Curator Dashboard

Multiscale Microscopy Core at OHSU is electron microscopy core that provides services and training to academic and corporate users.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries.

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• SciCrunch
• 17 years ago - by Anonymous

Core provides cell analysis and sorting services. Instruments include Cytek Aurora, Beckman Coulter CytoFLEX S, Thermo Fisher Attune CytPix, SONY MA900, and BD FACSSymphony S6.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

A set of online services created in support of MIRIAM, a set of guidelines for the annotation and curation of computational models. The core of MIRIAM Resources is a catalogue of data types (namespaces corresponding to controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP). MIRIAM Resources are developed and maintained under the BioModels.net initiative, and are free for use by all. MIRIAM Resources are composed of four components: a database, some Web Services, a Java library and this web application. * Database: The core of the system is a MySQL database. It allows us to store the data types (which can be controlled vocabularies or databases), their URIs and the corresponding physical URLs, and other details such as documentation and resource identifier patterns. Each entry contains a diverse set of details about the data type: official name and synonyms, root URI, pattern of identifiers, documentation, etc. Moreover, each data type can be associated with several resources (or physical locations). * Web Services: Programmatic access to the data is available via Web Services (based on Apache Axis and SOAP messages). In addition, REST-based services are currently being developed. This API allows one to not only resolve model annotations, but also to generate appropriate URIs, based upon the provision of a resource name and accession number. A list of available web services, and a WSDL are provided. A browser-based online demonstration of the Web Services is also available to try. * Java Library: A Java library is provided to access the Web Services. The documentation explains where to download it, its dependencies, and how to use it. * Web Application: A Web application, using an Apache Tomcat server, offers access to the whole data set via a Web browser. It is possible to browse by data type names as well as browse by tags. A search engine is also provided.

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• SciCrunch
• 16 years ago - by Anonymous

Shared resource dedicated to unlocking power of electronic health records for clinical and translational research in cancer care. Electronic phenotyping involves querying electronic health record systems and other clinical information systems and databases to identify patients who meet specific set of clinical characteristics. Can be used to support clinical and translational research pursuits, such as hypothesis generation, retrospective data gathering and hypothesis testing, research planning and grant preparation, subject recruitment for prospective clinical trials, and development of prospective research registries. Provides consultative and technical services.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data.

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• SciCrunch
• 14 years ago - by Anonymous

Provides microscopes and imaging stations. Expert staff offers guide to non-expert users. Facility offers imaging expertise in Electron Microscopy, Optical Microscopy, In Vivo Imaging, and Histology.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data.

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• SciCrunch
• 12 years ago - by Anonymous

Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts.

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• SciCrunch
• 4 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.

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• SciCrunch
• 15 years ago - by Anonymous

Software R package to correct systematic errors in nanopore sequencing reads of gene libraries. Retrieves true consensus sequences of variants identified by barcode, needing only few reads per variant.

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• SciCrunch
• 4 years ago - by Anonymous

A reference ontology that models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.

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• SciCrunch
• 13 years ago - by Anonymous

Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models.

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• RRID
• 4 years ago - by Anonymous

An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples.

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• SciCrunch
• 13 years ago - by Anonymous

Core laboratory for nucleic acid sequencing and bioinformatics. Mission includes research support, education, and training.Services encompass range of genomic techniques and applications, sequencing technologies, and bioinformatics analyses. GGBC operates multiple platforms for short-, long-, and single-molecule sequencing reads (i.e., Illumina MiSeq and NextSeq, PacBio Sequel, and Oxford Nanopore MinIon). We also write letters of support (LOS) to offer our capabilities and expertise for grant applications submitted to funding agencies.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts.

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• SciCrunch
• 14 years ago - by Anonymous

Open online platform for single cell RNA-seq. Provides data management and analytics. Used to analyze public and private datasets and you can choose between several best practices workflows and browse existing analyses.

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• RRID
• 4 years ago - by Anonymous

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.

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• SciCrunch
• 13 years ago - by Anonymous

Core to develop and utilize proteomics techniques to answer both basic and translational scientific questions.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core facility that provides the following services: Advanced ultrasound imaging. The mission of the Advanced Fetal Care Center (AFCC) is to provide the finest diagnosis and care for a mother carrying a baby with a congenital anomaly. For these families, our center offers entry to a continuum of care and support that extends throughout childhood--from prenatal diagnosis and counseling, through treatment and long-term follow-up. On rare occasions, our team will recommend and perform intervention during fetal life. Our physicians, who represent all pediatric subspecialty areas, work with a wide range of babies with anomalies. Together, they have developed ground-breaking procedures in fetal medicine and surgery.

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• SciCrunch
• 13 years ago - by Anonymous