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simularium / vivarium-models

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Define test models in Cytosim and MEDYAN #3

Open blairlyons opened 2 years ago

blairlyons commented 2 years ago

Use Case

We as developers need example models to test the VIvarium integrations with MEDYAN and Cytosim. These models should be as similiar as possible in Cytosim and MEDYAN.

Acceptance Criteria

Input files for each model for each of the two engines.

Details

  1. very simple model: a few filaments diffusing in a box
  2. model from a 2019 MEDYAN paper: download data from https://drum.lib.umd.edu/handle/1903/21856, it's the "Non-treadmilling bundle results and input files", once you unzip, use inputs in /2mUNI/alpha:A_0.1_wdata/M:A_0.675. The outputs in /run1 are visualized here https://simularium.allencell.org/viewer?trajFileName=medyan_Chandrasekaran_2019_UNI_alphaA_0.1_MA_0.675.simularium

These models will also help us work toward endocytosis models in both engines.

mattakamatsu commented 2 years ago

very simple actin model: image (33)

cytosim config file (rename to .cym): actin_vivarium.txt

the list of actin points: actin_points.txt