139 results found
    1. Computational and Systems Biology

    Simplifying the development of portable, scalable, and reproducible workflows

    Stephen R Piccolo et al.
    Descriptions, examples, and tools to enable biologists to use the Common Workflow Language for data processing and to facilitate computational reproducibility.
    1. Neuroscience

    Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era

    Aurel A Lazar et al.
    FlyBrainLab is an open-source computing platform that integrates 3D exploration and visualization of diverse Drosophila connectomic/synaptomic datasets with interactive exploration of the functional logic of modeled executable brain circuits.
  1. Science Forum: A community-led initiative for training in reproducible research

    Susann Auer et al.
    The Reproducibility for Everyone initiative aims to provide researchers at all career stages and across many disciplines with training in reproducible research practices via customizable workshop material.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Genetic mapping of etiologic brain cell types for obesity

    Pascal N Timshel et al.
    Unbiased computational integration of single-cell- and human genetics data shows that susceptibility to obesity is driven by a broad set of neuronal populations across the brain.
    1. Computational and Systems Biology
    2. Evolutionary Biology

    A community-maintained standard library of population genetic models

    Jeffrey R Adrion et al.
    The stdpopsim library, a community-driven open source project, is presented which provides easy access to a standard catalog of published simulation models for population genetics aimed at field-wide standardization.
    1. Cell Biology
    2. Computational and Systems Biology

    TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics

    Raphaël Etournay et al.
    A computational framework called TissueMiner, complete with tutorials, will allow a wide range of users to perform quantitative multiscale analysis of tissue morphogenesis.
    1. Neuroscience

    Creating and controlling visual environments using BonVision

    Gonçalo Lopes et al.
    BonVision is an open-source software for real-time rendering and control of 2D and 3D visual environments that also enables easy replication of experiments.
    1. Stem Cells and Regenerative Medicine

    A fully automated high-throughput workflow for 3D-based chemical screening in human midbrain organoids

    Henrik Renner et al.
    Automated liquid handling, whole mount staining, and clearing allow unbiased 3D quantitation of cell markers in human neural organoids with diameters of up to 1 mm at the single-cell level.
    1. Neuroscience

    Cellular cartography of the organ of Corti based on optical tissue clearing and machine learning

    Shinji Urata et al.
    A method of generating comprehensive maps of cochlear cells was created and enabled researchers to study characteristics of cellular damage in aged and noise-exposed inner ear.
    1. Biochemistry and Chemical Biology

    Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping

    Siqi Tian et al.
    A new biochemical method tests whether or not the pre-existing RNA structural correlations couple small molecule binding to gene expression in a paradigmatic riboswitch.

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