Curator Dashboard

Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data.

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• RRID-Legacy
• 7 years ago - submitted by Chao Yang

Facility offers NMR technologies to determine content and purity of sample as well as its molecular structure, interactions and chemometrics of biological mixtures.

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• RRID
• 1 year ago - by Anonymous

A web server for functional annotation of novel and publicly known genetic variants that was developed to assess the potential significance of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models in order to identify the phenotypically important variants. A broader range of variations have been incorporated such as insertions / deletions, block substitutions, IUPAC codes submission and region-based analysis, expanding the query size limit, and most importantly including additional categories for the assessment of functional impact. SNPnexus provides a comprehensive set of annotations for genomic variation data by characterizing related functional consequences at the transcriptome/proteome levels of seven major annotation systems with in-depth analysis of potential deleterious effects, inferring physical and cytogenetic mapping, reporting information on HapMap genotype/allele data, finding overlaps with potential regulatory elements, structural variations and conserved elements, and retrieving links with previously reported genetic disease studies.

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• SciCrunch
• 13 years ago - by Anonymous

A service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted. The JGA accepts only de-identified data approved by JST-NBDC. The JGA implements access-granting policy whereby the decisions of who will be granted access to the data resides with the JST-NBDC. After data submission the JGA team will process the data into databases and archive the original data files. The accepted data types include manufacturer-specific raw data formats from the array-based and new sequencing platforms. The processed data such as the genotype and structural variants or any summary level statistical analyses from the original study authors are stored in databases. The JGA also accepts and distributes any phenotype data associated with the samples. For other human biological data, please contact the NBDC human data ethical committee.

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• SciCrunch
• 13 years ago - by Anonymous

Centralized knowledge base of the human pancreas for diabetes research. Integrates diverse type 1 diabetes (T1D) datasets with expert-curated knowledge in centralized, open-source data hub. Since users will ultimately be able to contribute their own data, this will be repository for reproducible, collaborative research within the pancreas and T1D realms.

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• dkNET
• 1 year ago - submitted by Ko-Wei Lin

A Java application to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing. This tool may be used on a single RNASeq sample to identify genes with multiple spliceforms, on a pair of samples to identify differential splicing between the two, or on groups of samples to identify statistically significant group level differences in splicing patterns. SpliceSeq can be run from the install page as a java web start application to explore the sequencing data on their server or can be installed locally to analyze your own mRNA-Seq data.

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• SciCrunch
• 13 years ago - by Anonymous

GTAC offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users. Full service facility, from hypothesis to publication. Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms.

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• RRID-Legacy
• 7 years ago - submitted by Nate Herzog

Program of University of Wisconsin Population Health Institute, highlights policies and practices that can help everyone be as healthy as possible. Aims to grow shared understanding of health, equity and power of communities to improve health for all.

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• RRID
• 1 year ago - by Anonymous

A Web service that annotates textual metadata (e.g. journal abstract) with relevant ontology concepts. NCBO uses this Web service to annotate resources in the NCBO Resource Index. They also provide this Web service as a stand-alone service for users. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Their service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.

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• SciCrunch
• 15 years ago - by Anonymous

Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data.

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• dkNET
• 7 years ago - submitted by Ko-Wei Lin

Core provides services for genomics analysis, from sample processing through data generation. Available technologies focus on Illumina RNA and DNA sequencing. RNA-seq can be performed from a variety of sample types, including purified total RNA, cell populations (including low input samples of 50-1000 cells), or single cells (either plate-sorted rare populations or high-throughput 10x single-cell analyses). DNA-seq pipelines can also be performed, including bulk CUT and Tag/CUT and RUN, and ATAC-seq and single cell ATACseq and multiome capture. Custom prepared libraries can also be submitted for sequencing. Core laboratory houses Illumina sequencers, NextSeq2000 instruments and Miseq, plus 10x Chromium X and 10x CytAssist. Additional equipment includes ThermoFisher Kingfisher Flex, for extracting nucleic acid from variety of sample types using magnetic bead technology with throughput of up to 96 samples. Qiagen QIAcube Connect instruments automate extraction of nucleic acid using spin column technology. Ancillary equipment for sample processing includes Formulatrix Mantis Liquid Handler, Agilent TapeStation 4200 and Tecan NanoQuant.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data that is distributed on top of the core Kepler scientific workflow system.

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• SciCrunch
• 13 years ago - by Anonymous

Contract Research Org. specializing in custom protein analysis. Services Provided include SDS PAGE analysis, Western Blotting, Mass Spectrometry, protein staining ( silver,coomassie) for academia, federal institutions and industry.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core focused on metabolomics, lipidomics, medicinal chemistry, and small molecule analysis. Offers services, expertise, and collaboration for the research community. Instrumentation includes high field nuclear magnetic resonance (NMR), liquid chromatography–mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), high-performance liquid chromatography (HPLC), circular dichroism spectrometer (CD), inductively coupled plasma optical emission spectrometry (ICP-OES), and fluorimeter. Consulting is available to assist with experimental design and data interpretation.

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• RRID
• 1 year ago - by Anonymous

The American Society for Investigative Pathology (ASIP) is a society of biomedical scientists who investigate mechanisms of disease. Investigative pathology is an integrative discipline that links the presentation of disease in the whole organism to its fundamental cellular and molecular mechanisms. It uses a variety of structural, functional, and genetic techniques and ultimately applies research findings to the diagnosis and treatment of diseases. ASIP advocates for the practice of investigative pathology and fosters the professional career development and education of its members. The mission of the Society is to promote the discovery, advancement, and dissemination of basic and translational knowledge in experimental pathology and related disciplines. This shall be achieved by fostering investigation into the pathogenesis, classification, diagnosis, and manifestations of disease through meetings, publications, and educational activities. ASIP welcomes basic and clinical biomedical research scientists as active members.

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• SciCrunch
• 15 years ago - by Anonymous

Software tool to accompany existing resources such as Python programming language resource and comprehensive Perl archive network (CPAN) resource. Perl is family of two high level, general purpose, interpreted, dynamic programming languages. Perl refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned sister language, Perl 6, before name was officially changed to Raku in October 2019.

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• RRID-Legacy
• 7 years ago - by Anonymous

Core provides training, education, statistics and data management services. Services include: experimental design of new studies, advising on outcomes selection, determining or justifying sample size, designing randomization schemes,designing and writing the statistical analysis/modeling section(s), advising on appropriate database design and implementation methods, advising on the use of national data registries, health system data, grant writing on relevant sections within our specialties, creating custom databases and data entry portals for prospective studies, creating custom datasets or extracts from existing data sources for analysis, merging complex or multi-sourced data in concert with research aims and objectives, implementing blind, double-blind and other randomization schemes and more.

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• RRID
• 1 year ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. Mouse brains displayed in the Microsoft Silverlight PivotViewer from the Mouse Brain Library (MBL) which consist of high-resolution images of brains from many genetically characterized strains of mice. PivotViewer makes it easier to interact with massive amounts of data on the web in ways that are powerful, informative, and fun. By visualizing thousands of related items at once, users can see trends and patterns that would be hidden when looking at one item at a time. Because PivotViewer leverages Deep Zoom, it displays full, high-resolution content without long load times, while the animations and natural transitions provide context and prevent users from feeling overwhelmed by large quantities of information. This simple, inviting interaction model encourages exploration and longer audience engagement times, and applies broadly to a variety of content types.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2020. Software tool as automated Gene Ontology based multi species gene set generator for gene set enrichment analysis. Used to generate gene sets required for Gene Set Enrichment Analysis for almost any organism for which GO term association data exists.
Gene set collections can be automatically created for wide variety of species.

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• RRID-Legacy
• 7 years ago - by Anonymous

Interdisciplinary unit organized under University of Michigan's Medical School - Department of Radiology, dedicated to supporting research on structures and functions of brain that underlie cognitive and affective processes, and research on functional MRI and associated research tools. Provides equipped physical facility and intellectual support services for investigators.

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• RRID
• 1 year ago - submitted by Edyta Vieth