Codes for simulations and analyses in Ghandour, Haga, Ohkawa et al., "Dual roles of idling moments for past and future memories".
Codes depend on Python 3, numpy, scipy, matplotlib, and a UNIX shell script (bash). With Anaconda (or Miniconda), you can run conda env create -f env_engramtobe.yml then conda activate engramtobe to create an appropreate environment.
For running the codes, execute bash batch.sh on a UNIX shell (we ran codes in Ubuntu 20.04 and 22.04). Otherwise, manually execute commands written in the batch.sh.
Codes execute 5 simulations for each of four conditions (with and without sleep, homeostatic plasticity OFF, LTD-OFF). Each simulation generates a .npz file that contains results. After 5 simulations, results are summarized to output .csv and .tiff files that show cell-type ratios, coincidence and correlation of neural activities, and matching ratios as presented in the paper.
It took approximately 10 minutes to finish all calculations by a workstation with Xeon-W7-3445.