Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies.

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• SciCrunch
• 17 years ago - by Anonymous

Web application for creating, collecting, testing, and sharing metadata. It provides templates for metadata models or structures, and is capable of testing those models quickly using real data.

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• SciCrunch
• 9 years ago - submitted by Jeffrey Grethe

Bioinformatics Core Facility at the John G. Rangos Sr. Research Center provides bioinformatics as well as biostatistics services across a wide range of disease domains. The next-generation sequencing data analysis includes, but is not limited to, whole genome-, whole exome-, bulk and single cell epigenome-, bulk and single cell transcriptome, spatial transcriptome, microbiome, metabolome, proteome and lipidome data analysis. The facility specializes in T-, and B- cell repertoire data analysis, multi-omics initiatives, and multimodal analysis. Shiny dashboard and other web application development is also supported.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways.

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• SciCrunch
• 17 years ago - by Anonymous

Software application for PhoxX® Diode Laser to support Omicron products. It is related to uManager open source microscopy software for control of microscopes.

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• RRID-Legacy
• 9 years ago - by Anonymous

Facility, couples cytometry with microscopy, genomics and proteomics using instrumentation, expertise and services. Utilizes advanced super resolution microscopy techniques to gain understanding of cell sorting, analysis and enable cutting-edge spatial and single cell and multi-omics services.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Data set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available.
Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.

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• SciCrunch
• 17 years ago - by Anonymous

Program based on convolutional neural networks for spike detection from calcium traces. It is written in Python and Keras.

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• RRID-Legacy
• 9 years ago - by Anonymous

Core is located on the fourth floor of the Pharmaceutical Sciences Center, is ready to help you with your histology and pathology research. Open to any USC researcher and has everything you will need to make microscope slides from tissue samples. Tissues can be paraffin embedded, sectioned and stained in the laboratory. Sectioning can involve making microtome, vibratome and cryostat thin slices. You can also make color photographs of your microscopic images for publication. Expert advice is available concerning staining techniques and the interpretation of microscopic images.

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• SciCrunch
• 14 years ago - by Anonymous

Dataset consisting of a community sample of individuals ranging in age from 18 to 60 years old with at least two 7.5-minute resting state fMRI scans. During the resting state scan participants were instructed to relax while keeping their eyes open. In part of the sample eye status was randomized between scans. The particular eye status for each scan is indicated in the phenotypic information. No visual stimulus was presented. A subset of participants completed the ICS and PANAS affective behavior scales. The following data are released for every participant: * Scanner Type: Siemens, 3T Trio Tim * 7.5-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * Demographic information, inluding ICS and PANAS scores (included in the release file).

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• SciCrunch
• 13 years ago - by Anonymous

Supplier of mice for research purposes.

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• SciCrunch
• 9 years ago - submitted by Mason Pairish

Multi-purpose core research facility with sub-cores. Genetics, Analytical, Autoclave and Cell Culture Cores. Genetics Core provides Next Generation Sequencing, DNA/RNA and protein quantitation, nucleic acid QC, Real-Time PCR, and Droplet Digital PCR. Analytical Core houses analytical instruments such as UV-Vis, nanoparticle analyzers and plate readers. Some basic molecular biology equipment are also available. Cell Culture Core for researchers who need access to BSL1/BSL2 cell culture facility. Also includes autoclaves or labware sterilization and biohazardous waste disposal.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Biorepository of samples collected from patients with ALS, ALS-frontotemporal dementia (ALS-FTD), primary lateral sclerosis (PLS), progressive muscular atrophy (PMA), hereditary spastic paraplegia (HSP) and multisystem proteinopathy (MSP). Used by Consortium members and the scientific community to advance therapeutic development through study of the relationship between clinical phenotype and underlying genotype, and also through the discovery and development of biomarkers.

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• RRID-Legacy
• 8 years ago - submitted by Anita Bandrowski

Core specializes in production of pure, functional proteins for structural, biophysical, and biochemical studies. Has ability to produce and purify milligram amount of protein.

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• SciCrunch
• 14 years ago - by Anonymous

Assessment test that measures speed of processing by asking participants to discern whether two side-by-side pictures are the same or not. Participants' raw score is the number of items correct in a 90-second period. The items are designed to be simple to most purely measure processing speed. The test overall takes approximately 3 minutes to administer. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested.

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• SciCrunch
• 13 years ago - by Anonymous

Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins.

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• SciCrunch
• 8 years ago - submitted by Anita Bandrowski

Web analysis tool for validating predictive biomarkers of chemotherapy/hormonal therapy/anti-HER2 therapy using transcriptomic data of breast cancer patients. Designed to validate and rank new predictive biomarker candidates in real time. Platform provides resource for researchers to mine database and to validate and rank future biomarker candidates.

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• RRID
• 2 years ago - submitted by Susan Kasper

A self reporting scale to assess if adult patients are suffering from symptoms of attention deficit-hyperactivity disorder (ADHD). The Symptom Checklist is an instrument consisting of the eighteen DSM-IV-TR criteria. Six of the eighteen questions were found to be the most predictive of symptoms consistent with ADHD. These six questions are the basis for the ASRS v1.1 Screener and are also Part A of the Symptom Checklist. Part B of the Symptom Checklist contains the remaining twelve questions.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies.

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• RRID-Legacy
• 8 years ago - submitted by Shaofeng Lin