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http://www.tbi-impact.org/?p=impact%2Fcalc&btn_calc=GO+TO+CALCULATOR

A calculator that calculates the prediction models for 6 month outcome after Traumatic Brain Injury. Based on extensive prognostic analysis the IMPACT investigators have developed prognostic models for predicting 6 month outcome in adult patients with moderate to severe head injury (Glasgow Coma Scale <=12) on admission. By entering the characteristics into the calculator, the models will provide an estimate of the expected outcome at 6 months. We present three models of increasing complexity (Core, Core + CT, Core + CT + Lab). These models were developed and validated in collaboration with the CRASH trial collaborators on large numbers of individual patient data (the IMPACT database). The models discriminate well, and are particularly suited for purposes of classification and characterization of large cohorts of patients. Extreme caution is required when applying the estimated prognosis to individual patients. The sequential prediction models may be used as an aid to estimate 6 month outcome in patients with severe or moderate traumatic brain injury (TBI). However, the prediction rule can only complement, never replace, clinical judgment and can therefore be used only as a decision-support system.

Proper citation: IMPACT Prognostic Calculator (RRID:SCR_004730) Copy   

•   Source: SciCrunch Registry

http://aws.amazon.com/1000genomes/

A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow.

Proper citation: 1000 Genomes Project and AWS (RRID:SCR_008801) Copy   

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

Data tables providing an overview of information about stem cells that have been derived from mice and humans. The tables summarize published research that characterizes cells that are capable of developing into cells of multiple germ layers (i.e., multipotent or pluripotent) or that can generate the differentiated cell types of another tissue (i.e., plasticity) such as a bone marrow cell becoming a neuronal cell. The tables do not include information about cells considered progenitor or precursor cells or those that can proliferate without the demonstrated ability to generate cell types of other tissues. The tables list the tissue from which the cells were derived, the types of cells that developed, the conditions under which differentiation occurred, the methods by which the cells were characterized, and the primary references for the information.

Proper citation: National Institutes of Health Stem Cell Tables (RRID:SCR_008359) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012a-2518-fb6c-5617-794280000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics.

Proper citation: Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) Copy   

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https://github.com/dorianps/LESYMAP

Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit.

Proper citation: LESYMAP (RRID:SCR_017967) Copy   

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http://www.loni.usc.edu/

Biomedical technology resource center specializing in novel approaches and tools for neuroimaging. It develops novel strategies to investigate brain structure and function in their full multidimensional complexity. There is a rapidly growing need for brain models comprehensive enough to represent brain structure and function as they change across time in large populations, in different disease states, across imaging modalities, across age and sex, and even across species. International networks of collaborators are provided with a diverse array of tools to create, analyze, visualize, and interact with models of the brain. A major focus of these collaborations is to develop four-dimensional brain models that track and analyze complex patterns of dynamically changing brain structure in development and disease, expanding investigations of brain structure-function relations to four dimensions.

Proper citation: Laboratory of Neuro Imaging (RRID:SCR_001922) Copy   

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http://www.cs.tau.ac.il/~shlomito/tissue-net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Network visualizations in which the expression and predicted flux data are projected over the global human network. These network visualizations are accessible through the supplemental website using the publicly available Cytoscape software (Cline, Smoot et al. 2007). Since many high degree nodes exist in the network, special layouts are required to produce network visualizations that are readily interpretable. To this end we produced network visualizations in which hub nodes are repeated multiple times and hence layouts with a small number of edge crossings can be generated. Contains entries for brain compartments and brain pathways.

Proper citation: Network-based Prediction of Human Tissue-specific Metabolism (RRID:SCR_007392) Copy   

•   Source: SciCrunch Registry

http://www.tmslab.org/tmscore.php

At the Berenson-Allen Center for Noninvasive Brain Stimulation (CNBS) at Beth Israel Deaconess Medical Center and Harvard Medical School we have three distinct missions: Research, Education and Patient Care. Our research explores brain-behavior relations, brain plasticity and its modulation, employing different noninvasive brain stimulation techniques combined with careful task design, electroencephalography, and functional brain imaging. Educational efforts feature several Continuing Medical Education Courses including a week long intensive course in noninvasive brain stimulation offered 3 times per year. Our clinical program offers noninvasive brain stimulation for treatment of neuropsychiatric disorders such as depression and schizophrenia, epilepsy, and chronic pain. Clinical work also includes studies of central motor conduction time, cortical excitability, and noninvasive cortical mapping.

Proper citation: BIDMC Transcranial Magnetic Stimulation Core (RRID:SCR_011022) Copy   

•   Source: SciCrunch Registry

http://www.emcdda.europa.eu/eib

The EIB provides assessment tests for substance disorder related clinical instruments that are freely available. Details regarding copyright and/or possible use restrictions are specified for each instrument. Instruments are generally classed according to the intervention field they are designed to be used in (treatment, prevention, or harm reduction), though some instruments may be usable in more than one field.

Proper citation: Evaluation Instruments Bank (RRID:SCR_013246) Copy   

•   Source: SciCrunch Registry

https://www.umassmed.edu/shrna/

Facility houses complete collections of human and mouse lentiviral short hairpin RNA (shRNA) libraries from Open Biosystems/GE Dharmacon, Mammalian Gene Collection (MGC) cDNA Library, and human and mouse CRISPR/Cas9 GeCKO v2 libraries from Addgene.

Proper citation: Massachusetts University Medical School RNAi Core Facility (RRID:SCR_017727) Copy   

•   Source: SciCrunch Registry

https://sdrc.stanford.edu/sdrc-research-cores/dimc/home/

Core facility that provides immune monitoring assays at the RNA, protein, and cellular level, as well as archiving, reporting, and data mining support for clinical and translational studies related to Diabetes. The DIMC is a specialized subcore of the Human Immune Monitoring Center (HIMC) at Stanford.

Proper citation: Stanford Diabetes Research Center Diabetes Immune Monitoring Core (RRID:SCR_016210) Copy   

•   Source: SciCrunch Registry

http://www.lgfus.ca

Provides system for Splicing isoform Annotation. This LISA platform allows high throughput annotation and functional analysis of Alternate Splicing in humans.

Proper citation: Quebeck Sherbrooke University Genomic Core Facility (RRID:SCR_017785) Copy   

•   Source: SciCrunch Registry

https://ipsc.bsd.uchicago.edu/

Core provides training to use latest episomal techniques to reprogram, expand and characterize human and mice iPS cells from skin or blood tissues of healthy subjects and diseased patients. Develops capability to differentiate iPS cells into specific somatic cells, such as neutrons, cardiomyocytes, and hepatocytes.

Proper citation: Chicago University iPSC Core Facility (RRID:SCR_017918) Copy   

•   Source: SciCrunch Registry

https://ki.mit.edu/sbc/escell

Core provides service support to all MIT investigators who utilize specialized in vitro cells such as stem cells, organoids, or primary cell lines and/or novel mouse models to study human diseases such as cancer. Projects involve generation of new model system, such as CRISPR-mediated gene editing in mouse to introduce mutation that mimics one found in patients. Helps with projects required optimization of finicky cell cultures and other challenges.Provides customizable set of service options to match specific needs of each project, including consultative advice and troubleshooting, complete tissue culture and microinjection services within our facilities or hands-on training to enable investigators to perfom these experiments either at their own laboratory or within our facilities.Services Include:Gene Targeting genomic modification through traditional or CRISPR/Cas9 locus targeting, assistance with targeting strategies and vector designs;Embryonic Stem Cells generation of new ES lines from mouse strains, importation and testing of lines from outside sources, differentiation of ES lines into specific cell lineages or cell types and more;Microinjection injection of mouse ES cells into blastocysts to generate chimeras and injection of DNA, RNA or CRISPR RNPs into the pronucleus of fertilized mouse eggs to generate transgenic and edited mice;Specialized Tissue Culture establishemnt of new primary cell cultures from a tumor, tissue or organ; Isolation of fibroblasts (MEFs) from mice for culture and analysis;Tissue Culture for Xenograft and Syngenic Modeling optimization, validation and testing of cell lines for orthotopic placement into mice, coordinated with Preclinical Testing Facility;Repository of Reagent Mice Commonly used wild type mice such as C57BL/6j as well as KrasG12D-based models of cancers are maintained on campus for efficient distrubution;Training and Troubleshooting for all aspects of embryonic stem cells, primary cultures, animal breeding etc.;Serum, DMEM, LIF and other media components that have been tested and verified for use with ES cells.

Proper citation: Massachusetts Institute of Technology Koch Institute Preclinical Modeling Core Facility (RRID:SCR_017899) Copy   

•   Source: SciCrunch Registry

http://www.cti.northwestern.edu/

Core is Northwestern Radiology research facility providing translational imaging capabilities that promote pre-clinical and clinical research efforts. CTI occupies space in basement of Olson building housing imaging equipment along with research staff. Services include Cardiovascular Imaging for development, analysis and application of MRI methods providing insights into structure and function of cardiovascular system,NeuroImaging for functional MRI using spectroscopy and diffusion-weighted imaging to studying human anatomy and physiology during development and disease,Small Animal Imaging for molecular and functional imaging of biological processes in living animal models to study diseases and responses to intervention.

Proper citation: Northwestern University Center for Translational Imaging Core Facility (RRID:SCR_017878) Copy   

•   Source: SciCrunch Registry

http://www.cnbc.cmu.edu/

CNBC is joint venture of University of Pittsburgh and Carnegie Mellon University. Our center leverages the strengths of the University of Pittsburgh in basic and clinical neuroscience and those of Carnegie Mellon in cognitive and computational neuroscience to support a coordinated cross-university research and educational program of international stature. In addition to our Ph.D. program in Neural Computation, we sponsor a graduate certificate program in cooperation with a wide variety of affiliated Ph.D. programs.

Proper citation: Center for the Neural Basis of Cognition (RRID:SCR_002301) Copy   

•   Source: SciCrunch Registry

http://dunham.gs.washington.edu/protocols.shtml

A portal for Maitreya Dunham's lab, which works on the genomic analysis of experimental evolution in yeast using microarrays and the chemostat. Research interests of the lab include experimental evolution of genetic networks in yeast, aneuploidy and copy number variation, comparative genomics, technology development and human genetics in yeast.

Proper citation: Maitreya Dunham's Lab (RRID:SCR_000784) Copy   

•   Source: SciCrunch Registry

http://biosciencedbc.jp/

The National Bioscience Database Center (NBDC) intends to integrate all databases for life sciences in Japan, by linking each database with expediency to maximize convenience and make the entire system more user-friendly. We aim to focus our attention on the needs of the users of these databases who have all too often been neglected in the past, rather than the needs of the people tasked with the creation of databases. It is important to note that we will continue to honor the independent integrity of each database that will contribute to our endeavor, as we are fully aware that each database was originally crafted for specific purposes and divergent goals. Services: * Database Catalog - A catalog of life science related databases constructed in Japan that are also available in English. Information such as URL, status of the database site (active vs. inactive), database provider, type of data and subjects of the study are contained for each database record. * Life Science Database Cross Search - A service for simultaneous searching across scattered life-science databases, ranging from molecular data to patents and literature. * Life Science Database Archive - maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata in a unified format, and to access and download the datasets with clear terms of use. * Taxonomy Icon - A collection of icons (illustrations) of biological species that is free to use and distribute. There are more than 200 icons of various species including Bacteria, Fungi, Protista, Plantae and Animalia. * GenLibi (Gene Linker to bibliography) - an integrated database of human, mouse and rat genes that includes automatically integrated gene, protein, polymorphism, pathway, phenotype, ortholog/protein sequence information, and manually curated gene function and gene-related or co-occurred Disease/Phenotype and bibliography information. * Allie - A search service for abbreviations and long forms utilized in life sciences. It provides a solution to the issue that many abbreviations are used in the literature, and polysemous or synonymous abbreviations appear frequently, making it difficult to read and understand scientific papers that are not relevant to the reader's expertise. * inMeXes - A search service for English expressions (multiple words) that appear no less than 10 times in PubMed/MEDLINE titles or abstracts. In addition, you can easily access the sentences where the expression was used or other related information by clicking one of the search results. * HOWDY - (Human Organized Whole genome Database) is a database system for retrieving human genome information from 14 public databases by using official symbols and aliases. The information is daily updated by extracting data automatically from the genetic databases and shown with all data having the identifiers in common and linking to one another. * MDeR (the MetaData Element Repository in life sciences) - a web-based tool designed to let you search, compare and view Data Elements. MDeR is based on the ISO/IEC 11179 Part3 (Registry metamodel and basic attributes). * Human Genome Variation Database - A database for accumulating all kinds of human genome variations detected by various experimental techniques. * MEDALS - A portal site that provides information about databases, analysis tools, and the relevant projects, that were conducted with the financial support from the Ministry of Economy, Trade and Industry of Japan.

Proper citation: NBDC - National Bioscience Database Center (RRID:SCR_000814) Copy   

•   Source: SciCrunch Registry

http://cvr.yorku.ca/home/

The Centre for Vision Research focuses on interdisciplinary research into human and machine vision and visual processes, into vision's interactions with other senses and with motor and cognitive processes, and in applications such as visually-guided robotics or clinical diagnosis and treatment. The Centre for Vision Research includes the following major research themes: - Human Visual Performance - Visual Human-Computer Interaction, Graphics and Virtual Reality - Visual Psychophysics - Eye Movements and Hand-Eye Coordination - Computational Modeling and Computer Vision - Electrophysiology - Clinical and Developmental Studies - Brain Imaging

Proper citation: Centre for Vision Research (RRID:SCR_002879) Copy   

•   Source: SciCrunch Registry

https://cnprc.ucdavis.edu/

Center for investigators studying human health and disease, offering the opportunity to assess the causes of disease, and new treatment methods in nonhuman primate models that closely recapitulate humans. Its mission is to provide interdisciplinary programs in biomedical research on significant human health-related problems in which nonhuman primates are the models of choice.

Proper citation: California National Primate Research Center (RRID:SCR_006426) Copy   

•   Source: SciCrunch Registry