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http://learn.genetics.utah.edu/content/addiction/

A physiologic and molecular look at drug addiction involving many factors including: basic neurobiology, a scientific examination of drug action in the brain, the role of genetics in addiction, and ethical considerations. Designed to be used by students, teachers and members of the public, the materials meet selected US education standards for science and health. Drug addiction is a chronic disease characterized by changes in the brain which result in a compulsive desire to use a drug. A combination of many factors including genetics, environment and behavior influence a person's addiction risk, making it an incredibly complicated disease. The new science of addiction considers all of these factors - from biology to family - to unravel the complexities of the addicted brain. * Natural Reward Pathways Exist in the Brain: The reward pathway is responsible for driving our feelings of motivation, reward and behavior. * Drugs Alter the Brain's Reward Pathway: Drugs work over time to change the reward pathway and affect the entire brain, resulting in addiction. * Genetics Is An Important Factor In Addiction: Genetic susceptibility to addiction is the result of the interaction of many genes. * Timing and Circumstances Influence Addiction: If you use drugs when you are an adolescent, you are more likely to develop lifetime addiction. An individual's social environment also influences addiction risk. * Challenges and Issues in Addiction: Addiction impacts society with many ethical, legal and social issues.

Proper citation: New Science of Addiction: Genetics and the Brain (RRID:SCR_002770) Copy   

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http://www.cnl.salk.edu/

The long range goal of this laboratory is to understand the computational resources of brains from the biophysical to the systems levels. The central issues being addressed are how dendrites integrate synaptic signals in neurons, how networks of neurons generate dynamical patterns of activity, how sensory information is represented in the cerebral cortex, how memory representations are formed and consolidated during sleep, and how visuo-motor transformations are adaptively organized. Additionally, new techniques have been developed for modeling cell signaling using Monte Carlo methods (MCell) and the blind separation of brain imaging data into functionally independent components (ICA).

Proper citation: Computational Neurobiology Laboratory at the Salk Institute (RRID:SCR_002809) Copy   

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http://www.cnsforum.com/educationalresources/imagebank/

A collection of downloadable central nervous system (CNS) images for teaching, presentations, articles, and other purposes. The following major categories of images are as follows: Brain anatomy, Brain physiology, Anxiety, Depression, Schizophrenia, Dementia, Parkinson's disease, Stroke, and Others.

Proper citation: CNSforum: Image Bank (RRID:SCR_002718) Copy   

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http://www.rbwb.org/

The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States.

Proper citation: Rodent Brain WorkBench (RRID:SCR_002727) Copy   

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http://sumsdb.wustl.edu/sums/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

Proper citation: SumsDB (RRID:SCR_002759) Copy   

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http://sncid.stanleyresearch.org/

A database of 1749 neuropathological markers measured in 12 different brain regions from 60 brains in the Consortium Collection from the Stanley Medical Research Institute combined with microarray data and statistical tools. Fifteen brains each are from patients diagnosed with schizophrenia, bipolar disorder, or major depression, and unaffected controls. The four groups are matched by age, sex, race, postmortem interval, pH, side of brain, and mRNA quality. A Repository of raw data is also included. Users must register for access.

Proper citation: Stanley Neuropathology Consortium Integrative Database (RRID:SCR_002749) Copy   

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http://www.mrn.org/

Non-profit organization focused on imaging technology that is dedicated to advancing the diagnosis and treatment of mental illness and brain injury. MRN consists of an interdisciplinary association of scientists located at universities, national laboratories and research centers around the world and is focused on imaging technology and its emergence as an integral element of neuroscience investigation. The MRNs initial plan called for the building of state-of-the-art magnetic resonance imaging (MRI) and magnetoencephalogram (MEG) neuroimaging systems to be applied to studies of mental illness. This important task was carried out by Minds initial collaborators: Massachusetts General Hospitals Martinos Biomedical Imaging Center (Harvard and MIT), the University of Minnesota, the University of New Mexico, and Los Alamos National Laboratory. Since both the Network and the mission have expanded beyond building neuroimaging tools, a comprehensive understanding of mental illness and more fundamental and systematic understanding of the brain, is possible. The MRN Mobile Imaging system is a custom designed one-of-a-kind facility.

Proper citation: Mind Research Network (RRID:SCR_002925) Copy   

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http://www.fmrib.ox.ac.uk/fsl/

Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.

Proper citation: FSL (RRID:SCR_002823) Copy   

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http://studyforrest.org

An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data.

Proper citation: studyforrest.org (RRID:SCR_003112) Copy   

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http://www.fly-trap.org/

Flytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use.

Proper citation: flytrap (RRID:SCR_003075) Copy   

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http://brainmap.org/

A community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results

Proper citation: brainmap.org (RRID:SCR_003069) Copy   

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http://www.genepaint.org

Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution.

Proper citation: GenePaint (RRID:SCR_003015) Copy   

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http://briansimulator.org/

Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator.

Proper citation: Brian Simulator (RRID:SCR_002998) Copy   

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http://developingmouse.brain-map.org/

Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself.

Proper citation: Allen Developing Mouse Brain Atlas (RRID:SCR_002990) Copy   

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http://braininfo.rprc.washington.edu

Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.

Proper citation: BrainInfo (RRID:SCR_003142) Copy   

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http://science.education.nih.gov/home2.nsf/feature/index.htm

The NIH Office of Science Education (OSE) coordinates science education activities at the NIH and develops and sponsors science education projects in house. These programs serve elementary, secondary, and college students and teachers and the public. Activities * Develop curriculum supplements and other educational materials related to medicine and research through collaborations with scientific experts at NIH * Maintain a website as a central source of information about NIH science education resources * Establish national model programs in public science education, such as the NIH Mini-Med School and Science in the Cinema * Promote science education reform as outlined in the National Science Education Standards and related guidelines The OSE was established in 1991 within the Office of Science Policy of the Office of the Director of the National Institutes of Health. The NIH is the world''s foremost biomedical research center and the U.S. federal government''s focal point for such research. It is one of the components of the Department of Health and Human Services (HHS). The Office of Science Education (OSE) plans, develops, and coordinates a comprehensive science education program to strengthen and enhance efforts of the NIH to attract young people to biomedical and behavioral science careers and to improve science literacy in both adults and children. The function of the Office is as follows: (1) develops, supports, and directs new program initiatives at all levels with special emphasis on targeting students in grades kindergarten to 16, their educators and parents, and the general public; (2) advises NIH leadership on science education issues; (3) examines and evaluates research and emerging trends in science education and literacy for policy making; (4) works closely with the NIH extramural, intramural, women''s health, laboratory animal research, and minority program offices on science education special issues and programs to ensure coordination of NIH efforts; (5) works with NIH institutes, centers, and divisions to enhance communication of science education activities; and (6) works cooperatively with other public- and private-sector organizations to develop and coordinate activities.

Proper citation: NIH Office of Science Education (RRID:SCR_005603) Copy   

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http://www.nimh.nih.gov/educational-resources/brain-basics/brain-basics.shtml

Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, and ongoing research that helps us better understand and treat disorders. Mental disorders are common. You may have a friend, colleague, or relative with a mental disorder, or perhaps you have experienced one yourself at some point. Such disorders include depression, anxiety disorders, bipolar disorder, attention deficit hyperactivity disorder (ADHD), and many others. Some people who develop a mental illness may recover completely; others may have repeated episodes of illness with relatively stable periods in between. Still others live with symptoms of mental illness every day. They can be moderate, or serious and cause severe disability. Through research, we know that mental disorders are brain disorders. Evidence shows that they can be related to changes in the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions of cells in the body, the results can affect many aspects of life. Scientists are continually learning more about how the brain grows and works in healthy people, and how normal brain development and function can go awry, leading to mental illnesses. Brain Basics will introduce you to some of this science, such as: * How the brain develops * How genes and the environment affect the brain * The basic structure of the brain * How different parts of the brain communicate and work with each other * How changes in the brain can lead to mental disorders, such as depression.

Proper citation: Brain Basics (RRID:SCR_005606) Copy   

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http://brainstars.org

BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API.

Proper citation: BrainStars (RRID:SCR_005810) Copy   

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http://vibez.informatik.uni-freiburg.de/

An imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with precisely aligned gene expression patterns (1����m^3 resolution), an anatomical atlas, and a software. This software creates high-quality data sets by fusing multiple confocal microscopic image stacks, and aligns these data sets to the standard larva. The ViBE-Z database and atlas are stored in HDF5 file format. They are freely available for download. ViBE-Z provides a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality through fusion and attenuation correction of multiple confocal microscope stacks per specimen and uses a fluorescent stain of cell nuclei for image registration. It automatically detects 14 predefined anatomical landmarks for aligning new data with the reference brain. ViBE-Z performs colocalization analysis in expression databases for anatomical domains or subdomains defined by any specific pattern. The ViBE-Z database, atlas and software are provided via a web interface.

Proper citation: ViBE-Z (RRID:SCR_005895) Copy   

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https://gene-atlas.brainminds.jp/

Database of gene expression in the marmoset brain.Comparative anatomy of marmoset and mouse cortex from genomic expression. Atlas comparing brain of neonatal marmoset with mouse using in situ hybridization.

Proper citation: Expression Atlas of the Marmoset (RRID:SCR_005760) Copy   

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