Curator Dashboard

Web tool as HMM plus similar protein based gene prediction. Used for multiple gene prediction in genomic DNA with using information from similar protein. Used if you know protein sequence similar with protein which is encoded by gene in your sequence.

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• SciCrunch
• 6 years ago - by Anonymous

Web server for macromolecular structure model optimisation and databank of optimised structure models. Focuses on automating final steps of crystallographic process: optimisation of structure model through refinement, rebuilding, and validation. Can automatically optimise most of crystallographic structure models based on input model and diffraction data. Web server works on user provided data, databank has updated versions of Protein Data Bank entries based on original experimental data that were deposited with atomic coordinates in PDB.

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• RRID-Legacy
• 6 years ago - by Anonymous

Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains.

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• RRID-Legacy
• 6 years ago - by Anonymous

High-speed fluorescence-activated cell sorter (FACS) used in biological and medical research to analyze and physically separate specific types of cells from a complex mixture. It works by passing individual cells in a fluid stream past lasers and capturing target cells based on their unique light-scattering and fluorescent properties. Cell sorter features hardware and software enhancements that improve overall ease of use, flexibility,and aseptic capability. Offers new options in lasers and nozzles to support more advanced multicolor applications. Built on fixed alignment technology. FACSAria II cell sorter is first generation of BD FACSAria system where flow cell is in true fixed alignment with laser, to reduce startup time and improve reproducibility.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.

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• RRID-Legacy
• 6 years ago - by Anonymous

Microplate Reader from Molecular Devices is ideal for UV-Vis life science applications, especially DNA analysis. Multi channel design mimics dual beam spectrophotometer. Each sample has discrete sample beam and reference beam so that each well is measured directly, eliminating error due to variations in light output between optic fibers. System consists of eight sample beams and detectors and eight reference beams and detectors to deliver both precision and speed of reading across microplate through 4.0 OD. Detects 16 ng per well of DNA and quantitates 50 ng of DNA.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software R package to produce publication ready volcano plots with enhanced colouring and labeling. Used to visualise results of differential expression analyses.

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• RRID-Legacy
• 6 years ago - submitted by Christopher Haga

Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

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• SciCrunch
• 6 years ago - by Anonymous

Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software.

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• SciCrunch
• 6 years ago - by Anonymous

Software fast and lightweight tool for processing sequences in FASTA or FASTQ format.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software drug discovery platform to integrate purchasable chemical space with molecular modeling tools. Chemical marketplace for drug discovery with services based around small molecule compound sourcing. Integrated molecular modeling tools, compound database, IT infrastructure and compound procurement service with web interface. Virtual screens can be run to identify new hits and modeling applications can be used to improve their affinity and other properties.

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• SciCrunch
• 6 years ago - by Anonymous

Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays. Developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays. Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix.

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• RRID-Legacy
• 6 years ago - by Anonymous

Pipeline developed in collaboration with Bing Ren lab and supports processing of BICCN single-cell/nucleus ATAC-seq datasets. Pipeline uses python module SnapTools to align and process paired reads in form of FASTQ files. Produces hdf5-structured Snap file that includes cell-by-bin count matrix. Final outputs also include GA4GH compliant aligned BAM and QC metrics.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.

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• SciCrunch
• 6 years ago - submitted by Michele Ceccarelli