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An online tool for managing and viewing datasets. Data can be viewed in 2D or 3D with activation points as points clouds or projections on the cortex surface. Data can be imported as a NIfTI file or a list of activation peaks and results can be exported as a PDF file.
Proper citation: linkRbrain (RRID:SCR_014562) Copy
https://gemini.readthedocs.io/en/latest/
Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.
Proper citation: GEMINI (RRID:SCR_014819) Copy
Consortium to coordinate epigenome mapping and characterization worldwide to avoid redundant research effort, to implement high data quality standards, to coordinate data storage, management and analysis and to provide free access to the high resolution reference human epigenome maps for normal and disease cell types to the research community. Promotes data sharing. You may view, search and download the data already released by the different IHEC associated projects via the IHEC Data Portal.
Proper citation: International Human Epigenome Consortium (RRID:SCR_016937) Copy
https://software.broadinstitute.org/software/discovar/blog/
Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.
Proper citation: Discovar assembler (RRID:SCR_016755) Copy
http://www.bx.psu.edu/~giardine/vision/
International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.
Proper citation: ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) Copy
Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.
Proper citation: Allen Brain Atlas (RRID:SCR_017001) Copy
https://www.iigm.it/site/index.php?l=ENG
Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience.
Proper citation: Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) Copy
Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.
Proper citation: Data Archive BRAIN Initiative (RRID:SCR_017114) Copy
SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short.
Proper citation: SPARC Portal (RRID:SCR_017041) Copy
https://www.sciencescott.com/pyminer
Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.
Proper citation: PyMINEr (RRID:SCR_016990) Copy
http://pathwaynet.princeton.edu/
Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.
Proper citation: PathwayNet (RRID:SCR_017353) Copy
https://ccb-web.cs.uni-saarland.de/tissueatlas
Human miRNA tissue atlas. Database showing distribution of miRNA expression across human tissues.
Proper citation: TissueAtlas (RRID:SCR_017352) Copy
Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data.
Proper citation: Human Neocortical Neurosolver (RRID:SCR_017437) Copy
http://www.ariesepigenomics.org.uk/
Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time.
Proper citation: Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) Copy
http://www.epigenomes.ca/data-release/
Network to connect Canadian epigenetics researchers and expand their reach to broader health research community in Canada and beyond. Curated epigenomics sequence focused on common human diseases.
Proper citation: Canadian Epigenetics, Environment and Health Research Consortium Network (RRID:SCR_017491) Copy
https://hirnetwork.org/consortium/hpac
Consortium is investigating physical and functional organization of human islet tissue environment, cell-cell relationships within pancreatic tissue ecosystem, and contributions of non endocrine components (acinar, ductal, vascular, perivascular, neuronal, lymphatic, immune) to islet cell function and dysfunction. HPAC consists of research grants as well as the Human Pancreas Analysis Program (HPAP).
Proper citation: HIRN Human Pancreas Analysis Consortium (RRID:SCR_017583) Copy
Software Java tool for quantitative analysis of behavior. Used to address any theoretical problem that requires complex sequence of actions to be scored by human observer. Runs on microcomputer providing Java Virtual Machine[TM] and has been tested on Windows[TM] and Macintosh[TM] systems. Legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while Version 1.0 works well on Macintosh OS-X and Windows XP systems. JWatcher Video works best on Windows XP systems and has reduced functionality running in Macintosh OS-X. JWatcher-Palm can be used to acquire data on Palm OS[TM] equipped device and analyze it on your main computer.
Proper citation: JWatcher (RRID:SCR_017595) Copy
National research consortium designed to discover and perform preliminary characterization of range of molecular transducers that underlie effects of physical activity in humans. Used to study molecular changes that occur during and after exercise and to advance understanding of how physical activity improves and preserves health. Six year program into mechanisms of how physical activity improves health and prevents disease led by NIH Office of Strategic Coordination, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute on Aging, and National Institute of Biomedical Imaging and Bioengineering.
Proper citation: MoTrPAC Data Hub (RRID:SCR_017611) Copy
http://www.biorag.org/index.php
Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona.
Proper citation: Bio Resource for Array Genes Database (RRID:SCR_000748) Copy
http://www.eideneurolearningblog.blogspot.com/
Weekly articles related to brain-based learning and learning styles, problem-solving and creativity, kids, families, and parenting, gifted and visual learners, dyslexia, attention deficit disorders, autism, and more.
Proper citation: Eide Neurolearning Blog (RRID:SCR_000680) Copy
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