Curator Dashboard

Core offers micro 3D X-ray imaging of small samples in high resolution and provides images and quantitative analyses of internal structures of ex vivo samples without any destructive procedures.Scanco CT40 system allows for visualization, measurement, and quantification of the structure of mineralized specimens. Contrast reagents permit visualization of soft tissue structures such as blood vessels.System creates 3D model from stack of 2D X-ray images taken around single axis of rotation. High-resolution scanner can capture detail at resolution of 6 to 32 microns. Non- destructive nature of this technology allows investigators to carry out complementary analyses of the same sample. There are two dedicated workstations for analyzing microCT data, the SCANCO analysis software or the Amira software package with XImagePAQ extension.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Software Python suite to convert electron diffraction images to SMV format. Used in three dimensional electron crystallography.Developed to accomplish tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination.

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• RRID-Legacy
• 5 years ago - by Anonymous

Cryo-electron microscopy (cryo-EM) facility providesTitan Krios cryo-transmission electron microscope that is fully equipped for high-throughput data collection of the utmost quality possible. It has the ability to determine the atomic structure of a single protein or view molecules interacting in their cellular context. Provides guidance, training or data collection for researchers at the College of Medicine.Equipment includes Zeiss LSM 980 Cryo-Confocal Microscope,300 kV Krios Cryo-TEM for SPA and tomography, Equipped with Volta phase plates, bioquantum energy filter and K3 direct electron detector,200 kV thermionic JEOL 2100 for cryo-imaging, cryo-tomography, and standard imaging of stained grids.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Animal Cage Enclosures for use in in vivo models that require control of experimental gases such as O2, CO2, NO, or CO. May be used together with gas controllers from BioSpherix. Chamber is outfitted with adjustable ventilation holes which permit ventilation of animal vapors and gases while simultaneously ensuring stable control of experimental conditions within. Available in three standard sizes.

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• SciCrunch
• 5 years ago - submitted by Ray Gould

Controller for live cell microscopy provides two identical streams of any mix of oxygen and carbon dioxide gas without use of premixed gas cylinders. Eliminates need for pre-mixed gas. Controller is used primarily to pre-condition perfusion media while simultaneously conditioning headspace above culture.

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• SciCrunch
• 5 years ago - submitted by Ray Gould

Hypoxia cell culture system includes hypoxia incubator and cell culture hood with glove sleeves.

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• SciCrunch
• 5 years ago - submitted by Ray Gould

Software tool to combine multiple subreads of same SMRTbell molecule using statistical model to produce one highly accurate consensus sequence, also called HiFi read, along with base quality values. This tool powers Circular Consensus Sequencing workflow in SMRT Link.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.

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• RRID-Legacy
• 5 years ago - by Anonymous

Visualization and analysis software for Hi-C data.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool for computing scaffold ordering that maximizes colinearity to collection of maps, including genetic, physical or comparative maps into final chromosome build.Robust scaffold ordering based on multiple maps.

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• RRID-Legacy
• 5 years ago - by Anonymous

a package for automated de novo identification of repeat families from genomic sequences Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes.

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• RRID-Legacy
• 5 years ago - by Anonymous

Database of repetitive DNA elements.Database of prototypic sequences representing repetitive DNA from different eukaryotic species. Used in genome sequencing projects worldwide as reference collection for masking and annotation of repetitive DNA.

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• RRID-Legacy
• 5 years ago - by Anonymous

Open collection of Transposable Element DNA sequence alignments, hidden Markov Models, consensus sequences, and genome annotations.Dfam 3.2 provides early access to uncurated, de novo generated families.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool for assembly free construction of UTRs from short read RNA-Seq data on basis of coding sequence annotation.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed eggNOG v5.0 clusters and phylogenies.

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• RRID-Legacy
• 5 years ago - by Anonymous

Curated component of UniProtKB (produced by the UniProt consortium). It contains hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool for phylogenomic inference.

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• RRID-Legacy
• 5 years ago - by Anonymous

Public knowledge base for information on evolutionary timescale of life. Data from thousands of published studies are assembled into searchable tree of life scaled to time.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies.

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• RRID-Legacy
• 5 years ago - by Anonymous