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http://ranchobiosciences.com/gse4271/

Curated data set from a study that investigated 77 primary high-grade astrocytomas and 23 matched recurrences so that changes in gene expression related to both survival and disease progression can be identified. Samples in the study include WHO grade III and IV astrocytomas with a wide range of survival times.

Proper citation: GSE4271 (RRID:SCR_003643) Copy   

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http://www.chibi.ubc.ca/WhiteText/

Freely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology.

Proper citation: Automated recognition of brain region mentions in neuroscience literature. (RRID:SCR_002731) Copy   

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http://www.mri-resource.kennedykrieger.org/

Biomedical technology research center that provides expertise for the design of quantitative magnetic resonance imaging (MRI) and spectroscopy (MRS) data acquisition and processing technologies that facilitate the biomedical research of a large community of clinicians and neuroscientists in Maryland and throughout the USA. These methods allow noninvasive assessment of changes in brain anatomy as well as in tissue metabolite levels, physiology, and brain functioning while the brain is changing size during early development and during neurodegeneration, i.e. the changing brain throughout the life span. The Kirby Center has 3 Tesla and 7 Tesla state of the art scanners equipped with parallel imaging (8, 16, and 32-channel receive coils) and multi-transmit capabilities. CIS has an IBM supercomputer that is part of a national supercomputing infrastructure. Resources fall into the following categories: * MRI facilities, image acquisition, and processing * Computing facilities and image analysis * Novel statistical methods for functional brain imaging * Translating laboratory discoveries to patient treatment

Proper citation: National Resource for Quantitative Functional MRI (RRID:SCR_006716) Copy   

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https://scicrunch.org/scicrunch/data/source/nlx_154697-8/search?q=*

A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references.

Proper citation: Integrated Nervous System Connectivity (RRID:SCR_006391) Copy   

•   Source: SciCrunch Registry

http://mindhacks.com/

Mind Hacks: Neuroscience and psychology tricks to find out what's going on inside your brain. Mind Hacks is also a book by Tom Stafford and Matt Webb.

Proper citation: Mind Hacks (RRID:SCR_000170) Copy   

•   Source: SciCrunch Registry

http://www.nesys.uio.no/Database/

This site contains the NeSys archive on structure and structure-function data about brain map transformations in the cerebellar system of the rat. This archive presents data not illustrated in the original publications, downloadable original data sets, interactive illustration sequences, including 3-D models. The repository is based on 5 original publications. The publications deal with: - organization of projections to the pontine nuclei from three cortical areas: primary and secondary somatosensory areas (SI and SII), and the primary motor cortex (MI) - organization of pontine neurons projecting to somatosensory representations in the posterior cerebellum The data are also included in the FACCS application, a relational database application with embedded analytical tools, available via the The Rodent Brain Workbench (www.rbwb.org). Sponsors: NeSys Research and Database development is supported by The Research Council of Norway, The European Community (grants QLRT-2000-02256 and QLG3-CT 1999-00763), The Norwegian Consortium for High Performance Computing, and The Jahre Foundation.

Proper citation: Database on Brain Map Transformations in Cerebellar Systems (RRID:SCR_008052) Copy   

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http://experimentalman.com/blog/

Blog about how leading-edge bio-science and technology is impacting individuals and society. This blog is an outgrowth of David Ewing Duncan''s new book, Experimental Man: What one mans body reveals about youy future, your health, and our toxic world. In the book he reports taking over 250 tests in the realms of genes, environment, brain and body and explore what these tests can tell us about one persons health, past, present, and future.

Proper citation: Experimental Man Blog (RRID:SCR_008378) Copy   

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https://bbgre.brc.iop.kcl.ac.uk

A database and associated tools for investigating the genetic basis of neurodisability. It combines phenotype information from patients with neurodevelopmental and behavioral problems with clinical genetic data, and displays this information on the human genome map. Basic access to genetic information (deletions, duplications) relating to participants with neurodevelopmental disorders is provided without an account; access to the full dataset requires an account. The genetic information that is available to view comprises potentially pathogenic copy number variation across the genome, detected by array comparative genome hybridization (aCGH) using a customized 44K oligonucleotide array.

Proper citation: Brain and Body Genetic Resource Exchange (RRID:SCR_008959) 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   

•   Source: SciCrunch Registry

http://banyanbio.com/

Banyan Biomarkers was founded in 2002 by Ron Hayes, PhD , Kevin Wang, PhD, and Nancy Denslow, PhD to create the first Point of Care (POC) Blood Test to diagnose traumatic brain injury (TBI) and to diagnose neurological diseases. Initially inspired by research conducted at the University of Florida and The Evelyn F. and William McKnight Brain Institute, Banyan Biomarkers has made significant progress in developing and clinically validating novel enzyme linked immunosorbent assays (ELISAs) for traumatic brain injury (TBI). Banyan scientists have created an extensive pipeline of potential biomarkers and the company has a robust intellectual property portfolio. Jackson Streeter, Banyan''s CEO, has extensive experience in development of medical devices for acute brain injury. Currently no blood test exists for use by physicians to detect the presence and severity of brain trauma. Banyan Biomarkers'' research has identified unique and proprietary biomarkers present in the patient''s blood following injury to the brain. The detection and quantification of these biomarkers may provide early indications of brain trauma essential for earlier intervention and management. Banyan Biomarkers, Inc. offers preclinical and clinical sample analyses with a proven panel of neurological, psychiatric, neurodegenerative disease, and organ toxicity biomarker assays. The company provides analytical services to a wide range of customers including pharmaceutical companies, biotechnology companies and investigators at academic research institutes.

Proper citation: Banyan Biomarkers (RRID:SCR_004515) Copy   

•   Source: SciCrunch Registry

http://www.strokecenter.org/radiology/

The Internet Stroke Center at Washington University is pleased to offer this module for viewing CT, MR, and angiogram images of cerebrovascular and neurological diseases. While this project is still being perfected -- and many more cases have yet to be added -- we hope that you will find this collection useful in your education and practice. The images presented here are for educational use only. This information may not be used for diagnosis or treatment. All images are protected property of the Internet Stroke Center at Washington University and may not be reproduced without permission. Permission may be granted to students and professionals to borrow images from this site for educational purposes and/or presentations; we just ask that an email be sent detailing both the desired material and the intended use. Please direct all comments, questions, and requests to the Site Editor of the Internet Stroke Center.

Proper citation: Neurology Image Library from The Internet Stroke Center (RRID:SCR_013633) Copy   

•   Source: SciCrunch Registry

http://www.cdtdb.neuroinf.jp/CDT/Top.jsp

A platform that allow users to visualize and analyze transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain. Users can search for cerebellar development genes by name, ID, keyword, expression, and tissue specificity. Search results include general information, links, temporal, spatial, and tissue information, and gene category.

Proper citation: Brain Transcriptome Database (RRID:SCR_014457) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/barres_lab/brain_rnaseq.html

Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

Proper citation: Brain RNA-Seq (RRID:SCR_013736) Copy   

•   Source: SciCrunch Registry

http://netbio.bgu.ac.il/tissuenet/

Database of human tissue protein-protein interactions (PPIs) that associates each interaction with human tissues that express both pair mates. This was achieved by integrating current data of experimentally detected PPIs with extensive data of gene and protein expression across 16 main human tissues. Users can query TissueNet using a protein and retrieve its PPI partners per tissue, or using a PPI and retrieve the tissues expressing both pair mates. The graphical representation of the output highlights tissue-specific and tissue-wide PPIs. Thus, TissueNet provides a unique platform for assessing the roles of human proteins and their interactions across tissues.

Proper citation: TissueNet - The Database of Human Tissue Protein-Protein Interactions (RRID:SCR_002052) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/db/Search

Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.

Proper citation: Genes to Cognition Database (RRID:SCR_002735) Copy   

•   Source: SciCrunch Registry

https://bams1.org/cells/list.php, https://bams1.org/cells/search_bams_ref.php, https://bams1.org/cells/search_by_brain_region.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein.

Proper citation: BAMS Cells (RRID:SCR_003531) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/DRG

Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome.

Proper citation: Drug Related Gene Database (RRID:SCR_003330) Copy   

•   Source: SciCrunch Registry

http://hendrix.imm.dtu.dk/services/jerne/brede/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments.

Proper citation: Brede Database (RRID:SCR_003327) Copy   

•   Source: SciCrunch Registry

http://brainatlas.mbi.ufl.edu/ImageGallery.php

Image Gallery of a 3D MRI Atlas of an Adult C57BL/6J Mouse Brain showing Slice Animation and 3D Animation including Axial, Coronal, Sagittal views. RealPlayer or Windows Media Player needs to be installed for viewing these animations.

Proper citation: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery (RRID:SCR_007032) Copy   

•   Source: SciCrunch Registry

http://www.nybb.hs.columbia.edu/

A brain bank which collects postmortem human brains to meet the needs of neuroscientists investigating specific psychiatric and neurological disorders. NYBB disburses tissue samples to investigating clinicians or scientists whose research has been approved by their Institutional Review Board. The tasks of the NYBB include: collection and processing of human postmortem brain samples for research; neuropathological evaluation and diagnosis; storage and computerized inventory of brain samples; and distribution of brain samples to investigating clinicians and scientists. Brains from individuals without neurological or psychiatric disorders are used as normal controls.

Proper citation: New York Brain Bank at Columbia University (RRID:SCR_007142) Copy   

•   Source: SciCrunch Registry