Parameter scans for microtubule growth dynamics

simularium / readdy-models

Tools for building computational biology models in ReaDDy.

BSD 3-Clause "New" or "Revised" License

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Open mogres opened 2 years ago

mogres commented 2 years ago

As a modeler, I want to find parameter sets that result in microtuble growth.

[ ] Subset(s) of parameters for which consistent microtubule growth is observed
[ ] Analysis functions to obtain metrics for microtubule growth:
- [x] Length of protofilaments over time
- [x] Growth, shrinkage, attachment, and detachment events over time

mogres commented 2 years ago

[x] Debug timing issues Incorporated difference between number of simulation steps and visualization steps in scaled_time_step_us

mogres commented 2 years ago

[ ] Debug protofilament lengths for disappearing neighbors for microtubules_scan_growth_attach_20220418_x100_growth_x100_attach_1.h5
- [ ] Requires re-analyzing h5 file with correct box size
- [ ] Requires looking into site#remove agents