diff --git a/README.md b/README.md index 0bc6574d3db58fa024f10fb62be3c75f8c13c156..4d271473277def126b0d9379174d7f8f39561185 100644 --- a/README.md +++ b/README.md @@ -31,10 +31,14 @@ We separate the structure of the network (defined by population sizes, synapse numbers/indegrees etc.) from its dynamics (neuron model, neuron parameters, strength of external input, etc.). The complete set of default parameters for all components of the framework is defined -in `default_params.py`. +in `multiarea_model/default_params.py`. + +A description of the requirements for the code can be found at the end of this README. -------------------------------------------------------------------------------- +### Preparations + To start using the framework, the user has to define a few environment variables in a new file called `config.py`. The file `config_template.py` lists the required environment variables that need to specified by the user. @@ -92,10 +96,11 @@ Note that it can sometimes be necessary to execute `snakemake --touch` to avoid ## Running a simulation -A simple simulation can be run in the following way: -1. Define custom parameters - custom_params = ... - custom_simulation_params = ... +The files `run_example_downscaled.py` and `run_example_fullscale.py` provide examples. A simple simulation can be run in the following way: + +1. Define custom parameters. + See `multi_area_model/default_params.py` for a full list of parameters. All parameters can be customized. + 2. Instantiate the model class together with a simulation class instance. M = MultiAreaModel(custom_params, simulation=True, sim_spec=custom_simulation_params) @@ -110,8 +115,7 @@ The files `start_jobs.py` and `run_simulation.py` provide the necessary framewor for doing this in an automated fashion. The procedure is similar to a simple simulation: 1. Define custom parameters - custom_params = ... - custom_simulation_params = ... + 2. Instantiate the model class together with a simulation class instance. M = MultiAreaModel(custom_params, simulation=True, sim_spec=custom_simulation_params) @@ -119,8 +123,6 @@ The procedure is similar to a simple simulation: Call `start_job` to create a job file using the `jobscript_template` from the configuration file and submit it to the queue with the user-defined `submit_cmd`. -The file `run_example_fullscale.py` provides an example. - Be aware that, depending on the chosen parameters and initial conditions, the network can enter a high-activity state, which slows down the simulation drastically and can cost a significant amount of computing resources. ## Simulation modes