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https://commonfund.nih.gov/hubmap
Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.
Proper citation: The Human BioMolecular Atlas Program (RRID:SCR_016922) Copy
Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.
Proper citation: Kidney Precision Medicine Project (RRID:SCR_016920) Copy
https://github.com/zuoxinian/CCS
Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.
Proper citation: Connectome Computation System (RRID:SCR_017342) Copy
Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces.
Proper citation: Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) Copy
https://portal.brain-map.org/atlases-and-data/rnaseq
Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus.
Proper citation: Transcriptomics Explorer (RRID:SCR_017567) Copy
https://scdevdb.deepomics.org/
Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes.
Proper citation: Single Cell Developmental Database (RRID:SCR_017546) Copy
Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems.
Proper citation: EBRAINS Knowledge Graph (RRID:SCR_017612) Copy
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
An accurate and reliable method for identifying athletes with head trauma, and a strong candidate rapid sideline screening test for concussion. The test is able to capture impairments of eye movement, attention, language and other symptoms of impaired brain function. It is a physical method of evaluating visual tracking and saccadic eye movements is based on the time to perform rapid number naming. It involves reading aloud a series of single digit numbers from left to right on three test cards. Participants are asked to read the numbers on each card from left to right as quickly as possible but without making any errors. The sum of the three test card time scores constitutes the summary score for the entire test. The test is a proven indicator of oculomotor inefficiencies regarding eye movements during reading. Published medical studies have determined that deficiencies in saccadic eye movements can be an indicator of mild Traumatic Brain Injury (mTBI) or concussions. Studies have shown that there is a significant relationship between poor oculomotor functions and learning disabilities (including dyslexia detection). Saccadic eye movement deficiencies can be improved with training and correspondingly reading performance also can be improved. Simply put, subjects who don''t perform well on this test are not efficient readers, although because there are many reasons for poor reading unrelated to eye movements, some poor readers do fine on the test. They believe that the test should be in the hands of teachers in order to help them determine if a student''s poor reading performance is related to deficiencies in their ability to move their eyes efficiently.
Proper citation: King-Devick Test (RRID:SCR_004500) Copy
The Department of Neurology & Psychiatry aims to 1) provide the best psychiatric and neurological care to patients and their families, 2) discover and investigate new treatments for psychiatric and nervous system disorders, 3) study psychosocial processes in psychiatric and neurological illness, and 4) educate the next generation of practitioners, as well as our patients and the lay community. The Department of Neurology & Psychiatry (DNP) was established on June 1, 2007. The Department has 34 faculty members and is planning continued expansion. There are 7 psychiatrists, 18 neurologists, 4 child neurologists, and 5 NIH-supported PhD investigators. The DNP is one of five departments in the country that combines the disciplines of neurology and psychiatry. We are unique in having two strong residency programs and are the only that attempts to establish a new paradigm in care of patients with neurological and psychiatric disease through co-management initiatives. * Division of Psychiatry: The Psychiatrists work within four areas: Adult, Geriatric, Community, and Forensic Psychiatry. * Division of Neurology: The division has an extremely active stroke/intensive care and general neurology service. We are expanding services in neurocritical care and interventional neurology. * Education: The DNP has approximately 25 residents/fellows in each discipline. * Research: The DNP has robust programs in clinical, basic, and translational research. We emphasize 3 areas in this overview of the DNP. ** Clinical Research Unit ** Psychosocial Processes Group ** Translational Neuromuscular Disease VISION STATEMENT All members of the Saint Louis University Department of Neurology & Psychiatry will collaborate to support state-of-the-art neurological and psychiatric education, compassionate patient care, and a growing research enterprise. The Department will develop the most exciting intellectual environment in the Nation for investigation, treatment, and training in psychiatry and neurology. We will fulfill this Vision in an environment of mutual respect and collaboration.
Proper citation: St. Louis University Department of Neurology and Psychiatry (RRID:SCR_004297) Copy
Infrastructure for sharing cardiovascular data and data analysis tools. Human ExVivo heart data set and canine ExVivo normal and failing heart data sets are available. Canine hearts atlas and human InVivo atlases are available.
Proper citation: CardioVascular Research Grid (CVRG) (RRID:SCR_004472) Copy
https://www.hupo.org/human-antibody-initiative/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.The mission of the Human Antibody Initiative (HAI) aims to promote and facilitate the use of antibodies for proteomics research. The initiative consists of two separate activities; (1) the generation of a catalogue of validated antibodies from many different sources and (2) a protein atlas for the expression and localization of human proteins in normal and disease tissue. The two separate activities have as their primary deliverables to generate databases with free public accessibility. The Antibody Resource database (www.antibodypedia.org) is aimed to produce a comprehensive catalogue of validated antibodies towards human proteins. This initiative depends on input from a large number of academic groups and commercial companies. The Protein Atlas initiative (www.proteinatlas.org) is aimed to provide comprehensive and annotated database of high-resolution images showing tissue profiles in normal and cancer tissues. Both databases will be open to the public without restriction (no passwords).
Proper citation: HUPO Antibody Initiative (RRID:SCR_004568) Copy
National Brain Tumor Society (NBTS) is a nonprofit organization committed to finding a cure for brain tumors. We aggressively drive strategic research, advocate for public policies that meet the critical needs of the brain tumor community, and provide patient information. Headquartered in Watertown, Massachusetts, with offices in San Francisco, California and Wilmington, Delaware, we host activities throughout the United States. Formed in 2008 by the merger of two leading organizations that had served the brain tumor community, the National Brain Tumor Foundation and the Brain Tumor Society, the National Brain Tumor Society is now the largest brain tumor nonprofit organization in the country. Both legacy organizations had been formed in the 1980s by parents and other people who were committed to increasing both research funding and access to resources specific to brain tumors. In 2010, the Kelly Heinz-Grundner Foundation, a Delaware-based organization, joined NBTS as a wholly-owned subsidiary. Founded in 2005, after the death of Kelly Heinz-Grundner to a brain tumor, the group has contributed to NBTS''s efforts to pursue research and public policies that benefit the brain tumor community. NBTS grant programs are effective for academic researchers, inclusive of industry expertise, and promising for the patient community. All funding is open to both the domestic and international research communities. The Innovation Research Grant Program supports catalytic transformative projects that will significantly move the field forward. These may include out-of-the-box projects or research that is critical to move therapies down the pipeline. Research that represents an incremental advance is not considered innovative. NBTS will accept Innovation Letters of Intent throughout the year. Researchers in academic or industry labs and at all stages of their career may be funded through this program.
Proper citation: National Brain Tumor Society (RRID:SCR_004744) Copy
The Alabama Head Injury Foundation (AHIF) was founded in 1983 to increase public awareness of Traumatic Brain Injury (TBI) and to stimulate the development of supportive services. Today, AHIF is among the largest state brain injury associations in the nation with model programs and statewide services. Its mission is to improve the quality of life for people who have survived traumatic brain injuries and for their families. Whether the injury is mild or severe the life of the injured person and their family is changed forever. The impact can be both emotionally and financially devastating. AHIF provides the information to help clients and families understand the results of injury. AHIF helps access available resources and provides services and programs which meet the unique needs of individuals with traumatic brain injury (TBI) as well as spinal cord injury (SCI) in certain programs.
Proper citation: Alabama Head Injury Foundation (RRID:SCR_004580) Copy
http://www.floridabraintumor.com/homepage.htm
The mission of the Florida Brain Tumor Association (FBTA) is to provide hope, support and education to brain tumor survivors, their families and friends; to conquer brain tumors by funding research into their causes and cures; and to enrich the quality of life of those touched by brain tumors. In October, 1991, the Florida Brain Tumor Association (formerly South Florida Brain Tumor Association) began due to a desperate need from brain tumor survivors and families who were searching for support and a safe place to share their life changing experiences. Beginning in Boca Raton, Florida, as a grass roots organization and a handful of people, the first support group was conceived. Today, there are many additional FBTA support groups, from coast to coast in the state of Florida. The Florida Brain Tumor Association (FBTA) has become a major force in the brain tumor community. We host many fundraisers yearly, donating funds for research to brain tumor centers. The FBTA has hosted over 20 three day conferences, seminars and meetings, attracting thousands of survivors, families and health care professionals in the United States and Canada. Many of the most renowned physicians in the world travel from far and near to present at FBTA conferences. We are proud and grateful for their commitment and dedication to our cause. The FBTA is a not-for-profit 501(c)(3) organization that is supported by contributions from individuals, corporations, and foundations. We are the only organization of this kind, relying on the strength and dedication of our members, who are brain tumor survivors, family members and friends. Our Medical Advisory Board is also voluntary; we are very thankful to them for their generous gifts of time.
Proper citation: Florida Brain Tumor Association (RRID:SCR_004739) Copy
http://www.braintumorkids.org/
Established in 1983 in Atlanta, GA, the Brain Tumor Foundation for Children (BTFC) was the first nonprofit organization in the United States to focus on pediatric brain tumor disease. The mission of the Brain Tumor Foundation for Children is to provide financial assistance, social support, and information for families of children with brain and spinal cord tumors; fund research projects that improve treatment options and search for a cure; and raise public awareness of the disease and advocate on behalf of children who are affected.
Proper citation: Brain Tumor Foundation For Children (RRID:SCR_004735) Copy
http://spot.colorado.edu/~dubin/talks/brodmann/brodmann.html
Reference atlas of Brodmann Areas in the Human Brain with an Emphasis on Vision and Language. Other Pages include: Flat Brodmann Maps, Brodmann Area Names (with locational Descriptions), Flat Visual Area Maps, Language Areas, PopUp Gyri Maps
Proper citation: Brodmann Areas in the Human Brain with an Emphasis on Vision and Language (RRID:SCR_004857) Copy
The Brain Tumor Action Network is a not-for-profit 501(c)(3) organization established to bring awareness to the general public about brain tumors and to educate and empower brain tumor survivors, their families and friends. We foster grassroots advocacy on federal and state legislative issues affecting brain tumor survivors, their families and friends by providing information on brain tumor-related public issues and effective advocacy. BTAN has the following goals: * To encourage those living with brain tumors, their families and friends to become advocates for brain tumor awareness. * To foster grassroots advocacy on federal and state legislative issues affecting brain tumor survivors, their families and friends by providing information (and training) on brain tumor related public issues and effective advocacy. * To work independently and in collaboration with other brain tumor related organizations on behalf of the brain tumor community family. * To increase brain tumor awareness nationally through the Hidden Under Our Hats, National Brain Tumor Awareness Project in Washington, DC and at various treatment centers, conferences and fund raisers. * To raise funds to support specific research projects. * To create a PILOT respite care program for brain tumor survivors and their families at Moffitt Cancer Center & Research Institute (Tampa, FL). The respite care fund would assist brain tumor patients and their family members with additional care and support from home health care workers.
Proper citation: Brain Tumor Action Network (RRID:SCR_004733) Copy
An interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes / protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB''s mapping interface. All of SMPDB''s images, image maps, descriptions and tables are downloadable.
Proper citation: Small Molecule Pathway Database (RRID:SCR_004844) Copy
http://www.pencerbraintrust.com/
The Gerry & Nancy Pencer Brain Trust is a not-for-profit organization with a mandate to make a difference in the quality of life of people living with brain tumors. This registered charity is the primary source of funding for The Gerry & Nancy Pencer Brain Tumor Centre, and carries out annual fundraising events to support its'' ongoing research and patient care activities. The Gerry & Nancy Pencer Brain Tumor Centre is located in Toronto, Canada at the world-renowned Princess Margaret Hospital. The Centre provides multidisciplinary care, treatment, support, and education for brain tumor patients and their families, and promotes brain tumor research in the hopes of one day finding a cure for brain cancer. All of this is made possible through your very generous donations.
Proper citation: Gerry and Nancy Pencer Brain Trust (RRID:SCR_004762) Copy
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