Cell-memory

The subfolders contain codes to generate the results obtained by numerical simulations in the eLife article,

Cells use molecular working memory to navigate in changing chemoattractant fields

The codes have been tested successfully with versions of Python (at least 2.7) on Windows and macOS.

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Using the framework

Polarity model : Kymographs in Figure 1D, Figure 1 - figure supplement 1D-H, Figure 4- figure supplement 1A,C, Figure 4- figure supplement 2A,C

Physical model of single-cell chemotaxis : Cell shapes in Figure 1E, Figure 4B, Figure 4 - figure supplement 1B,D, Figure 4- figure supplement 2B,D

Each folder has a file with name ending '_main.py'. This file combines different objects (functions) defined in linked files in the same folder.

For example: In the folder /Cell-memory/Polarity model, the 'EgfrPtpSde_main.py' loads the model equations and parameters from 'Models.py' file.

Excecution of Polarity model:

model = EgfrPtp()
initial_condition = around_steadystate()
lbo = Periodic()
stimulus = single_gradient()

rd = ReactionDiffusion1D(model, initial_condition, lbo,stimulus)
rd.simulate()

Execution of Physical model of single-cell chemotaxis: 'LevelSet_main.py' file loads kymograph corresponding to Figure 1D and generate cell shapes in Figure 1E. A single CPU of a normal desktop computer (eg. with Intel64 Family 6 processor) requires ~24 hrs for completion.