This is the README file for the script to perform simulations of the bleaching protocol from: Denizot, A., M. Arizono, U. V. Nägerl, H. Berry, & E. De Schutter. Control of Ca2+ signals by astrocyte nanoscale morphology at tripartite synapses, Glia, Sep. 2022, doi: 10.1002/glia.24258 This model requires STEPS software, which is freely available at http://steps.sourceforge.net/STEPS/default.php HOW TO RUN THE CODE ----------- First, you need to download STEPS at http://steps.sourceforge.net/STEPS/default.php or directly at https://github.com/CNS-OIST/STEPS Dependencies for STEPS are described on the README file at https://github.com/CNS-OIST/STEPS. The model requires that the following packages are installed: - numpy - pickle - sys - pyqtgraph The model is divided in 2 python files: **** ip3r_model_mesh.py This file contains 2 functions: - getModel(), that defines all molecules, reactions, reaction constants involved in the model - gen_geom(), that imports the geometry from the meshes "5nodes_ratio1.inp", "5nodes_ratio1.inp" and "5nodes_ratio1.inp", which correspond to astrocytic branchlets with shaft width of d0, d0/2 and d0/3, respectively. **** 3d_neurostim_failure.py This file sets initial conditions and runs the simulation while recording data in a file. To run this script, simply call the function with python with an integer i as an argument that will be the seed for the given simulation as well as the name of the mesh file 'filename'. The 3rd argument corresponds of the probability of failure of a node stimulation p and the 4th argument to the time interval t, expressed in seconds, between each stimulation event. The output file, out.filename.T=t.pfail=p.i', contains in each line the number of ca_GCaMP6s, of IP3 molecules and the number of open IP3R channels in Node 5 (denoted node_4 in the code). Time between two lines corresponds to 1 ms. Example command: python 3d_neurostim_failure.py 1 5nodes_ratio3.inp 0.25 100 -> output out.5nodes_ratio3.inp.T=100.pfail=0.25.1 MESH FILES ----------- "5nodes_ratio1.inp", "5nodes_ratio1.inp" and "5nodes_ratio1.inp" correspond to astrocytic branchlets with shaft width of d0, d0/2 and d0/3 CONTACT ----------- audrey.denizot3@oist.jp