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Subcellular modeling pipeline
0.1.0
Subcellular modeling pipeline
0.1.0

Contents

  • Overview

Workflow notebooks

  • Simulations
  • Analysis
  • Visualization

API reference

  • simulation
    • simulation.batch_simulations
    • simulation.cytosim
      • simulation.cytosim.post_processing
    • simulation.post_processing
    • simulation.readdy
      • simulation.readdy.data_structures
      • simulation.readdy.loader
      • simulation.readdy.parser
      • simulation.readdy.post_processor
  • analysis
    • analysis.compression_metrics
      • analysis.compression_metrics.compression_analysis
      • analysis.compression_metrics.compression_metric
      • analysis.compression_metrics.constants
      • analysis.compression_metrics.polymer_trace
      • analysis.compression_metrics.vectors
    • analysis.dimensionality_reduction
      • analysis.dimensionality_reduction.fiber_data
      • analysis.dimensionality_reduction.pacmap_dim_reduction
      • analysis.dimensionality_reduction.pca_dim_reduction
    • analysis.tomography_data
      • analysis.tomography_data.tomography_data
    • analysis.wall_clock_time
      • analysis.wall_clock_time.log_data
  • visualization
    • visualization.combined_trajectory
    • visualization.dimensionality_reduction
    • visualization.display_data
    • visualization.fiber_points
    • visualization.histogram_plots
    • visualization.individual_trajectory
    • visualization.scatter_plots
    • visualization.spatial_annotator
    • visualization.tomography

Project links

  • GitHub
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analysis.wall_clock_timeΒΆ

Wall clock time analysis methods and notebooks.

analysis.wall_clock_time.log_data

Methods for analyzing simulation logs.
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