fm/
A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model.
Proper citation: FMA (RRID:SCR_003379) Copy
A hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. The tools and resources include a repository of interactive applets, computational and graphing tools, instructional and course materials. The core SOCR educational and computational components include the following suite of web-based Java applets: * Distributions (interactive graphs and calculators) * Experiments (virtual computer-generated games and processes) * Analyses (collection of common web-accessible tools for statistical data analysis) * Games (interfaces and simulations to real-life processes) * Modeler (tools for distribution, polynomial and spectral model-fitting and simulation) * Graphs, Plots and Charts (comprehensive web-based tools for exploratory data analysis), * Additional Tools (other statistical tools and resources) * SOCR Java-based Statistical Computing Libraries * SOCR Wiki (collaborative Wiki resource) * Educational Materials and Hands-on Activities (varieties of SOCR educational materials), * SOCR Statistical Consulting In addition, SOCR provides a suite of tools for volume-based statistical mapping (http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_AnalysesCommandLine) via command-line execution and via the LONI Pipeline workflows (http://www.nitrc.org/projects/pipeline). Course instructors and teachers will find the SOCR class notes and interactive tools useful for student motivation, concept demonstrations and for enhancing their technology based pedagogical approaches to any study of variation and uncertainty. Students and trainees may find the SOCR class notes, analyses, computational and graphing tools extremely useful in their learning/practicing pursuits. Model developers, software programmers and other engineering, biomedical and applied researchers may find the light-weight plug-in oriented SOCR computational libraries and infrastructure useful in their algorithm designs and research efforts. The three types of SOCR resources are: * Interactive Java applets: these include a number of different applets, simulations, demonstrations, virtual experiments, tools for data visualization and analysis, etc. All applets require a Java-enabled browser (if you see a blank screen, see the SOCR Feedback to find out how to configure your browser). * Instructional Resources: these include data, electronic textbooks, tutorials, etc. * Learning Activities: these include various interactive hands-on activities. * SOCR Video Tutorials (including general and tool-specific screencasts).
Proper citation: Statistics Online Computational Resource (RRID:SCR_003378) Copy
Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.
Proper citation: Proteomics Identifications (PRIDE) (RRID:SCR_003411) Copy
The Institute for Sensory Research (ISR) defines itself as a world class research center dedicated to the discovery and application of knowledge of the sensory systems. Integration of engineering, life, and physical sciences, combining rigorous experimental methodology with mathematical analysis is stressed. Our multidisciplinary approach to bioengineering, sensory neuroscience, graduate, and undergraduate education, makes ISR a unique academic research center. At ISR, we study sensory systems, our gateways to the world. Our ears, eyes, skin, and mouth are channels through which we experience sound, light, texture, etc. These are functions that we usually take for granted until problems arise. Engineers, scientists, and students at ISR investigate both the basic sensory principles used by the brain, and also how the sensory systems can be best utilized, modified, and repaired if necessary to better communicate with our surroundings and with one another. In addition to basic research in hearing, touch, vision, and oro-facial biomechanics, recent projects include the design and testing of sensory-aid devices such as cochlear implants, hearing aids, ear protectors, and tactile aids for the visually and hearing impaired. Additional projects involve visual-depth perception, chewing and swallowing, oto-acoustic emissions, and personal care products such as oral rinses and skin lotions. Research * Auditory * Somatosensory * Vision
Proper citation: Syracuse University; Institute for Sensory Research (RRID:SCR_003377) Copy
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Main_Page
Laboratory portal, including software, web-based tools, databases and data sets, related to their research that focuses on the development and application of biophysical and bioinformatics methods aimed at understanding the structural and energetic origins of protein-protein, protein-nucleic acid, and protein-membrane interactions. Their work includes fundamental theoretical research, the development of software tools, and applications to problems of biological importance. In this regard they maintain an active collaborative computational and experimental research program on the molecular basis of cell-cell adhesion. Other problems of current interest include protein structure prediction, the organization of protein sequence/structure space, the prediction of protein function based on protein structure, the structural origins of specificity in protein-DNA interactions, RNA function and, more generally, the electrostatic properties of biological macromolecules.
Proper citation: Honig Lab (RRID:SCR_003410) Copy
https://www.marquette.edu/grad/programs-neuroscience.php
Neuroscience specialization in Graduate Program in Biological Sciences at Marquette University brings together researchers from Departments of Biological and Biomedical Sciences at Marquette to offer quality graduate education in the field of neuroscience with the goal of training students for careers as neuroscience researchers and educators. The specialization is for students who wish to pursue a Ph.D. degree. The collaborative and multi-disciplinary neuroscience research environment at Marquette is supported by the Integrative Neuroscience Research Center (INRC), a consortium of researchers committed to advancing neuroscience research and education at Marquette. The Neuroscience Graduate Program offers the opportunity to conduct research in a collaborative, intellectually rigorous environment, with access to the most modern research tools.
Proper citation: Marquette University, Neuroscience (RRID:SCR_003404) Copy
http://www.ichip.de/software/SplicingCompass.html
Software for detection of differential splicing between two different conditions using RNA-Seq data.
Proper citation: SplicingCompass (RRID:SCR_003249) Copy
https://cabig.nci.nih.gov/tools/caTRIP
THIS RESOURCE IS NO LONGER IN SERVICE documented June 4, 2013. Allows users to query across a number of caBIG data services, join on common data elements (CDEs), and view results in a user-friendly interface. With an initial focus on enabling outcomes analysis, caTRIP allows clinicians to query across data from existing patients with similar characteristics to find treatments that were administered with success. In doing so, caTRIP can help inform treatment and improve patient care, as well as enable the searching of available tumor tissue, enable locating patients for clinical trials, and enable investigating the association between multiple predictors and their corresponding outcomes such as survival caTRIP relies on the vast array of open source caBIG applications, including: * Tumor Registry, a clinical system that is used to collect endpoint data * cancer Text Information Extraction System (caTIES), a locator of tissue resources that works via the extraction of clinical information from free text surgical pathology reports. while using controlled terminologies to populate caBIG-compliant data structures * caTissue CORE, a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation * Cancer Annotation Engine (CAE), a system for storing and searching pathology annotations * caIntegrator, a tool for storing, querying, and analyzing translational data, including SNP data Requires Java installation and network connectivity.
Proper citation: caTRIP (RRID:SCR_003409) Copy
Faculty of the Department of Neuroscience participate in the teaching of courses in the Interdisciplinary Program in Neuroscience and the School of Medicine. A Ph.D. in Neuroscience is offered through the Interdisciplinary Program in Neuroscience. Support for graduate training is offered through the Department, the research grants of individual faculty, as well as through three NIH training grants directed by Neuroscience faculty. * Training in Recovery of Function after CNS Injury. Program Director: Barbara S. Bregman, Ph.D. * Training Program in Drug Abuse. Program Director: Barbara S. Bayer, Ph.D. * Training in Neural Injury and Plasticity. Program Director: Jean R. Wrathall, Ph.D. Scientists in the Department of Neuroscience participate in a wide array of research activities with a focus on understanding both the normal and injured nervous system. The theme of neuroplasticity characterizes much of the research in the Department. We study neuroplasticity during normal development and in the adult in response to activity (e.g., learning) or drugs. Our research is also focused on studying the plasticity that ensues after traumatic (such as spinal cord injury) or ischemic damage to the nervous system and over the course of developmental or neurodegenerative diseases (such as Specific Language Impairment, autism, or Parkinson's and Alzheimer's Diseases). The specific research interests of each of the principal investigators falls under four broad subheadings: *CNS disorders ( Faden, Mocchetti, Rebeck, Riesenhuber,Ullman) *Cognitive/Computational (Riesenhuber, Ullman) *Development, Regeneration and recovery of function after injury (Bregman, Faden, Kromer, Ullman, Wrathall) *Neuroimmunology and Drugs of Abuse (Bayer, Faden, Kromer, Mocchetti) Under this common theme, a variety of diverse techniques and models are employed by the faculty. They range from molecular studies of gene function to studies on humans using Event-Related Potentials (ERPs) and functional MRI. Experimental models include cell culture systems, rodent genetic and experimental models of nervous system injury and disorders, as well as the use of computer simulations to understand higher cortical processing.
Proper citation: Georgetown, Neuroscience (RRID:SCR_003363) Copy
Child language component of TalkBank system. TalkBank is system for sharing and studying conversational interactions. Includes software developed for speech recognition and analysis as well as behavior recognition. Database contains transcript and media data collected from conversations between young children and their playmates and caretakers. Conversations with older children and adults are available from TalkBank. All of data is transcribed in CHAT and CA/CHAT formats.
Proper citation: Child Language Data Exchange System (CHILDES) (RRID:SCR_003241) Copy
Catalog containing information about 547 biological pathway related resources and molecular interaction related resources. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.
Proper citation: PathGuide: the pathway resource list (RRID:SCR_003248) Copy
Portal of geological information, including geology maps, reports, and GIS datasets, to help with the exploration, development and conservation of Alberta's resources.
Proper citation: Alberta Geological Survey (RRID:SCR_003402) Copy
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