vivarium_csu_sanofi_multiple_myeloma

Cite as:

Matthew Kappel, Yongquan Xie, James Collins, Alison Bowman, & Abraham Flaxman. (2021). ihmeuw/vivarium_csu_sanofi_multiple_myeloma: Archival release (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.5542097

Research repository for the vivarium_csu_sanofi_multiple_myeloma project.

Contents

• Installation
• Usage
• Running Simulations

Installation

You will need git, git-lfs and conda to get this repository and install all of its requirements. You should follow the instructions for your operating system at the following places:

• git
• git-lfs
• conda

Once you have all three installed, you should open up your normal shell (if you're on Linux or macOS) or the git bash shell if you're on Windows. You'll then make an environment, clone this repository, then install all necessary requirements as follows:

:~$ conda create --name=vivarium_csu_sanofi_multiple_myeloma python=3.8
...conda will download python and base dependencies...
:~$ conda activate vivarium_csu_sanofi_multiple_myeloma
(vivarium_csu_sanofi_multiple_myeloma) :~$ git clone https://github.com/ihmeuw/vivarium_csu_sanofi_multiple_myeloma.git
...git will copy the repository from github and place it in your current directory...
(vivarium_csu_sanofi_multiple_myeloma) :~$ cd vivarium_csu_sanofi_multiple_myeloma
(vivarium_csu_sanofi_multiple_myeloma) :~$ pip install -e .
...pip will install vivarium and other requirements...

Note the -e flag that follows pip install. This will install the python package in-place, which is important for making the model specifications later.

Cloning the repository should take a fair bit of time as git must fetch the data artifact associated with the demo (several GB of data) from the large file system storage (git-lfs). If your clone works quickly, you are likely only retrieving the checksum file that github holds onto, and your simulations will fail. If you are only retrieving checksum files you can explicitly pull the data by executing git-lfs pull.

Vivarium uses the Hierarchical Data Format (HDF) as the backing storage for the data artifacts that supply data to the simulation. You may not have the needed libraries on your system to interact with these files, and this is not something that can be specified and installed with the rest of the package's dependencies via pip. If you encounter HDF5-related errors, you should install hdf tooling from within your environment like so:

(vivarium_csu_sanofi_multiple_myeloma) :~$ conda install hdf5

The (vivarium_csu_sanofi_multiple_myeloma) that precedes your shell prompt will probably show up by default, though it may not. It's just a visual reminder that you are installing and running things in an isolated programming environment so it doesn't conflict with other source code and libraries on your system.

Usage

You'll find six directories inside the main src/vivarium_csu_sanofi_multiple_myeloma package directory:

• artifacts

  This directory contains all input data used to run the simulations. You can open these files and examine the input data using the vivarium artifact tools. A tutorial can be found at https://vivarium.readthedocs.io/en/latest/tutorials/artifact.html#reading-data

• components

  This directory is for Python modules containing custom components for the vivarium_csu_sanofi_multiple_myeloma project.

• data

  This directory contains small scale external data for use in the simulation.

• model_specifications

  This directory holds all model specifications and branch files associated with the project.

• results_processing

  The post-processing and analysis code is stored in this directory.

• tools

  This directory holds Python files used to run scripts used to prepare input data or process outputs.

Running Simulations

With your conda environment active, you can then run simulations by, e.g.:

(vivarium_csu_sanofi_multiple_myeloma) :~$ simulate run -v /<REPO_INSTALLATION_DIRECTORY>/vivarium_csu_sanofi_multiple_myeloma/src/vivarium_csu_sanofi_multiple_myeloma/model_specifications/united_states_of_america.yaml

The -v flag will log verbosely, so you will get log messages every time step. For more ways to run simulations, see the tutorials at https://vivarium.readthedocs.io/en/latest/tutorials/running_a_simulation/index.html and https://vivarium.readthedocs.io/en/latest/tutorials/exploration.html