Curator Dashboard

Software for de novo data simulation. It uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and GC%-depth bias.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool for protein structure alignment based on TM-score.Used to identify structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming. Used for sequence independent protein structure comparisons.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Accepts and provides access to geoscience data, primarily marine, collected from oceanographic expeditions in the Antarctic region. The synthesis began in 2003 as the Antarctic Multibeam Bathymetry and Geophysical Data Synthesis (AMBS) with a focus on multibeam bathymetry field data and other geophysical data from the Southern Ocean collected with the R/V N. B. Palmer. In 2005, the effort was expanded to include all routine underway geophysical and oceanographic data collected with both the R/V N. B. Palmer and R/V L. Gould, the two primary research vessels serving the US Antarctic Program. Data available include seafloor bathymetry, subbottom profiling, trackline gravity and magnetics, meteorological, and water column data as well as basic cruise information for all Palmer and Gould expeditions. Seafloor bathymetry data are provided both as raw swath data as well as in gridded form through the Global Multi-Resolution Topography (GMRT) synthesis. This gridded compilation of seafloor bathymetry data can be accessed through GeoMapApp, Create Maps and Grids and through an OGC-compliant Web Map Service. GeoMapApp is an integrated mapping application that provides access to many additional regional bathymetric grids, seismic, radar, gravity and magnetics profiles as well as other map and grid compilations for the Antarctic continent including LIMA.

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• SciCrunch
• 14 years ago - by Anonymous

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.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software Python package for wavelet analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Assists scientists in finding Antarctic scientific data of interest and submitting data for long-term preservation in accordance with their obligations under the National Science Foundation (NSF) Office of Polar Programs (OPP) Data Policy.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Core that provides services in genotyping, sequencing, biobanks, and genetic epidemiology. It also offers access to the Amish exome variant database, basic molecular services, and viral vector construction and development.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Microscopy facility specializes in areas of optical microscopy, electron microscopy, and histology. Facility is equipped with confocal microscopes, research fluorescence microscopes, and transmission and scanning electron microscopes. Research staff engage in experimentation, training, project collaboration, and consultation.

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• SciCrunch
• 3 years ago - submitted by Craig Praul

An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

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• SciCrunch
• 12 years ago - by Anonymous

Core that provides pathology research service, live microscopy service, and confocal imaging to facilitate morphologic studies in digestive diseases.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A powerful and modular medical image viewer/editor. It should be particularly useful to Undergraduates, Postdocs and Researchers in Medical Imaging to visualize data and to easily make attractive figures (for papers or presentations). It will also in a near future offer a number of advanced algorithms for medical image processing. Look at the video to get an idea ! http://www.benoitscherrer.com/MisterI/videos.html

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• SciCrunch
• 14 years ago - by Anonymous

Core composed of the Viral Unit, which provides labeled andn unlabeled viral components, and Bacterial Unit, which provides bacteria and bacterial proteins for research. The retroviral unit focues on the viral components of the retrovirus HIV-1.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Core for drug discovery and prototyping. Provides chemical probes for biological pathways and supports small molecule custom synthesis.Provides expertise in medicinal chemistry to biologists and clinicians at Stanford. Expertise in each step of drug development process, including hit generation, drug design and optimization, and clinical selection. Provides instrumentation to support synthesis, purification and analysis of small molecules.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides custom designed monoclonal antibodies made in mice, rats and rabbits. Services include design of antigens, immunization and screening strategies; hybridoma cell line production and optimization; and custom designed antibodies for biomarker discovery.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Stable Isotope Biogeochemistry Laboratory at Stanford University's School of Earth Sciences provides analytical facilities and technical expertise to members of Stanford community who need to determine stable isotope ratios of variety of organic and inorganic materials from both terrestrial and marine environments.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium.

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• SciCrunch
• 17 years ago - by Anonymous

Core that provides importation/exportation, colony management, customized mouse models, rederivation and creation of genetically-modified mutant mice (e.g. CRISPR), and re-animation of a variety of models cryopreserved within the KOMP or MMRRC repositories. It also provides ancillary services and procedures, including blood sampling for in vivo testing for glucose tolerance tests and insulin tolerance tests.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Procures and provides needed tissue specimens to Stanford Cancer Institute investigators to support cancer related research. Services include collecting and banking freshly frozen tumor and normal tissue from surgical material and autopsy specimens;Providing fresh tumor tissue for viable cell studies;Processing and banking blood from cancer patients;Maintaining tissue database with links to clinicopathological data;Providing histological staining and pathological review;Coordinating patient consent and assuring regulatory compliance.Provides portal to virtual bank which links inventories of specialized satellite repositories, including collections of hematological and neurosurgical specimens.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth