Starting simulations via command line

Alternative Mechanisms

1. Start cardiacmodelling/ap-nimbus-app-manager and call its endpoint from the command line.
   See Running cardiacmodelling/ap-nimbus-app-manager.
2. Run cardiacmodelling/appredict-with-emulators or cardiacmodelling/appredict-no-emulators in isolation/standalone.
   See Running cardiacmodelling/appredict-no-emulators or cardiacmodelling/appredict-with-emulators.
3. Start cardiacmodelling/ap-nimbus-app-manager and a database as you normally would for cardiacmodelling/ap-nimbus-client-direct (see Prerequisites), but rather than use the client-direct UI, instead invoke cardiacmodelling/ap-nimbus-client-direct from the command line as below.

Invoking cardiacmodelling/ap-nimbus-client-direct as a CLI

Apart from using the web front-end in the form of client-direct, cardiacmodelling/ap-nimbus-client-direct also offers a command-line tool for starting simulations. In order to call this tool, it needs a setup with Python, the same installed components as the web front-end and access to the database (see Prerequisites). The most conveniant way to achieve this is to start a docker component specifically for the purpose of starting simulations in command line.
The example below starts a docker component and shows the various command line options available.

Note

Any path to PK data files is local to the docker component.

sudo docker run -it \
                --rm \
                --net ap-nimbus-network \
                -v volume-client:/opt/django/media \
                --env-file env \
                cardiacmodelling/ap-nimbus-client-direct:<version> \
                python manage.py start_simulation -h

usage: manage.py start_simulation [-h] [--model_year MODEL_YEAR] [--model_version MODEL_VERSION] [--notes NOTES] [--pacing_frequency PACING_FREQUENCY] [--maximum_pacing_time MAXIMUM_PACING_TIME] [--ion_current_type ION_CURRENT_TYPE] [--ion_units ION_UNITS] [--concentration_type PK_OR_CONCS]
                                  [--minimum_concentration MINIMUM_CONCENTRATION] [--maximum_concentration MAXIMUM_CONCENTRATION] [--intermediate_point_count INTERMEDIATE_POINT_COUNT] [--intermediate_point_log_scale INTERMEDIATE_POINT_LOG_SCALE] [--PK_data_file PK_DATA] [--concentration_point CONCENTRATION_POINT]
                                  [--current_inhibitory_concentration <current> concentration hill coefficient saturation level spread of uncertainty] [--version] [-v {0,1,2,3}] [--settings SETTINGS] [--pythonpath PYTHONPATH] [--traceback] [--no-color] [--force-color] [--skip-checks]
                                  title author_email model_name

positional arguments:
  title                 Title to identify sumulations. Please note: use quotes if the title contains spaces or quotes.
  author_email          Email address of the author for which the simulation is run
  model_name            The name of the model to use. If the name is not unique, please also specify year and/or version. Please note: use quotes if the model name contains spaces or quotes.

optional arguments:
  -h, --help            show this help message and exit
  --model_year MODEL_YEAR
                        The year for a specified model, to tell models with the same name apart e.g. 2020
  --model_version MODEL_VERSION
                        The model version, where a model has multiple versions e.g. CiPA-v1.0
  --notes NOTES         Textual notes for the simulation. Please note: use quotes if the notes contain spaces or quotes.
  --pacing_frequency PACING_FREQUENCY
                        (in Hz) Frequency of pacing (between 0.05 and 5).
  --maximum_pacing_time MAXIMUM_PACING_TIME
                        (in mins) Maximum pacing time (between 0 and 120).
  --ion_current_type ION_CURRENT_TYPE
                        Ion current type: (pIC50 or IC50)
  --ion_units ION_UNITS
                        Ion current units. (-log(M), M, µM, or nM)
  --concentration_type PK_OR_CONCS, --pk_or_concs PK_OR_CONCS
                        Concentration specification type. (compound_concentration_range, compound_concentration_points, or pharmacokinetics)
  --minimum_concentration MINIMUM_CONCENTRATION
                        (in µM) at least 0.
  --maximum_concentration MAXIMUM_CONCENTRATION
                        (in µM) > minimum_concentration.
  --intermediate_point_count INTERMEDIATE_POINT_COUNT
                        Count of plasma concentrations between the minimum and maximum (between 0 and 10).
  --intermediate_point_log_scale INTERMEDIATE_POINT_LOG_SCALE
                        Use log scale for intermediate points.
  --PK_data_file PK_DATA, --PK_data PK_DATA
                        File format: tab-seperated values (TSV). Encoding: UTF-8 Column 1 : Time (hours) Columns 2-31 : Concentrations (µM).
  --concentration_point CONCENTRATION_POINT
                        Specify compound concentrations points one by one. For example for points 0.1 and 0.2 specify as follows: --concentration_point 0.1 --concentration_point 0.2
  --current_inhibitory_concentration <current> concentration hill coefficient saturation level spread of uncertainty
                        Inhibitory concentrations, one by one e.g. --current_inhibitory_concentration INa 0.5 1 0 0
  --version             Show program's version number and exit.
  -v {0,1,2,3}, --verbosity {0,1,2,3}
                        Verbosity level; 0=minimal output, 1=normal output, 2=verbose output, 3=very verbose output
  --settings SETTINGS   The Python path to a settings module, e.g. "myproject.settings.main". If this isn't provided, the DJANGO_SETTINGS_MODULE environment variable will be used.
  --pythonpath PYTHONPATH
                        A directory to add to the Python path, e.g. "/home/djangoprojects/myproject".
  --traceback           Raise on CommandError exceptions.
  --no-color            Don't colorize the command output.
  --force-color         Force colorization of the command output.
  --skip-checks         Skip system checks.