Hybrid model simulations: Hamiltonian terms dataset

Status: Public

Type: dataset

Hybrid model simulations: Hamiltonian terms dataset

Description:

Overview

This dataset contains simulated data from the Hamiltonian terms series using the hybrid agent-based modeling framework ARCADE v3.1.4.

Simulation conditions test different combinations of Cellular Potts Model Hamiltonian terms. All simulations use the prefix HAMILTONIAN_TERMS_FOV. Simulation keys include the following:

• VA = Hamiltonian terms include volume constraint and adhesion terms
• VAU = Hamiltonian terms include volume constraint, adhesion terms, and differential substrate adhesion

Simulations are run with 10 replicates (random seeds 0 - 9) initialized from select FOVs by placing the filtered and sampled cell and nuclear shapes in the center of a 500 μm x 500 μm x 500 μm environment (for VA) or the bottom of a 1 mm x 1 mm x 125 μm environment immediately above the substrate (for VAU) using a spatial resolution of 1 μm/voxel. Simulations are run for 5,760 ticks at a temporal resolution of 1 minute/tick representing 4 days of growth. All adhesion parameters (cell-cell, cell-media, subcellular, and cell-substrate) are set to baseline value of 50. Snapshots are taken every 5 minutes (5 ticks).

The dataset has the following structure:

.
├── analysis
│   └── analysis.BASIC_METRICS
│       └── (name)_(superkey).BASIC_METRICS.csv
├── data
│   ├── data.CELLS
│   │   └── (name)_(key)_(seed).CELLS.tar.xz
│   └── data.LOCATIONS
│       └── (name)_(key)_(seed).LOCATIONS.tar.xz
├── inits
│   ├── inits.CELLS
│   │   └── (name)_(seed).CELLS.json
│   └── inits.LOCATIONS
│       └── (name)_(seed).LOCATIONS.json
├── results
│   └── (name)_(key)_(seed).csv
├── setups
│   └── (name).xml
├── simulations
│   └── (name)_(key).json
└── README.md

• analysis = various analysis files
  • analysis.BASIC_METRICS = all results compiled into files grouped by superkey
• data = compressed simulation outputs for each condition and seed
  • data.CELLS = individual cell agent data for each tick (including cell id, parent id, population, age, number of divisions, cell state and phase, volume, and height)
  • data.LOCATIONS = individual location data for each tick (including cell id and list of voxels belonging to the cell)
• inits = simulation initialization files for each seed
• results = tidy formatted data parsed from simulation outputs, for each condition and seed
• setups = all simulation setup files
• simulations = simulation summary output files for each condition

Usage

For documentation on how to use and interact with this dataset please refer to https://docs.quiltdata.com/walkthrough/getting-data-from-a-package.

License

For questions on licensing please refer to https://www.allencell.org/terms-of-use.html.