Curator Dashboard

Software tool for identifying hub objects and sub-networks from complex interactome. Predicts and explore nodes and subnetworks in given network by several topological algorithms. Provides interface to analyze topology of protein-protein interaction networks, such as human, yeast, rat, mouse, fly etc. Plugin works with Cytoscape 2.6 or above, which requires Java 1.5 or above.

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• RRID-Legacy
• 7 years ago - submitted by Yanming Liu

Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution.

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• SciCrunch
• 7 years ago - submitted by Haris Zafeiropoulos

Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community.

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• NIF
• 7 years ago - by Anonymous

Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more.

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• RRID-Legacy
• 7 years ago - submitted by Edyta Vieth

Software tool to dig out more robust and reliable differentially expressed genes between two groups. Samples from different groups will be re-sampled randomly associated with total number of samples.

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• RRID-Legacy
• 7 years ago - by Anonymous

Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program.

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• RRID-Legacy
• 7 years ago - submitted by Joe Menke

Software tool for dendritic spine analysis that enables to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo and in vitro imaging sessions, automatically aligns images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics such as length, thickness, and overall number, for accurate quantitative comparison.

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• RRID-Legacy
• 7 years ago - submitted by Maci Heal

Software tool as ultra fast, multi channel resonant scanning laser confocal microscope system for rapid 2D and 3D slide scanning, and cleared tissue imaging. System for imaging of slide mounted specimens and cleared tissue imaging. Utilizes strip mosaic scanning process to rapidly and accurately collect fluorescent image data while stage moves specimen continuously in y-axis.

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• RRID-Legacy
• 7 years ago - submitted by Maci Heal

Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays.

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• RRID-Legacy
• 7 years ago - submitted by Maci Heal

Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses.

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• RRID-Legacy
• 7 years ago - submitted by Maci Heal

Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses.

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• RRID-Legacy
• 7 years ago - submitted by Maci Heal

Software tool to automatically align sections to visualize brains in 3D. Assists with cell mapping, cytoarchitectonics and other areas requiring characterization of neuronal circuitry to create comprehensive anatomical reference. Automatically creates full resolution, 3D reconstructions of entire brain or any organ from serial sections of whole slide images. Allows to view cells, structures, and lesions, locate neurons expressing particular gene or visualize axonal projections of specific neurons with full anatomical context.

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• RRID-Legacy
• 7 years ago - submitted by Maci Heal

Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene.

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• RRID-Legacy
• 7 years ago - submitted by Jenna Oberstaller

Condor project maintains, distributes, and supports variety of computing systems that are deployed by commercial and academic interests world wide. Explores social and technical problems of cooperative computing on scales ranging from desktop to world wide computational Grid.

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

Galaxy-based web service for analysis of Chromatin Immuno Precipitation (ChIP) data. Integrative platform for transcriptional regulation studies. Data analysis platform based on Galaxy open source framework. Besides standard Galaxy functions, Cistrome has ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. Used to conduct data integration to mine hidden biological insights from publicly available high throughput data.

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• dkNET
• 7 years ago - submitted by Ko-Wei Lin

Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language.

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• SciCrunch
• 7 years ago - submitted by Justin Bedo

Language for representing scientific findings in life sciences in reusable, shareable, and computable form. Captures causal and correlative relationships in context, where context can include information about biological and experimental system in which relationships were observed, supporting publications cited and process of curation.

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• SciCrunch
• 7 years ago - submitted by Charles Hoyt

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
• 7 years ago - submitted by Charles Hoyt

Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications.

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• SciCrunch
• 7 years ago - submitted by Charles Hoyt

Omics database for spaceflight experiments. Interactive, open access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Enables exploration of molecular network responses of terrestrial biology to space environment. Contains curated omics data, metadata and radiation dosimetry for model organisms. Supports standard guidelines for submission of datasets, MIAME for microarray, ENCODE Consortium Guidelines for RNA-seq and MIAPE Guidelines for proteomics.

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• RRID-Legacy
• 7 years ago - by Anonymous