Installation and Remote Access#

Installation at your desktop computer#

Connection to server and sandbox folder structure#

We are preparing a new tutorial to run ABMShare with tailored Google Colab notebooks. Now you can clone the original repozitory and run it locally,

The sandbox folder#

The sandbox folder contains all the necessary files for running abmSHARE. The folder is updated for all users after each system update. Previous version of the system are stored with the system update date appended as sandbox_[date]. The sandbox folder always contains the updated settings. Please check new/old keys in new and old configuration files for possible changes. Changes are documented in the Changelog page.

Structure of the sandbox folder#

sandbox
    |   
    +-- input_data
    |   +-- data
        |   +-- Czechia.json
        |   +-- NUTS2_mobility_data.csv
        |   +-- population_age_distribution.csv
    |   +-- simulation_configuration_files
        |   +-- simulation_interventions.csv
        |   +-- simulation_global_pars.csv
        |   +-- simulation_region_pars.csv
        |   +-- simulation_vacciness.csv
        |   +-- simulation_variants.csv
    |   +-- simulation_immunity_files
        |   +-- immunity_input_files.csv
        |   +-- vaccine_dose_pars.csv
        |   +-- vaccine_variant_pars.csv
        |   +-- variants_cross_immunity.csv
        |   +-- variants_pars.csv
    |   +-- synthpops_configuration_files
        |   +-- pars_file.csv
        |   +-- synthpops_input_files.csv
        |   +-- synthpops_region.csv
    |   +-- synthpops_input_data
        |   +-- Various files in here        
    |   +-- main_configuration.json
    |   +-- report_configuration.json
    |   +-- main_configuration.json
    |   +-- simulation_configuration.json
    |   +-- synthpops_configuration.json
    +-- logs
    +-- outputs
        | 
    +-- parameters.py
    +-- results.sh
    +-- start.sh

Input data folder#

This folder contains all configuration files for each module as well as all input data needed for the abmSHARE model to run. These inputs are defined in json and/or csv files.

Configuration files#

main_configuration.json file contains all important parameters for all other modules. More information can be found here.
synthpops_configuration.json file is the synthetic population module configuration file responsible for creating synthetic populations that can serve as inputs into the abmSHARE model. More information can be found here.
simulation_configuration.json file defines the main features of the simulation. It can specify the population created by synthetic population model. More information about settings of this module can be found here.
report_configuration.json file creates outputs of each simulation in csv format as well as a summary of the simulation. More information about this module can be found here.
Other files are available at download page.

Data folder#

Folder name: data
This folder contains three files by default, which can be shared across simulation and synthetic population module.

Czechia.json contains the geographic data for Czechia. It is used for creating synthetic populations and for running simulations.
NUTS2_mobility_data.csv contains the mobility data for Czechia. It is used for creating synthetic populations and for running simulations.
population_age_distribution.csv contains the age distribution data for Czechia. It is used for creating synthetic populations and for running simulations.

Simulation configuration files folder#

Folder name: simulation_configuration_files
These files are used for defining the simulation parameters. They are used in the simulation module. More info about thouse files you can find T5 Simulation.

simulation_interventions.csv contains the interventions for the simulation. It is used for defining interventions in the simulation module.
simulation_global_pars.csv contains the global parameters for the simulation. It is used for defining global parameters in the simulation module.
simulation_region_pars.csv contains the region-specific parameters for the simulation. It is used for defining region-specific parameters in the simulation module.
simulation_vaccines.csv contains the vaccine parameters for the simulation. It is used for defining vaccine parameters in the simulation module.
simulation_variants.csv contains the variant parameters for the simulation. It is used for defining variant parameters in the simulation module.

Simulation immunity files folder#

Folder name: simulation_immunity_files
These files are used for defining the immunity parameters. They are used in the simulation module. More info about thouse files you can find T5.3 Simulation - Immunity and variants.

immunity_input_files.csv contains the input files for the immunity. It is used for defining the input files in the immunity module.
vaccine_dose_pars.csv contains the vaccine dose parameters for the immunity. It is used for defining the vaccine dose parameters in the immunity module.
vaccine_variant_pars.csv contains the vaccine variant parameters for the immunity. It is used for defining the vaccine variant parameters in the immunity module.
variants_cross_immunity.csv contains the cross-immunity parameters for the immunity. It is used for defining the cross-immunity parameters in the immunity module.
variants_pars.csv contains the variant parameters for the immunity. It is used for defining the variant parameters in the immunity module.

Synthetic population configuration files folder#

Folder name: synthpops_configuration_files
These files are used for defining the synthetic population parameters. They are used in the synthetic population module. More info about thouse files you can find Synthetic popilation configuration file and on T4 Creating population.

pars_file.csv contains the parameters for the synthetic population. It is used for defining the parameters in the synthetic population module.
synthpops_input_files.csv contains the input files for the synthetic population. It is used for defining the input files in the synthetic population module.
synthpops_region.csv contains the region-specific parameters for the synthetic population. It is used for defining the region-specific parameters in the synthetic population module.

Synthetic population other specific input data folder#

Folder name: synthpops_input_data
These files are used for defining more specific parameters for synthetic population creator. More info about thouse files you can find on T4.1 Population input data.

Outputs folder#

This folder contains several outputs from a simulation. The outputs folder can be set as a default folder in Auto save settings, or it can be used for manually saved outputs defined in various configuration files. Each simulation output is saved to a new folder with a time stamp in the folder name (YY_mm_DD_HH_MM)

    |
    +-- outputs
        |   +-- Output_2023_01_31_24_00
            |   +-- Configuration   
            |   +-- output_reports
            |   +-- pop_configurations
            |   +-- pops
            |   +-- sims

Each simulation result folder has its own subdirectories:

Configuration holds all input configuration files used for the simulation.
output_reports contains all generated csv and xlsx outputs defined in the Report module.
pop_configuration contains configuration files used as inputs in the Synthetic population module for creating population.
pops holds all generated population objects from Synthetic population module. These can be used in Simulation module as popfile key.
sims saves instances of simulations for later analysis and exploration. These are covasim.MultiSim() objects.

Other individual files#

Start file#

(file: start.sh)

After editing all configuration files, a abmSHARE simulation is started by typing ./start.sh in the command line. It is important to be in the located (cd) in the sandbox directory or to insert an absolute path for the start.sh file. If you want to validate the input configuration for the model, run ./start.sh -v. The validation process will check for correct input data types and file paths.