Curator Dashboard

Software tool as coordinate free approach for comparing biological shapes using landmark data.

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• RRID-Legacy
• 4 years ago - by Anonymous

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

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• SciCrunch
• 13 years ago - by Anonymous

Open source statistical package written in Python 3 and based mostly on Pandas and NumPy. Designed for users who want simple yet exhaustive stats functions.

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• RRID
• 4 years ago - by Anonymous

Software package that uses hidden Ising models to identify enriched genomic regions in ChIP-chip data.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 18, 2022. A tumor bank that provides a large collection of cancer specimens, from breast and other cancers, annotated with clinical information. The CBCF TB enables researchers to address unanswered questions concerning the prognosis and treatment of breast cancer and other cancers. The CBCF TB website is also directed to participants interested in donating tumor tissue or blood. Biological specimens such as blood, urine, bone marrow, and ascites (fluid that sometimes collects in the abdomen) contain genetic information, just as tumor tissue does. These samples can be used in studies that may help researchers see how people with certain genetic make-ups respond to certain treatments. It can also explain why different people have different health problems. CBCF TB, formerly ARTB, was created by a merger of components of two existing Tumor-banking initiatives, the CLS Repository in Calgary and the Tumor bank of the PolyomX Program in Edmonton.

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• SciCrunch
• 16 years ago - by Anonymous

Contains data to inform healthcare decision-making from Cochrane and other systematic reviews, clinical trials, and more. Cochrane reviews bring you the combined results of the worlds best medical research studies, and are recognized as the gold standard in evidence-based health care. Consists of a regularly updated collection of evidence-based medicine databases, including The Cochrane Database of Systematic Reviews. This database includes systematic reviews of healthcare interventions that are produced and disseminated by The Cochrane Collaboration. It is published on a monthly basis and made available both on CD-ROM and the Internet. The review abstracts are available to browse and search free of charge on this website. The Cochrane Library Users'' Group (CLUG) provides a forum for discussion of usability, readability, searchability, and formatting issues related to the use of The Cochrane Library. The Cochrane Collaboration is an international not-for-profit and independent organization, dedicated to making up-to-date, accurate information about the effects of healthcare readily available worldwide. Funded by John Wiley and Sons Limited. The individual entities of The Cochrane Collaboration are funded by a large variety of governmental, institutional and private funding sources, and are bound by organisation-wide policy limiting uses of funds from corporate sponsors.

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• SciCrunch
• 14 years ago - by Anonymous

Open source framework for single cell characterization and visualization.Graphical user interface, standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes.

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• RRID
• 4 years ago - submitted by Samantha White

GWASrap is a comprehensive web-based bioinformatics tool to systematically support variant representation, annotation and prioritization for data generated from genome-wide association studies (GWAS) and Next Generation Sequencing (NGS). Our web-based framework utilizes state-of-the-art web technologies to maximize user interaction and visualization of the results. For a given SNP dataset with its P-values, GWASrap will first provide a Circos-style plot to visualize any genetic variants at either the genome or chromosome level. The tool then combines different genomic features (SNP/CNV density, disease susceptibility loci, etc.) with comprehensive annotations that give the researcher an intuitive view of the functional significance of the different genomic regions. The detailed statistics of the underlying study are also displayed on the web page, including variant distribution in different functional categories, classic Manhattan plot and QQ plot. Users can perform interactive operations in the Manhattan panel, such as zooming in and out to search regions or markers of interest. The system can also display a comprehensive range of relevant information from variant genetic attributes to nearby genomic elements, such as enhancers or non-coding RNAs. Furthermore, researchers can obtain extensive functional predictions for various features including transcription factor-binding sites, miRNA and miRNA target sites, and their predicted changes caused by the genetic variants. Our system can re-prioritize genetic variants by combining the original statistical value and variant prioritization score based on a simple additive effect equation. Researchers can also re-evaluate the significance of a trait/disease-associated SNP (TAS) using the dynamic linkage disequilibrium (LD) panel or the tree-like network panel. The GWASrap supports input variants in different formats, not only common variants with a dbSNP rs ID but also rare variants from NGS data, which are represented by chromosome and locations. GWASrap provides a range of web services for data retrieving about the annotation information and effect prediction of each variant in dbSNP using the SOAP interface. The WSDL for each service is available in the API tab. Each service returns JSON string including all related information with key/value. GWASrap provides running results about some current published GWAS as well as a category view for each hot disease / trait. The dataset is brought from published database GWAS or curated from literature.

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• SciCrunch
• 15 years ago - by Anonymous

Core provides intravital imaging equipment to acquire advanced descriptive and quantitative data for imaging studies. Includes Olympus FVMPE-RS advanced multiphoton microscope, multichannel, multiphoton excitation system specifically tailored for intravital and deep tissue imaging.System is additionally equipped with 458 and 588 nm stimulation laser lines for photobleaching, light stimulation and/or photoactivation of various fluorescent or caged constructs. Uses Spectra-Physics InSight X3 dual-line, tunable multiphoton laser for ultrafast, multichannel imaging.Available Neurotar Mobile Home Cage allows researchers to integrate real-time imaging with behavioral/locomotion tracking. Offers training and access to imaging system, support in design of experimental procedures, acquisition of image data, and analysis of acquired images.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 8th,2024. Facility offers sequencing services on three platforms, gold standard Sanger sequencing on ABI capillary sequencers, next generation sequencing (NGS) on Ion Torrent PGM and S5 and, Illumina MiSeq along with experimental design and data analysis.NGS service includes library preparation for multiple applications including targeted sequencing, RNA-Seq and Exome-Seq. Capillary sequencers also enable microsatellite genotyping and fragment analysis for VNTR, SNaPshot and Human Cell Line Authentication. Molecular biological services include PCR, cloning, subcloning, mutagenesis, construct preparation and, plasmid DNA preps at different scales.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

It is an independent nonprofit organization established to provide meaningful trans-disciplinary experiential education to students by making the most cutting-edge instructional methods and technologies available to them to bring new inventions to the marketplace and to encourage knowledge sharing and collaboration among its numerous constituencies. The Center provides a comprehensive program in which its students learn and acquire real-world experience by assisting universities, private and public research institutions, companies, and entrepreneurs to evaluate new technologies and facilitate the creation and development of new ventures. By offering a virtual venue for students and other constituencies worldwide, our stakeholders and collaborators can connect and share knowledge, expertise, resources, best practices, and other important information. Employers, investors and others searching for talent place a premium on relevant experience. However, students, individuals seeking a change in their careers, and prospective entrepreneurs often find it difficult to obtain positions that can provide needed experience, even if they are willing to work without compensation. This conundrum often leads to people taking or staying in positions for which they have no passion and which do not make the best use of their abilities. The Centers program is designed to provide extensive, intensive and relevant experience to its participants, with particular emphasis on teaching them to adapt to and thrive in our lightning fast, rapidly changing and increasingly flat world. As an independent organization, the Centers program and activities are not restricted to any particular institution or jurisdiction. Thus the Center can attract students, clients, professionals and other stakeholders, establish collaborations, and pursue other opportunities appropriate to its mission almost anywhere. eductional resource.

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• SciCrunch
• 14 years ago - by Anonymous

Core is division of Genetics Core Facilities, University service center to provide consultation, training, and services in areas of cell culture and hybridomas. Stockroom serves University of Pennsylvania investigators and affiliate institutions by coordinating relations with various suppliers of molecular biological research materials. This involves not only bulk purchasing of these products, but negotiation of discounts and convenient delivery arrangements. Special ordering of non regularly stocked products is available from 28 bioreagent vendors with discounted pricing and overnight delivery.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Open-source software pipeline for population genomics. Designed for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium.

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• SciCrunch
• 14 years ago - by Anonymous

Core within Division of Gastroenterology provides services which�represents intersection between host and their microbes in both�preclinical and clinical human subject research.Offers human biospecimen repository with associated clinical metadata, instrumentation/access to critical analytic services to characterize expression (i.e. genomics, transcriptomics, metabolomics, microbial culture, etc.) in both microbes and�their mammalian hosts, as well as expertise to extend pre-clinical in vitro and animal model research into human clinical domain. �

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

FUN is an international organization that is focused on neuroscience education and research at the undergraduate level. FUNs members and supporters include businesses and organizations; private liberal arts colleges, state and research university departments and programs; and individual faculty and students, all sharing a common interest in undergraduate neuroscience.

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• SciCrunch
• 17 years ago - by Anonymous

Offers consultation and laboratory services for high-throughput sequencing (HTS) experiments, with particular expertise and interest in microbiome/metagenome and RNA-seq applications. Provides instrumentation, including Illumina NextSeq 2000 and single cell platforms from 10X genomics and 1CellBio. Offers full service options, as well as hands on instruction for trainees who want to learn best practices for wet lab aspects of genomics experiments. Offers consultation services for all phases of HTS studies, from study design to bioinformatics analysis.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Stroke Trials Registry is a continuously updated registry of randomized clinical trials in stroke and cerebrovascular disease. This project is a free public service from the Internet Stroke Center at Washington University School of Medicine; with support from the American Stroke Association and the National Institute of Neurological Disorders and Stroke. This registry will meet technical standards for inclusion in the International Clinical Trials Registry Platform of the World Health Organization. The information on this site is intended for health professionals. SPOTRIAS is an NIH-funded network of stroke research centers that perform early phase clinical projects, share data, and promote new approaches to therapy for acute stroke. clinical data, human, homo sapien, stroke, translational medicine

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• SciCrunch
• 14 years ago - by Anonymous

Software tools to register histological section images and cell count locations to mouse brain atlas. Semi automated workflow and GUI for automated brain slice histology alignment, registration, and cell quantification. Used to explore Allen Mouse Brain Atlas, register asymmetric slice images to atlas using manual input, and analyze region of interest data by registering locations of fluorescently labeled cells to standardized regions of Atlas.

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• SciCrunch
• 4 years ago - submitted by Jude Frie

A classification system developed by the National Institute on Aging and the Alzheimer's Association that can be used to integrate and compare Alzheimer's disease (AD) research portfolios from public and private organizations supporting AD research in the US and abroad. The CADRO was constructed as a three-tier classification system organized around seven major categories: five in research and two resource-related: * Category A. Molecular Pathogenesis and Pathophysiology of Alzheimer's Disease * Category B. Diagnosis, Assessment and Disease Monitoring * Category C. Translational Research and Clinical Interventions * Category D. Epidemiology * Category E. Care, Support and Health Economics of Alzheimer's Diseases * Category F. Research Resources * Category G. Consortia and Public Private Partnerships * Category H. Alzheimer's Disease - Related Dementias Using information from project abstracts and research aims, the above categories were stratified into research topics and these were further divided into research themes. The three levels of classification are meant to enable a fine-grained portfolio analysis that can inform strategic planning and funding decisions. The CADRO was developed as a dynamic portfolio analysis tool that can be used to: (i) capture the changing landscape of AD research funded by different organizations, (ii) identify opportunities for coordination of support for AD research, and (iii) identify funding gaps as well as areas of overlap within and across organizations.

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• SciCrunch
• 13 years ago - by Anonymous