Curator Dashboard

Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for similarity and expression correction for strain level identification and quantification in metaproteomics. Peptide intensity weighted proteome abundance similarity correction tool to correct identification and spectral counting based quantification results. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth