Curator Dashboard

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

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• SciCrunch
• 7 years ago - by Anonymous

Facility provides diverse range of equipment, expertise and training in field of biochemistry, molecular, structural and cellular biology. Facility consists of several research laboratories and support areas.

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• RRID
• 1 year ago - by Anonymous

Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert).

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• SciCrunch
• 16 years ago - by Anonymous

Core provides analytical and preparative flow cytometers, to facilitate range of experiments in biology of both normal and cancer cells. Experimental analyses, including:Complex, 19 fluorescence parameter immuno-phenotyping;DNA content, ploidy and cell cycle analysis; 17 fluorescence parameter cell sorting and single-cell flow cloning; High speed (10,000 � 30,000+ cells per second) and efficiency (95%+ purity) cell sorting;Assessment of apoptosis;Molecular cytogenetics;Cell function studies;Micro-biological applications;Multiplexed and micro-particle-based analysis;Mass cytometry analysis and imaging;Fluidigm Helios plasma mass cytometer. Cells are labeled with antibodies conjugated to heavy metal markers, vaporized in plasma and detected with time-of-flight mass spectrometry;Fluidigm Hyperion solid tissue imager provides simultaneous imaging of labeled solid tissue sections, for mass cytometry analysis. FCSR has bank of metal reagent kits (for custom antibody conjugation), available for purchase at favorable rates compared to those available commercially. The bank has 35 unique labeling metals, for users to create custom reagents and panels. Please contact FCSR for further information and pricing. Robotic automated cell transfer A.L.S. CellCelector automated cell transfer robot. For automated transfer of single cells and colonies from culture plates, without pre-treatment. Integral bio-safety cabinet for BSL-2 cultures.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core Facility for flow cytometry at the Ludwig-Maximilian-University Hospital Munich. Provides access and services for flow cytometry and cell sorters.

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• RRID
• 1 year ago - by Anonymous

Tennessee Donor Services (TDS) is a nonprofit, independent organization authorized by the Federal Government to accept anatomical gifts for transplantation and research. Its mission is to support families in our communities who have sustained the loss of a loved one by providing an opportunity for organ, eye and tissue donation and by facilitating the recovery and transplantation of these gifts to help others in need. In our area (TN & VA), over 4,600 people now wait for an organ transplant, (heart, liver, lungs, kidneys, intestine or pancreas). Annually, our service area has approximately 300 people who donate one or more organs upon death and over 900 who donate corneas and/or tissues annually. The need for transplants far exceeds the number of donations in the area covered by TDS, and across the nation. Currently, in the United States, more than 108,000 people wait for an organ transplant. One third of them will die waiting for a transplant. TDS'' designated service area includes 84 counties in Tennessee, 10 counties in Virginia, 3 counties in Georgia and 1 county in Kentucky.

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• SciCrunch
• 16 years ago - by Anonymous

Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.

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• RRID-Legacy
• 7 years ago - by Anonymous

Bioimaging Platform provides access to and support for wide variety of advanced microscopy and flow cytometry instruments, enabling researchers to perform studies from the tissue level and down to sub-cellular scales. Provides access to analytical imaging technologies. As such, the platform comprises of advanced microscopy systems for high resolution studies of fixed and live samples as well as for low-phototoxicity imaging of whole organs and organisms.Bioimaging platform includes seven advanced microscopy systems, two flow cytometers and several high-performance analysis workstations.

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• RRID
• 1 year ago - submitted by Paul Antony

A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them.

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• RRID-Legacy
• 7 years ago - submitted by Sergio Martinez-Bellver

Software R package for copy number prediction with correction for GC and mappability bias for HTS data.

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• RRID
• 1 year ago - submitted by Wei Lv

The Brain Tumor Funders'' Collaborative is a partnership among five private philanthropic and advocacy organizations: American Brain Tumor Association, Brain Tumour Foundation of Canada, Children''s Brain Tumor Foundation, James S. McDonnell Foundation, and Sontag Foundation. This Collaborative promotes research directly relating to brain tumors and offers grants to professors and institutions to conduct research.

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• SciCrunch
• 15 years ago - by Anonymous

Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets.

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

Software R package as dissimilarity-based functions for ecological analysis. Used for analyzing ecological data.

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• RRID
• 1 year ago - by Anonymous

A brain bank which has obtained brains from individuals who suffered from some form of dementia. Clinical records and a family history are obtained for each donor in order to better understand each dementing illness and to work towards the improvement of diagnosing, treating, and preventing these diseases.

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• SciCrunch
• 15 years ago - by Anonymous

Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.

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

Core Facility houses 600 MHz Bruker Avance Neo NMR spectrometer available for both collaborative and fee-for-service use. The facility is equipped with a 14.1 T Bruker system and a nitrogen-cooled Prodigy probe, enabling a range of 3D experiments on isotopically labeled biomolecules with enhanced sensitivity for challenging samples. Services include biomolecular structure determination, characterization of biomolecular motions, and stable isotope-resolved metabolomics for studying metabolic pathways.

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• RRID
• 1 year ago - submitted by Mike Sabo

Software that characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results.

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• SciCrunch
• 13 years ago - by Anonymous

GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome

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• SciCrunch
• 17 years ago - by Anonymous

Integrated Cell Browser features integrated single-cell RNA sequencing (scRNA-seq) and single cell ATAC-seq data from human donor-specific pancreatic islet cells. The browser enables detailed interrogation of single cell RNA-seq and single cell ATAC-seq data through intuitive visualizations. Within the single-cell browser, users can first identify and filter single-cell datasets and dataset collections. Users can visualize interactive plots of cell type clusters, gene expression, cell type abundance, and marker gene expression. Donors and their data were provided by external programs described here.

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