Curator Dashboard

Series of tutorial material covering a broad selection of topics in bioinformatics. Categories include: Bioinformatics APIs, Data integration, Events, Grid and Cloud Computing, Metabolic modelling, Reviews, Software Comparisons, Statistics, Systems Biology, Transcriptomics, Tutorials.

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• SciCrunch
• 15 years ago - by Anonymous

Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Software Python library for parallel and distributed computing. Enables parallel and out-of-core computation.

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• RRID
• 1 year ago - by Anonymous

Arabidopsis thaliana promoter binding element database that focuses on specific binding elements on known genes, found with experimental methods.

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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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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Public research university in Ann Arbor, Michigan. One of foremost research universities in United States.

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• SciCrunch
• 16 years ago - submitted by Stephen Larson

A Web-based Tool for High-throughput Primer and Probe Design. The program has its different utilities available on its web server. A standalone version is also available. Algorithms: * SSPD - Sequence Specific Primer Design: to design primers for each of the specific sequences given by the user in the query input file against any alternate potential hybridization with any of the sequences given in the database input file. * PSPD - Probe Specific Primer Design: to design primers it selects the gene-specific fragments (probes) to design primer pairs for their PCR amplification. * FSPD Fragment Specific Primer Design: primer design algorithm used when there is a very long query sequence for which multiple primers are required for its amplification. * Check Binding Specificity * Probe Design Only: Probe design algorithm could be used to find sequence-specific probes, which doesn''t show any blast hit against database. Such probe design has been used for targeted sequencing like agilent sure-select technology with next-generation sequencing.

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• SciCrunch
• 13 years ago - by Anonymous

Collections of Addgene plasmids, open access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists. Ordering or depositing plasmids related to COVID-19 research.

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• rapid-viraldb
• 7 years ago - submitted by Jeffrey Grethe

Histology core facility at the University of Michigan School of Dentistry provides histological services using standard histological techniques. The core specializes in sectioning of hard (demineralized) tissues.

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• RRID
• 1 year ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This course emphasizes genetic applications and approaches to drug addiction research through methodological instruction based on literature, data sets and informatics resources drawn from studies of addiction related phenotypes. The course includes plenary sessions on major progress in addiction genetics, and discussion sessions in which students present their work for discussion on applications of genetic methods. Students will leave the course able to design and interpret genetic and genomic studies of addiction as they relate to their specific research question, and will be able to make use of current bioinformatics resources to identify research resources and make use of public data sources in their own research.

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• SciCrunch
• 15 years ago - by Anonymous

Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops.

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• RRID-Legacy
• 7 years ago - by Anonymous

Core dedicated to developing technology to harness abundant, clean, and renewable marine energy in environmentally sustainable way and at competitive cost.

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• RRID
• 1 year ago - submitted by Edyta Vieth

A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool to simplify creation and management of computing environments in Neuroimaging.

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• NIF
• 7 years ago - by Anonymous

Alfalfa_DArTag_BI_Cornell_University 1.0 is an alfalfa DArTag genotyping panel of 3000 loci. DArTag assay uses custom designed oligos to amplify targeted SNPs, and their flanking sequences, prior to NGS sequencing. The sequenced amplicons are demultiplexed and targeted SNPs/haplotypes are analysed using DArT P/L’s proprietary pipeline (https://www.diversityarrays.com/services/targeted-genotying/). The markers were selected from a diverse set of 40 cultivated alfalfa parents and founders from North American breeding programs. The panel is suitable for genotyping tetraploid alfalfa for breeding decisions and selection. Usage of the panel on diploid Medicago was tested and resulted in higher missing data and fewer polymorphic data points. Usage of the panel outside of Medicago sativa is likely to result in higher missing data and fewer data points. Panel developed in collaboration between DArT and Breeding Insight at Cornell University.

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• RRID
• 1 year ago - submitted by Moira Sheehan

GlycomeDB is a database of all known carbohydrate structures. This was achieved by crosslinking several other databases of carbohydrate structures by using the GlycoCT XML language specification. We have analyzed all of the existing public databases and defined a sequence format based on XML (GlycoCT) capable of storing all structural information of carbohydrate sequences. We have implemented a library of parsers for the interpretation of the different encoding schemes for carbohydrates. With this library we have translated the carbohydrate sequences of all freely available databases (CFG , KEGG, GLYCOSCIENCES.de, BCSDB and Carbbank) to GlycoCT, and created a new database (GlycomeDB) containing all structures and annotations. During the process of data integration we found multiple inconsistencies in the existing databases which were corrected in collaboration with the responsible curators. With the new database, GlycomeDB, it is possible to get an overview of all carbohydrate structures in the different databases and to crosslink common structures in the different databases. Scientists are now able to search for a particular structure in the meta database and get information about the occurrence of this structure in the five carbohydrate structure databases.

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• SciCrunch
• 15 years ago - by Anonymous

Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.

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• RRID-Legacy
• 7 years ago - submitted by Nathan Anderson

Software R package provides interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. Allows users to integrate tools from various packages at different stages of analysis workflow.

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• RRID
• 1 year ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 11, 2012. FuncExpression is a web-based resource for functional interpretation of large scale genomics data. FuncExpression can be used for the functional comparison of plant, animal, and fungal gene name lists generated from genomics and proteomics experiments. Multiple gene lists can be classified, compared and visualized. FuncExpression supports two way-integration of plant gene functional information and the gene expression data, which allows for further cross-validation with plant microarray data from related experiments at BarleyBase. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous

EImaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method.

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• SciCrunch
• 7 years ago - submitted by Leah Booher