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http://www.regulomedb.org/

Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.

Proper citation: RegulomeDB (RRID:SCR_017905) Copy   

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http://www.broadinstitute.org/pubs/MitoCarta/

Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.

Proper citation: MitoCarta (RRID:SCR_018165) Copy   

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http://geno2mp.gs.washington.edu/Geno2MP/#/

Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community.

Proper citation: Geno2MP (RRID:SCR_016872) Copy   

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https://genefriends.org/

Human RNA-seq-based gene and transcript co-expression database.Functional genomics tool based on gene co-expression map that describes which genes tend to be activated and deactivated simultaneously in large number of RNAseq data samples.

Proper citation: GeneFriends (RRID:SCR_021625) Copy   

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http://www.catstests.com/Product08.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This free neuropsychological evaluation software, Repeat, examines performance on a serial reaction time task thought to depend upon implicit memory. Participant's acquisition of a repeating stimulus sequence is assessed in this task. Repeat is a modification of procedures reported by Nissen and Bullemer (1987) and by Lewick, Hill and Bizot (1988). The computer screen is divided into quadrants. A single X, appears in one of the quadrants. The participant's task is either, depending on response modality, to strike as quickly as possible the key (4, 5, 1, 2 on the numeric keypad) corresponding to the quadrant in which the X appears or to position the mouse pointer over the quadrant and click it. The X then appears according to a repeating pre-programmed sequence in a different quadrant and the participant is required to respond as quickly as possible to that X. A trial is made up of a series of the repeating sequence. Sequence order and length and the number of iterations of the sequence are predetermined by the experimenter. CATs Repeat also allows for the interleaving of a randomly positioned X between each sequenced X. Alternatively a series of random presentations can be programmed to allow for assessment of the baseline speed of responding, that is a condition under which the participant can acquire no anticipatory information to enhance speed of responding. Repeat also contains a dual-task or split attention component modeled after a task reported by Nissen and Bullemer (1987). This task is identical to the one described above except that either a low or high tone is presented with each X presentation and the participant is asked to count the number of low tones they heard during a trial. The relative frequency of low tones is experimenter definable. Finally Repeat allows for the assessment of the explicit knowledge the participant may have acquired of the sequence. This component of the task is modeled after the generate procedure reported by Nissen and Bullemer (1987). At any point in the experiment the participant can be asked to begin predicting where the X will appear next. At this time no normative data is available for this test.

Proper citation: Colorado Assessment Tests - Repeat (RRID:SCR_001565) Copy   

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http://www.nbrc.nite.go.jp/e/index.html

Collection of microbial resources and perform taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. NBRC is a member of WFCC, OECD Global BRC Network, ACM and JSCC. They are certified by quality management system ISO 9001. To provide attractive biological resources with useful information attached, they actively collect potentially useful biological resources (microorganisms and cloned genes) and distributes them to promote basic research as well as industrial applications. At the Biological Resource Center, they explore, isolate and identify microorganisms from various natural environments and at the same time accept scientifically and industrially useful microorganisms from researchers in academic and industrial sectors. The microbial DNA library constructed at the Biotechnology Development Center is also part of their collection. To improve and expand the collection, new methodologies for the isolation, identification and preservation of microorganisms and DNA will be investigated and developed so as to provide biological resources of higher quality. Their resources serve, for example, as the standard for determining antimicrobial activity, in aseptic tests as well as for the production of pharmaceutical substances and will be constantly reinforced for wider distribution to researchers in academia and industries. Please refer to the catalog shown at the NBRC website for details.

Proper citation: NBRC (RRID:SCR_002660) Copy   

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https://neuropsychological-assessment-tests.com/sanzen-tower-london-test

CATs Tower of London test is a free, computer-based software test originally developed by Shallice (1982) to investigate problem solving in subjects with damage to the frontal lobes. The CATs Tower of London Test comes with one preprogrammed test along with extensive normative data for that test. You can also create a test using your design. Briefly, subjects are required to move colored beads from a window on the left (working area) until they achieve the arrangement in the window on the right (goal position). Subjects are instructed to try to achieve the goal arrangement in as few moves as possible. The software contains a Tower of London test. The test contains trials with 3 beads and 3 pegs, 4 beads and 4 pegs, and 5 beads and 5 pegs. You can use the Setup screen to create a test using your design. A test can contain 3, 4, and 5 bead problems with varying number of moves required for the optimal solution. In Shallice's initial investigation using the Tower of London, patients with damage to the left anterior frontal lobe demonstrated impaired planning (i.e., greater number of moves required for solution). Patients with damage to the right anterior, and left or right posterior areas of the frontal lobes were not impaired. Thus, results from this initial study provided support for the view that the left anterior frontal lobe area is involved in the planning required for solving the Tower of London test. Recent studies using neuroimaging techniques support this notion. Studies using regional cerebral blood flow (rCBF) imaging indicate an involvement of the left frontal lobes in the planning required for successfully completing the Tower of London puzzle. Studies of patients with damage to the frontal lobes indicate less cortical specificity, but are consistent with the view that the frontal lobes are involved in the planning required for solving this puzzle.

Proper citation: Colorado Assessment Tests - Tower of London (RRID:SCR_003507) Copy   

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http://www.mdvu.org/library/

THIS RESOURCE IS NO LONGER IN SERVICE, documented April 15, 2016. The Movement Disorder Virtual University (MDVU) Resource Library contains detailed movement disorder information and resources including rating scales, scoring sheets, patient fact sheets, teaching slide sets, research news, meeting reports, anatomical illustrations, movement disorder treatment and rehabilitation directory, a glossary, support organizations, drug package information, and a library of links.

Proper citation: Movement Disorder Virtual University (MDVU): Resource Library (RRID:SCR_002719) Copy   

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http://fantom.gsc.riken.jp/4/

The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4. In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates. In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome. TOOLS *Genome Browser: graphical display of genomic features, such as promoters, exon structures, H3K9 acetylation, transcription factors positioning on the genome, coupled with gene and promoter activities. *EdgeExpressDB: regulatory interactions, such as transcriptional regulation, post-transcriptional silencing with miRNA, and PPI, coupled with gene and promoter activities. *SwissRegulon: FANTOM4 TF regulation is predicted using Motif Activity Response Analysis (MARA) developed by Erik van Nimwegen at Biozentrum. Follow the link to carry out MARA on your own dataset. *Custom Tracks on the UCSC Genome Browser: FANTOM4 tracks on the UCSC Genome Browser Database. *The RIKEN integrated database of mammals: Integration of FANTOM4 data with other mammalian resources, in particular, produced by RIKEN.

Proper citation: FANTOM DB (RRID:SCR_002678) Copy   

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http://metscape.ncibi.org

A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.

Proper citation: Metscape (RRID:SCR_014687) Copy   

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http://www.semel.ucla.edu/creativity/

The purpose of this center is to study the molecular, cellular, systems and cognitive mechanisms that result in cognitive enhancements and explain unusual levels of performance in gifted individuals, including extraordinary creativity. Additionally, by understating the mechanisms responsible for enhancements in performance we may be better suited to intervene and reverse disease states that result in cognitive deficits. One of the key topics addressed by the Center is the biological basis of cognitive enhancements, a topic that can be studied in human subjects and animal models. In the past much of the focus in the brain sciences has been on the study of brain mechanisms that degrade cognitive performance (for example, on mutations or other lesions that cause cognitive deficits). The Tennenbaum Center for the Biology of Creativity at UCLA enables an interdisciplinary team of leading scientists to advance knowledge about the biological bases of creativity. Starting with a pilot project program, a series of investigations was launched, spanning disciplines from basic molecular biology to cognitive neuroscience. Because the concept of creativity is multifaceted, initial efforts targeted refinement of the component processes necessary to generate novel, useful cognitive products. The identified core cognitive processes: 1.) Novelty Generation the ability to flexibly and adaptively generate products that are unique; 2.) Working Memory and Declarative Memory the ability to maintain, and then use relevant information to guide goal-directed performance, along with the capacity to store and retrieve this information; and 3.) Response Inhibition the ability to suppress habitual plans and substitute alternate actions in line with changing problem-solving demands. To study the basic mechanisms underlying these complex brain functions we use translational strategies. Starting from foundational studies in basic neuroscience, we forged an interdisciplinary strategy that permits the most advanced techniques for genetic manipulation and basic neurobiological research to be applied in close collaboration with human studies that converge on the same core cognitive processes. Our integrated research program aims to reveal the genetic architecture and fundamental brain mechanisms underlying creative cognition. The work holds enormous promise for both enhancing healthy cognitive performance and designing new treatments for diverse cognitive disorders. Sponsors: The Tennenbaum Center for the Biology of Creativity was inspired by the vision and generosity of Michael Tennenbaum.

Proper citation: Tennenbaum Center for the Biology of Creativity (RRID:SCR_000668) Copy   

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http://www.simulations-plus.com/Products.aspx?pID=13

Software program for advanced predictive modeling of Absorption, Distribution, Metabolism, Elimination, and Toxicity (ADMET) properties of chemical substances in the human body. ADMET Predictor can estimate a number of vital ADMET properties (listed below) from molecular structures and build predictive models of new properties from user's data.

Proper citation: ADMET Predictor (RRID:SCR_014903) Copy   

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http://neurobureau.projects.nitrc.org/ADHD200/Introduction.html

Preprocessed versions of the ADHD-200 Global Competition data including both preprocessed versions of structural and functional datasets previously made available by the ADHD-200 consortium, as well as initial standard subject-level analyses. The ADHD-200 Sample is pleased to announce the unrestricted public release of 776 resting-state fMRI and anatomical datasets aggregated across 8 independent imaging sites, 491 of which were obtained from typically developing individuals and 285 in children and adolescents with ADHD (ages: 7-21 years old). Accompanying phenotypic information includes: diagnostic status, dimensional ADHD symptom measures, age, sex, intelligence quotient (IQ) and lifetime medication status. Preliminary quality control assessments (usable vs. questionable) based upon visual timeseries inspection are included for all resting state fMRI scans. In accordance with HIPAA guidelines and 1000 Functional Connectomes Project protocols, all datasets are anonymous, with no protected health information included. They hope this release will open collaborative possibilities and contributions from researchers not traditionally addressing brain data so for those whose specialties lay outside of MRI and fMRI data processing, the competition is now one step easier to join. The preprocessed data is being made freely available through efforts of The Neuro Bureau as well as the ADHD-200 consortium. They ask that you acknowledge both of these organizations in any publications (conference, journal, etc.) that make use of this data. None of the preprocessing would be possible without the freely available imaging analysis packages, so please also acknowledge the relevant packages and resources as well as any other specific release related acknowledgements. You must be logged into NITRC to download the ADHD-200 datasets, http://www.nitrc.org/projects/neurobureau

Proper citation: ADHD-200 Preprocessed Data (RRID:SCR_000576) Copy   

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http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/BRIC/default.aspx

Imaging Core facility that provides a comprehensive research imaging service to meet the needs of investigators and research subjects using imaging facilities at Brigham and Women's Hospital (BWH). A unique feature of BRIC is the complete anonymity of research subjects. Research image scheduling, image acquisition and image storage are all kept completely separate from BWH clinical Radiology systems. The BRIC provides the administrative infrastructure, customer service architecture and institutional support to promote investigative applications of imaging technologies.

Proper citation: BWH Research Imaging Core (RRID:SCR_002708) Copy   

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http://www.hcp.med.harvard.edu/ncs/

The baseline NCS, fielded from the fall of 1990 to the spring of 1992, was the first nationally representative mental health survey in the U.S. to use a fully structured research diagnostic interview to assess the prevalences and correlates of DSM-III-R disorders. The baseline NCS respondents were re-interviewed in 2001-02 (NCS-2) to study patterns and predictors of the course of mental and substance use disorders and to evaluate the effects of primary mental disorders in predicting the onset and course of secondary substance disorders. In conjunction with this, an NCS Replication survey (NCS-R) was carried out in a new national sample of 10,000 respondents. The goals of the NCS-R are to study trends in a wide range of variables assessed in the baseline NCS and to obtain more information about a number of topics either not covered in the baseline NCS or covered in less depth than we currently desire. A survey of 10,000 adolescents (NCS-A) was carried out in parallel with the NCS-R and NCS-2 surveys. The goal of NCS-A is to produce nationally representative data on the prevalences and correlates of mental disorders among youth. The NCS-R and NCS-A, finally, are being replicated in a number of countries around the world. Centralized cross-national analysis of these surveys is being carried out by the NCS data analysis team under the auspices of the World Health Organization (WHO) World Mental Health Survey Initiative. In order to provide an easily accessible database which can be updated and checked on a regular basis, we have created a public use file system containing all the documents from the NCS and NCS-R programs. These file systems can be accessed through the Internet and either downloaded onto a disk or printed. We will update the system on a regular basis to add newly completed paper abstracts and other documents. In addition, the NCS and NCS-R data can be accessed through ICPSR (Inter-university Consortium for Political and Social Research). Any updates to the data to correct coding or classification errors will be made available along with written documentation of the changes in ICPSR''s quarterly newsletter.

Proper citation: National Comorbidity Survey (RRID:SCR_004588) Copy   

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http://www.grc.nia.nih.gov/

A research program of the NIA which focuses on neuroscience, aging biology, and translational gerontology. The central focus of the program's research is understanding age-related changes in physiology and the ability to adapt to environmental stress, and using that understanding to develop insight about the pathophysiology of age-related diseases. The IRP webpage provides access to other NIH resources such as the Biological Biochemical Image Database, the Bioinformatics Portal, and the Baltimore Longitudinal Study of Aging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Intramural Research Program (RRID:SCR_012734) Copy   

•   Source: SciCrunch Registry

http://www.cdc.gov/genomics/hugenet/default.htm

Human Genome Epidemiology Network, or HuGENet, is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. Its goals include: establishing an information exchange that promotes global collaboration in developing peer-reviewed information on the relationship between human genomic variation and health and on the quality of genetic tests for screening and prevention; providing training and technical assistance to researchers and practitioners interested in assessing the role of human genomic variation on population health and how such information can be used in practice; developing an updated and accessible knowledge base on the World Wide Web; and promoting the use of this knowledge base by health care providers, researchers, industry, government, and the public for making decisions involving the use of genetic information for disease prevention and health promotion. HuGENet collaborators come from multiple disciplines such as epidemiology, genetics, clinical medicine, policy, public health, education, and biomedical sciences. Currently, there are 4 HuGENet Coordinating Centers for the implementation of HuGENet activities: CDC''s Office of Public Health Genomics, Atlanta, Georgia; HuGENet UK Coordinating Center, Cambridge, UK; University of Ioannina, Greece; University of Ottawa , Ottawa, Canada. HuGENet includes: HuGE e-Journal Club: The HuGE e-Journal Club is an electronic discussion forum where new human genome epidemiologic (HuGE) findings, published in the scientific literature in the CDC''s Office of Public Health Genomics Weekly Update, will be abstracted, summarized, presented, and discussed via a newly created HuGENet listserv. HuGE Reviews: A HuGE Review identifies human genetic variations at one or more loci, and describes what is known about the frequency of these variants in different populations, identifies diseases that these variants are associated with and summarizes the magnitude of risks and associated risk factors, and evaluates associated genetic tests. Reviews point to gaps in existing epidemiologic and clinical knowledge, thus stimulating further research in these areas. HuGE Fact Sheets: HuGE Fact Sheets summarize information about a particular gene, its variants, and associated diseases. HuGE Case Studies: An on-line presentation designed to sharpen your epidemiological skills and enhance your knowledge on genomic variation and human diseases. Its purpose is to train health professionals in the practical application of human genome epidemiology (HuGE), which translates gene discoveries to disease prevention by integrating population-based data on gene-disease relationships and interventions. Students will acquire conceptual and practical tools for critically evaluating the growing scientific literature in specific disease areas. HUGENet Publications: Articles related to the HuGENet movement written by our HuGENet collaborators. HuGE Navigator: An integrated, searchable knowledge base of genetic associations and human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. HuGE Workshops: HuGENet has sponsored meetings and workshops with national and international partners since 2001. Available are detailed summaries, agendas or the ability to download speaker slides. HuGE Book: Human Genome Epidemiology: A Scientific Foundation for Using Genetic Information to Improve Health and Prevent Disease. (The findings and conclusions in this book are those of the author(s) and do not necessarily represent the views of the funding agency.) HuGENet Collaborators: HuGENet is interested in establishing collaborations with individuals and organizations working on population based research involving genetic information. HuGE Funding: Funding opportunities for specific population-based genetic epidemiology research projects are available. Research initiatives whose aims include assessing the prevalence of human genetic variation, the association between genetic variants and human diseases, the measurement of gene-gene or gene-environment interaction, and the evaluation of genetic tests for screening and prevention are compiled to create a posted listing. Additional information and application details can be found by clicking on the respective links.

Proper citation: Human Genome Epidemiology Network (RRID:SCR_013117) Copy   

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https://commonfund.nih.gov/hmp/

NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016.

Proper citation: Human Microbiome Project (RRID:SCR_012956) Copy   

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http://epigenomesportal.ca/ihec/

A data portal of the International Human Epigenome Consortium which provides access to comprehensive data sets of reference epigenomes relevant to health and disease. The IHEC Data Portal can be used to view, search and download data already released by different IHEC-associated projects. Data are organized by consortium, by tissue, and by assay category. Users can visualize data sets using the data grid provided or the UCSC Genome Browser.

Proper citation: International Human Epigenome Consortium Data Portal (RRID:SCR_014625) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://www.gencodegenes.org

Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.

Proper citation: GENCODE (RRID:SCR_014966) Copy   

•   Source: SciCrunch Registry