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http://hendrix.imm.dtu.dk/software/lyngby/

Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files.

Proper citation: Lyngby (RRID:SCR_007143) Copy   

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http://www.bmu.psychiatry.cam.ac.uk/software/

Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution.

Proper citation: Cambridge Brain Activation (RRID:SCR_007109) Copy   

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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   

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http://www.cidr.jhmi.edu/

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   

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https://bams1.org/

Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions.

Proper citation: Brain Architecture Management System (RRID:SCR_007251) Copy   

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http://jaxmice.jax.org/list/ra1642.html

Produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The impetus for the program resulted from the recognition that: * The value of genomic data would remain limited unless more information about the functionality of its individual components became available. * The task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e.N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. The resulting mutant mouse lines have been available to the scientific community for the last five years and over 700 NMF mice have been sent to interested investigators for research; these mutant mouse lines will remain available as frozen embryos (which can be re-derived on request) and can be ordered through the JAX customer service at 1-800-422-6423 (or 207-288-5845). The results of the work of the Neuroscience Mutagenesis Facility and that of two other neurogenesis centers, i.e. The Neurogenomics Project at Northwestern University, and the Neuromutagenesis Project of the Tennessee Mouse Genome Consortium, can also be seen at Neuromice.org, a common web site of these three research centers; in addition, information about all mutants produced by these groups has been recorded in MGI.

Proper citation: JAX Neuroscience Mutagenesis Facility (RRID:SCR_007437) Copy   

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http://www.nimh.nih.gov/funding/clinical-trials-for-researchers/practical/stard/index.shtml

A nationwide public health clinical trial conducted to determine the effectiveness of different treatments for people with major depression, in both primary and specialty care settings, who have not responded to initial treatment with an antidepressant. This is the largest and longest study ever done to evaluate depression treatment. The study is completed and no longer recruiting participants. Each of the four levels of the study tested a different medication or medication combination. The primary goal of each level was to determine if the treatment used during that level could adequately treat participants����?? major depressive disorder (MDD). Those who did not become symptom-free could proceed to the next level of treatment. The design of the STAR*D study reflects what is done in clinical practice because it allowed study participants to choose certain treatment strategies most acceptable to them and limited the randomization of each participant only to his/her range of acceptable treatment strategies. No prior studies have evaluated the different treatment strategies in broadly defined participant groups treated in diverse care settings. Over a seven-year period, the study enrolled 4,041 outpatients, ages 18-75 years, from 41 clinical sites around the country, which included both specialty care settings and primary medical care settings. Participants represented a broad range of ethnic and socioeconomic groups. All participants were diagnosed with MDD, were already seeking care at one of these sites, and were referred to the trial by their doctors. * STAR*D Study Medications: Citalopram (Celexa), Sertraline (Zoloft), Bupropion SR (Wellbutrin SR), Venlafaxine XR (Effexor XR), Buspirone (BuSpar), Mirtazapine (Remeron), Triiodothyronine (T3) (Cytomel), Nortriptyline (Pamelor, Aventyl), Tranylcypromine (Parnate), Lithium (Eskalith, Lithobid) *STAR*D Talk Therapy:Cognitive Therapy

Proper citation: Sequenced Treatment Alternatives to Relieve Depression Study (RRID:SCR_008051) Copy   

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http://national_databank.mclean.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. A publicly accessible data repository to provide neuroscience investigators with secure access to cohort collections. The Databank collects and disseminates gene expression data from microarray experiments on brain tissue samples, along with diagnostic results from postmortem studies of neurological and psychiatric disorders. All of the data that is derived from studies of the HBTRC collection is being incorporated into the National Brain Databank. This data is available to the general public, although strict precautions are undertaken to maintain the confidentiality of the brain donors and their family members. The system is designed to incorporate MIAME and MAGE-ML based microarray data sharing standards. Data from various types of studies conducted on brain tissue in the HBTRC collection will be available from studies using different technologies, such as gene expression profiling, quantitative RT-PCR, situ hybridization, and immunocytochemistry and will have the potential for providing powerful insights into the subregional and cellular distribution of genes and/or proteins in different brain regions and eventually in specific subregions and cellular subtypes.

Proper citation: National Brain Databank (RRID:SCR_003606) Copy   

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

A portal to educational resources.

Proper citation: NIMH Educational Resources (RRID:SCR_004045) Copy   

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http://brainarchitecture.org/

Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts

Proper citation: Brain Architecture Project (RRID:SCR_004283) Copy   

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http://yogo.msu.montana.edu/

A set of software tools created to rapidly build scientific data-management applications. These applications will enhance the process of data annotation, analysis, and web publication. The system provides a set of easy-to-use software tools for data sharing by the scientific community. It enables researchers to build their own custom-designed data management systems. The problem of scientific data management rests on several challenges. These include flexible data storage, a way to share the stored data, tools to curate the data, and history of the data to show provenance. The Yogo Framework gives you the ability to build scientific data management applications that address all of these challenges. The Yogo software is being developed as part of the NeuroSys project. All tools created as part of the Yogo Data Management Framework are open source and released under an OSI approved license.

Proper citation: Yogo Data Management System (RRID:SCR_004239) Copy   

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http://headit.ucsd.edu

Platform for sharing, download, and re-analysis or meta-analysis of sophisticated, fully annotated, human electrophysiological data sets. It uses EEG Study Schema (ESS) files to provide task, data collection, and subject metadata, including Hierarchical Event Descriptor (HED) tag descriptions of all identified experimental events. Visospatial task data also available from, http://sccn.ucsd.edu/eeglab/data/headit.html: A 238-channel, single-subject EEG data set recorded at the Swartz Center, UCSD, by Arnaud Delorme, Julie Onton, and Scott Makeig is al.

Proper citation: HeadIT (RRID:SCR_005657) Copy   

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http://www.matrics.ucla.edu/index.html

Cognitive deficits -- including impairments in areas such as memory, attention, and executive function -- are a major determinant and predictor of long-term disability in schizophrenia. Unfortunately, available antipsychotic medications are relatively ineffective in improving cognition. Scientific discoveries during the past decade suggest that there may be opportunities for developing medications that will be effective for improving cognition in schizophrenia. The NIMH has identified obstacles that are likely to interfere with the development of pharmacological agents for treating cognition in schizophrenia. These include: (1) a lack of a consensus as to how cognition in schizophrenia should be measured; (2) differing opinions as to the pharmacological approaches that are most promising; (3) challenges in clinical trial design; (4) concerns in the pharmaceutical industry regarding the US Food and Drug Administration''s (FDA) approaches to drug approval for this indication; and (5) issues in developing a research infrastructure that can carry out clinical trials of promising drugs. The MATRICS program will bring together representatives of academia, industry, and government in a consensus process for addressing all of these obstacles. Specific goals of the NIMH MATRICS are: * To catalyze regulatory acceptance of cognition in schizophrenia as a target for drug registration. * To promote development of novel compounds to enhance cognition in schizophrenia. * Leverage economic research power of industry to focus on important but neglected clinical targets. * Identify lead compounds and if deemed feasible, support human proof of concept trials for cognition in schizophrenia.

Proper citation: MATRICS - Measurement And Treatment Research to Improve Cognition in Schizophrenia (RRID:SCR_005644) Copy   

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http://www.nimh.nih.gov/about/advisory-boards-and-groups/namhc/reports/mri-research-safety-ethics.pdf

NIMH recognizes the need to consider safety and ethical issues related to both the administration of MR (magnetic resonance) facilities and the use of these facilities for research. This document summarizes the points to consider discussed by the National Advisory Mental Health Council (NAMHC) Workgroup. Examples of safe and ethical practices are discussed in relation to several issues. These examples are intended to be illustrative and should not be interpreted as an exhaustive or exclusive list. This document was presented to the full NIMH Council on September 15, 2006 and approved unanimously. By making the points to consider document available publicly, NIMH intends to provide a resource for researchers and institutions that use MRI in research. The agenda was organized into six topics, which provide the organization for the points to consider that follow: A. MRI screening B. Training, operating, and emergency procedures C. Physical facilities D. Scanning/participant health variables E. Context- Specific Considerations: University vs. medical settings F. Additional data needs and updating The NIMH believes that investigators, institutions and facilities can use this document as a resource for the development, administration, evaluation, and use of MRI research facilities.

Proper citation: MRI Research Safety and Ethics (RRID:SCR_005642) 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://www.nimh.nih.gov/research-funding/training/index.shtml

A portal to the National Institute of Mental Health''s Research Training, Career Development, and Related Programs. Topics cover Resources for Applicants, Individual Fellowship Programs, Individual Career Development Programs, Institutional Training Programs, Additional Career Development/Training-Related Opportunities, and Training Programs to Increase Workforce Diversity.

Proper citation: NIMH Resources for Research Training and Career Development (RRID:SCR_005624) Copy   

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http://www.patternlabforproteomics.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible

Proper citation: GOEx - Gene Ontology Explorer (RRID:SCR_005779) Copy   

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http://www.jneurosci.org/supplemental/18/12/4570/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest.

Proper citation: Hippocampal Slice Wave Animations (RRID:SCR_008372) Copy   

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http://grey.colorado.edu/emergent

emergent is a comprehensive, full-featured neural network simulator that allows for the creation and analysis of complex, sophisticated models of the brain in the world. With an emphasis on qualitative analysis and teaching, it also supports the workflow of professional neural network researchers. Its high level drag-and-drop programming interface, built on top of a scripting language that has full introspective access to all aspects of networks and the software itself, allows one to write programs that seamlessly weave together the training of a network and evolution of its environment without ever typing out a line of code. Networks and all of their state variables are visually inspected in 3d, allowing for a quick visual regression of network dynamics and robot behavior. This same 3d world sports a highly accurate Newtonian physics simulation, allowing you to create rich robotics simulations (for example, a car). As a direct descendant of PDP (1986) and PDP (1999), emergent has been in development for decades. In the most recent versions available strive to distill it down to its essential elements. Those that take the time to learn the best practices will be rewarded with the ability to create and understand the most complicated neural models ever published.

Proper citation: Emergent (RRID:SCR_008500) Copy   

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http://www.nimh.nih.gov/educational-resources/brains-inner-workings/the-brains-inner-workings-activities-for-grades-9-through-12.shtml

This comprehensive free collection of multimedia resources and inquiry-based activities tied to the National Science Education Standards help teachers and students learn about the structure, function and cognitive aspects of the human brain. The packet includes a teacher's manual, student manual, DVD of videos, and a CDROM of accompanying materials.

Proper citation: Brain's Inner Workings: Activities for Grades 9 through 12 (RRID:SCR_008842) Copy   

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