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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
The WEB ATLAS contains photographs of dissected brains showing important structures. The diagrams folder contains drawings showing functionally important parts of the brain as well as drawings of dissections adapted from C.G. Smith. We are particularly pleased to make Nan Cheney''s medical illustrations of the brain and the head available. The STROKE MODEL portion of the website has syndromes associated with strokes of different vessels of the brain as well as extensive diagrams and tables about the vessels of the brain. The 3D RECONSTRUCTIONS featured on this website were made from MRI scans through the brain - where indicated the source material was from the NIH Visible Human Project. The website will also contain material important for the neuroanatomy labs for med students at UBC. Weekly quizzes will help you keep up with studying the material, the podcasts will help you review material presented in the labs, and the weekly wikis will help you share information with your peers.
Proper citation: Neuroanatomy at UBC (RRID:SCR_008744) Copy
http://lrcv-crp-sante.s3-website-us-east-1.amazonaws.com/
A gene set analysis algorithm for biomarker identification in the cloud.
Proper citation: YunBe (RRID:SCR_008740) Copy
Gnuplot is a portable command-line driven graphing utility for linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don''t have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986. Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types. Demos here. Gnuplot supports many different types of output: interactive screen terminals (with mouse and hotkey input), direct output to pen plotters or modern printers, and output to many file formats (eps, fig, jpeg, LaTeX, metafont, pbm, pdf, png, postscript, svg, ...). Gnuplot is easily extensible to include new output modes. Recent additions include an interactive terminal based on wxWidgets and the creation of mousable graphs for web display using the HTML5 canvas element.
Proper citation: Gnuplot (RRID:SCR_008619) Copy
http://www.broadinstitute.org/cancer/cga/invex/
A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations.
Proper citation: InVEx (RRID:SCR_008734) Copy
An information extracting and processing package for biological literature that can be used online or installed locally via a downloadable software package, http://www.textpresso.org/downloads.html Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. The Textpresso project serves the biological and biomedical research community by providing: * Full text literature searches of model organism research and subject-specific articles at individual sites. Major elements of these search engines are (1) access to full text, so that the entire content of articles can be searched, and (2) search capabilities using categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or identify one (e.g., cell, gene, allele, etc). The search engines are flexible, enabling users to query the entire literature using keywords, one or more categories or a combination of keywords and categories. * Text classification and mining of biomedical literature for database curation. They help database curators to identify and extract biological entities and facts from the full text of research articles. Examples of entity identification and extraction include new allele and gene names and human disease gene orthologs; examples of fact identification and extraction include sentence retrieval for curating gene-gene regulation, Gene Ontology (GO) cellular components and GO molecular function annotations. In addition they classify papers according to curation needs. They employ a variety of methods such as hidden Markov models, support vector machines, conditional random fields and pattern matches. Our collaborators include WormBase, FlyBase, SGD, TAIR, dictyBase and the Neuroscience Information Framework. They are looking forward to collaborating with more model organism databases and projects. * Linking biological entities in PDF and online journal articles to online databases. They have established a journal article mark-up pipeline that links select content of Genetics journal articles to model organism databases such as WormBase and SGD. The entity markup pipeline links over nine classes of objects including genes, proteins, alleles, phenotypes, and anatomical terms to the appropriate page at each database. The first article published with online and PDF-embedded hyperlinks to WormBase appeared in the September 2009 issue of Genetics. As of January 2011, we have processed around 70 articles, to be continued indefinitely. Extension of this pipeline to other journals and model organism databases is planned. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 24 different literatures, among them Neuroscience, and can readily be extended to other corpora of text.
Proper citation: Textpresso (RRID:SCR_008737) Copy
Imaging center dedicated to fostering research in the social, behavioral, biological, engineering, and materials sciences where imaging methodologies play a central role. The SLEIC provides the Penn State research community with instrumentation, technological and substantive expertise, educational opportunities, and financial support for conducting magnetic resonance imaging (MRI) and electrophysiology (EEG, ERP) experiments.
Proper citation: Pennsylvania State University SLEIC (RRID:SCR_014922) Copy
http://www.sailing.cs.cmu.edu/main/?page_id=511
Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns.
Proper citation: SPEX2 (RRID:SCR_014923) Copy
https://sites.google.com/ucsd.edu/drc/home
Research center across five institutions for clinical research in diabetes. Collaborators include UC San Diego's School of Medicine, Salk Institute, Cedars-Sinai Medical Center, UC Los Angeles' School of Medicine, and LA Biomedical Research Center.
Proper citation: University of California San Diego - University of California Los Angeles Diabetes Research Center (RRID:SCR_015100) Copy
https://dogma.ccbb.utexas.edu/
Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
Proper citation: DOGMA (RRID:SCR_015060) Copy
Research center which operates in collaboration with the University of Alabama Birmingham Comprehensive Diabetes Center to promote excellence in diabetes research and patient care. The DRC supports the areas of animal physiology, human biology and intervention and translational research. It focuses on developing new methods to treat, prevent, and ultimately cure diabetes and its complications.
Proper citation: University of Alabama at Birmingham Diabetes Research Center (RRID:SCR_015107) Copy
https://diabetes.med.umich.edu/partners/michigan-diabetes-research-center-mdrc
Multidisciplinary unit of the University of Michigan funded by the National Institute of Diabetes and Digestive and Kidney Diseases/National Institute of Health. Promotes new discoveries and enhance scientific progress through the support of basic and clinical research related to diabetes, its complications, and related disorders. Creates environment that supports innovative research; attracts and retains early stage investigators and investigators new to diabetes research; provides core services that leverage funding and unique expertise; fosters interdisciplinary collaborations; raises awareness and interest in fundamental and clinical diabetes research at their institutions, as well as locally, regionally, and nationally.
Proper citation: Michigan Diabetes Research Center (RRID:SCR_015112) Copy
Consortium of laboratory-based and clinical investigators who research etiology, pathogenesis, treatment and cure of type 1 and type 2 diabetes, and their associated microvascular and atherosclerotic complications.
Proper citation: Boston Area Diabetes Endocrinology Research Center (RRID:SCR_015072) Copy
http://www.einstein.yu.edu/centers/diabetes-research/
Research center that facilitates the research of diabetes and related studies in obesity, metabolism and endocrinology
Proper citation: Einstein-Mount Sinai Diabetes Research Center (RRID:SCR_015070) Copy
http://bioinformatics.psb.ugent.be/orcae/
Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community.
Proper citation: Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) Copy
https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMBCX
Mass spectrometer that combines quadrupole, ion trap, and Orbitrap mass analysis.
Proper citation: LTQ-Orbitrap Fusion Tribrid Mass Spectrometer (RRID:SCR_014992) Copy
Statistical software for ROC curve analysis. MedCalc performs several statistical tests such as method comparison, method evaluation, reference intervals, and meta-analysis.
Proper citation: MedCalc (RRID:SCR_015044) Copy
https://www.nikoninstruments.com/en_EU/Products/Upright-Microscopes/Research/Eclipse-FN1
Fixed-stage microscope for electrophysiological research. Features include open design, noise reduction, 16x objective lens, and water dipping objective with depth induced aberration correction.
Proper citation: Nikon: Eclipse FN1 Microscope (RRID:SCR_014995) Copy
Private organization that offers resources and serves as a community for those recovering from addiction and to help patients find the highest quality care for a successful recovery.
Proper citation: AddictionResources (RRID:SCR_015048) Copy
https://www.agilent.com/cs/library/datasheets/Public/5991-2541EN.pdf
Hardware system which automates RNA, DNA, and protein sample QC, including sample loading, separation, and imaging.
Proper citation: Agilent: 2200 TapeStation Instrument (RRID:SCR_014994) Copy
This resource is not available. Documented on October 6, 2020.Software for the analysis of mass spectrometry data. MassHunter also works with software-specific packages to do more specialized analysis tasks.
Proper citation: Agilent Masshunter Quantitative Analysis software (RRID:SCR_015040) Copy
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
