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http://tela.biostr.washington.edu/cgi-bin/repos/bmap_repo/main-menu.pl

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. An experiment management system for researchers studying language organization in the brain. Data from thirteen patients are available as a public demo. Language Map EMS

Proper citation: Language Map Experiment Management System (RRID:SCR_004562) Copy   

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http://www.scandb.org/newinterface/about.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SCAN (RRID:SCR_005185) Copy   

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http://pdsp.med.unc.edu/

This service provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters. Bryan Roth MD, PhD (University of North Carolina Chapel Hill) will perform pharmacological and functional screening of novel compounds as a contractor to NIMH. Screening of compounds is provided to qualified academic investigators at no cost. * Assays using for a large number of cloned human or rodent cDNAs for CNS receptors, channels and transporters. For a list of current receptors/transporters go to:clones.html * Ki determinations * Functional assays to determine effects on second messenger systems, channel activity and transporter function * Cloned receptors are also available at no cost to qualified investigators. * Assays are now available for bioavailability predictions (CaCo2, MDR-1) and cardiovascular toxicity predictions (HERG, 5-HT2B) Who is eligible * Academic investigators involved in basic or clinical research relevant to mental health. * Projects from research and development areas in small businesses relevant to mental and behavioral science. * Areas of interest to NIMH include the design and development of new chemical entities and small molecules as research tools, probes, targeted drug delivery systems, and PET ligands for brain imaging. * Research areas of interest are described in the Division of Basic and Clinical Neuroscience Research webpage, http://www.nimh.nih.gov/about/organization/dnbbs/index.shtml.

Proper citation: NIMH Psychoactive Drug Screening Program (RRID:SCR_005630) Copy   

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http://www.sri.com/biosciences/nimh/

The purpose of the NIMH Toxicological Evaluation of Novel Ligands Program is to accelerate the discovery, development, and application of novel ligands for PET, SPECT, and MRI imaging in humans by providing toxicology and safety assessment of promising, target-selective compounds. The program will also provide limited assessment of novel psychoactive agents for clinical research and as potential therapeutics. Toxicology and safety data generated by the program will be used to support an Investigational New Drug (IND) application to the Food and Drug Administration (FDA), or for Radioactive Drug Research Committee (RDRC) evaluation of a compound for human studies. The contract will evaluate toxicity and safety of compounds submitted for testing which may include, but are not limited to, novel chemical entities, structural analogs of compounds with an IND, or analogs of FDA-approved drugs. The services available under this program fall under four general phases: (1) analytical, (2) pharmacokinetics, (3) preliminary safety, and (4) IND-directed toxicity including safety pharmacology. What is available A broad range of tasks are available for assessing the safety and/or pharmacokinetics of each ligand. Specific capabilities available to investigators include: * Validation of the analytical methods for quantitating drug concentrations in dosing solutions, biological fluids, and tissues, as required. Determination of plasma drug levels in animals administered the agent under study, and calculation of pharmacokinetic parameters derived from these data. * Determination of bioavailability of the drug after different routes of administration, including oral, intravenous (i.v.), subcutaneous (s.c.), intramuscular (i.m.), or intraperitoneal (i.p.), as needed. Calculation of the pharmacokinetic parameters from the derived data. * In vitro evaluation of hepatotoxicity in human and animal liver cells. * Preclinical acute toxicity evaluations on lead compounds, evaluating clinical observations, body weights, clinical pathology, histopathology, and plasma drug levels in rodents and non-rodent species. Other toxicology endpoints may be selected if needed. * Subacute and subchronic toxicity evaluations in rodents and large animal species, evaluating clinical observations, body weights, clinical pathology, and histopathology. * Genotoxicity assessments using a battery of appropriate assays. Since these preclinical studies are needed to demonstrate to the FDA that a candidate medication or imaging agent is understood well enough for designing appropriate clinical treatment regimens, most of the work to be conducted to achieve these objectives must be performed and the resulting data analyzed and reported in strict compliance with the FDA''s GLP regulations for nonclinical laboratory studies (21 CFR 58). These data must be obtained by carefully planned and skillfully executed methods that are specific, accurate, and precise. The applicable portions of the accumulated safety data will be included in documents submitted to the FDA in support of regulatory applications. Who is eligible Academic investigators involved in basic or clinical research relevant to mental health. Research areas are described on the NIMH website.

Proper citation: NIMH Toxicological Screens of Novel Ligands (RRID:SCR_005631) Copy   

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http://www.nimh.nih.gov/news/media/index.shtml

A provider for videos available from the National Institute of Mental Health (NIMH). Visitors may sort by topic and/or subscribe to RSS feeds.

Proper citation: NIMH Video (RRID:SCR_005594) Copy   

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http://www.neuroepigenomics.org/methylomedb/

A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database.

Proper citation: MethylomeDB (RRID:SCR_005583) Copy   

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http://code.google.com/p/lapdftext/

Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise.

Proper citation: lapdftext (RRID:SCR_006167) Copy   

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http://www.mbl.org/mbl_main/atlas.html

High-resolution electronic atlases for mouse strains c57bl/6j, a/j, and dba/2j in either coronal or horizontal section. About this Atlas: The anterior-posterior coordinates are taken from an excellent print atlas of a C57BL/6J brain by K. Franklin and G. Paxinos (The Mouse Brain in Stereotaxic Coordinates, Academic Press, San Diego, 1997, ISBN Number 0-12-26607-6; Library of Congress: QL937.F72). The abbreviations we have used to label the sections conform to those in the Franklin-Paxinos atlas. A C57BL/6J mouse brain may contain as many as 75 million neurons, 23 million glial cells, 7 million endothelial cells associated with blood vessels, and 3 to 4 million miscellaneous pial, ependymal, and choroid plexus cells (see data analysis in Williams, 2000). We have not yet counted total cell number in DBA/2J mice, but the counts are probably appreciably lower.The brain and sections were all processed as described in our methods section. The enlarged images have a pixel count of 1865 x 1400 and the resolution is 4.5 microns/pixel for the processed sections.Plans: In the next several years we hope to add several additional atlases of the same sort for other strains of mice. A horizontal C57BL/6J atlas and a DBA/2J coronal atlas were completed by Tony Capra, summer 2000, and additional atlases may be made over the next several years. As describe in the MBL Procedures Section is not hard to make your own strain-specific atlas from the high resolution images in the MBL.

Proper citation: Mouse Brain Atlases (RRID:SCR_007127) Copy   

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http://www.cpc.unc.edu/projects/addhealth

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

Proper citation: Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Copy   

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http://senselab.med.yale.edu/cellpropdb

A repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells. The database is presently focused on neurons but will eventually include other cell types, such as glia, muscle, and gland cells. This resource is intended to: * Serve as a repository for data on gene products expressed in different brain regions * Support research on cellular properties in the nervous system * Provide a gateway for entering data into the cannonical neuron forms in NeuronDB * Identify receptors across neuron types to aid in drug development * Serve as a first step toward a functional genomics of nerve cells * Serve as a teaching aid

Proper citation: Cell Properties Database (RRID:SCR_007285) Copy   

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https://github.com/denisecailab/minian

Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.

Proper citation: Minian (RRID:SCR_022601) Copy   

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https://github.com/Cai-Lab-at-University-of-Michigan/nTracer

Software tool as plug-in for ImageJ software. Used for tracing microscopic images.

Proper citation: nTracer (RRID:SCR_023032) Copy   

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https://CRAN.R-project.org/package=TrumpetPlots

Software R package to visualize relationship between allele frequency and effect size in genetic association studies.

Proper citation: TrumpetPlots (RRID:SCR_023742) Copy   

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https://portal.brain-map.org/atlases-and-data/bkp/abc-atlas

Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression.

Proper citation: Allen Brain Cell Atlas (RRID:SCR_024440) Copy   

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https://github.com/mne-tools/mne-bids/

Software Python package to link Brain Imaging Data Structure and MNE-Python software for analyzing neurophysiology data with goal to make analyses faster to code, more robust to errors, and easily shareable with colleagues. Provides programmable interface for BIDS datasets in electrophysiology with MNE-Python. Used for organizing electrophysiological data into BIDS format and facilitating their analysis.

Proper citation: MNE-BIDS (RRID:SCR_018766) Copy   

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https://portal.brain-map.org/explore/classes/nomenclature

Framework for creating brain cell type nomenclature, and include examples using published datasets. System allows designation of cell types with or without hierarchical organization. Nomenclature convention initially applied to brain cells and types, is intended to encompass existing naming strategies used in publications across diverse research teams. Allows tracking of many different taxonomies, including those from different organ systems or across diverse areas of bioscience.

Proper citation: Common Cell Type Nomenclature (RRID:SCR_021124) Copy   

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https://palamaralab.github.io/software/argon/

Software tool as fast simulator of genetic data that samples from Discrete Time Wright Fisher process backwards in time. Used to simulate long chromosomes and large samples under DTWF, with computational time comparable to recent coalescent simulators.

Proper citation: ARGON (RRID:SCR_021635) Copy   

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https://www.braintest.org/brain_test/BrainTest

A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help.

Proper citation: Brain Test (RRID:SCR_006212) Copy   

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http://intramural.nimh.nih.gov/gcap/index.htm

Schizophrenia related portal that aims to solve the mystery of genetic predisposition to psychosis, develop new methods for early diagnosis and prevention, and discover new treatments that will cure people suffering from it. Our objectives are to fully characterize: # neurobiological mechanisms related to susceptibility genes for schizophrenia and related clinical disorders; # genetic variation in aspects of cognition and emotionality associated with schizophrenia; and # small molecular targets for novel therapies. A unique feature of this Program is that its diverse scientific resources will be focused on a highly specific scientific agenda, that is to acquire the critical biological information about the susceptibility genes associated with schizophrenia and related illnesses. Our mission and goal, to understand the basic mechanisms of serious mental illness, has again guided us into new areas of research and to new insights. We have found evidence of new genes implicated in the cause of schizophrenia and involved in brain functions related to cognition and emotion and we have begun to explore how genes interact with each other and with the environment to individualize risk for these conditions. We are working now with over 20 genes related to schizophrenia. One of the key developments in our research over the past year has been the emergence of some targets for the development of novel therapeutics. We have discovered a new schizophrenia susceptibility gene, KCNH2, which represents the first clear target for the development of novel treatments. Just in this past year, for example, we published the first extensive statistical analysis of how schizophrenia genes may vary in their risk effects based on different genetic background (Nicodemus et al Hum Gen 2006), the first studies of schizophrenia genes interacting in effecting gene expression in brain (Lipska et al Hum Mol Genetics 2006a, Lipska et al Hum Mol Gen 2006 b); the first evidence that the mechanism of genetic association of NRG1 with schizophrenia involves a novel isoform of the gene in human brain (Law et al PNAS 2006), and the first evidence that MAOA may be linked to mood and impulse control because it effects critical mood regulatory neural networks (Meyer-Lindenberg et al PNAS 2006).

Proper citation: Genes Cognition and Psychosis Program (RRID:SCR_006292) Copy   

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http://vinovia.ncl.ac.uk/emagewebapp/pages/eadhb_home.jsf

Database of a set of standard 3D virtual models at different stages of development from Carnegie Stages (CS) 12-23 (approximately 26-56 days post conception) in which various anatomical regions have been defined with a set of anatomical terms at various stages of development (known as an ontology). Experimental data is captured and converted to digital format and then mapped to the appropriate 3D model. The ontology is used to define sites of gene expression using a set of standard descriptions and to link the expression data to an ''''anatomical tree''''. Human data from stages CS12 to CS23 can be submitted to the HUDSEN Gene Expression Database. The anatomy ontology currently being used is based on the Edinburgh Human Developmental Anatomy Database which encompasses all developing structures from CS1 to CS20 but is not detailed for developing brain structures. The ontology is being extended and refined (by Prof Luis Puelles, University of Murcia, Spain) and will be incorporated into the HUDSEN database as it is developed. Expression data is annotated using two methods to denote sites of expression in the embryo: spatial annotation and text annotation. Additionally, many aspects of the detection reagent and specimen are also annotated during this process (assignment of IDs, nucleotide sequences for probes etc). There are currently two main ways to search HUDSEN - using a gene/protein name or a named anatomical structure as the query term. The entire contents of the database can be browsed using the data browser. Results may be saved. The data in HUDSEN is generated from both from researchers within the HUDSEN project, and from the wider scientific community. The HUDSEN human gene expression spatial database is a collaboration between the Institute of Human Genetics in Newcastle, UK, and the MRC Human Genetics Unit in Edinburgh, UK, and was developed as part of the Electronic Atlas of the Developing Human Brain (EADHB) project (funded by the NIH Human Brain Project). The database is based on the Edinburgh Mouse Atlas gene expression database (EMAGE), and is designed to be an openly available resource to the research community holding gene expression patterns during early human development.

Proper citation: HUDSEN Human Gene Expression Spatial Database (RRID:SCR_006325) Copy   

•   Source: SciCrunch Registry