vivarium_ihme_obesity_washout

Research repository for the vivarium_ihme_obesity_washout project.

Contents

• Model Documentation Resources
• Installation
• Usage

Model Documentation Resources

CONCEPT MODEL: J:/Project/simulation_science/cvd/concept_model_obesity_washout.docx

Installation

These models require data from GBD databases. You'll need several internal IHME packages and access to the IHME cluster.

To install the extra dependencies create a file called ~/.pip/pip.conf which looks like this:

[global]
extra-index-url = http://pypi.services.ihme.washington.edu/simple
trusted-host = pypi.services.ihme.washington.edu

To set up a new research environment, open up a terminal on the cluster and run:

$> conda create --name=vivarium_ihme_obesity_washout python=3.6
...standard conda install stuff...
$> conda activate vivarium_ihme_obesity_washout
(vivarium_ihme_obesity_washout) $> conda install redis
(vivarium_ihme_obesity_washout) $> git clone git@github.com:ihmeuw/vivarium_ihme_obesity_washout.git
...you may need to do username/password stuff here...
(vivarium_ihme_obesity_washout) $> cd vivarium_ihme_obesity_washout
(vivarium_ihme_obesity_washout) $> pip install -e .

Usage

You'll find four directories inside the main src/vivarium_ihme_obesity_washout package directory:

• components

  This directory is for Python modules containing custom components for the vivarium_ihme_obesity_washout project. You should work with the engineering staff to help scope out what you need and get them built.

• external_data

  If you have small scale external data for use in your sim or in your results processing, it can live here. This is almost certainly not the right place for data, so make sure there's not a better place to put it first.

• model_specifications

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

• verification_and_validation

  Any post-processing and analysis code or notebooks you write should be stored in this directory.