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Case studies have been used in many disciplines (health sciences, social sciences, engineering and law) to create opportunities to provide learners with immersive environments in which to apply these problem solving skills. Digital case studies provide the additional benefits of interactivity and reproducibility to data science problems, but educators are faced with challenges understanding the ecosystem of tools that can be used to develop them. Over the course of the next few hours, you and your team will develop a simple digital case study based on publically-available data from Botswana. The focus of this case study will center on HIV prevalence in Botswana using three building blocks: Person, Place and Time.
You will build a digital case study with Jupyter Notebook and Docker. Click on the Binder Notebook link above. Wait a few minutes for the Binder service to complete its setup and launch. Enjoy the rest of the story after you launch the case study.
- Obtain a GitHub account.
- Note down your GitHub log in credentials (user name and password).
- The workshop facilitators will guide you during the log in process to this custom Jupyter Notebook server. (You may try to set this up on your local machine using the code from this repository: https://github.com/PHI-Toolkit/jupyterhub-deploy-docker-localhost.git. Note you may need to set up Docker and its associated tools to make this happen, and it may require you to have a local machine with the right hardware and software requirements. Local machine set up will not use GitHub authentication by default.)
- Once you have set up and launched the Docker-based Jupyter Notebook server, and have logged in using your GitHub credentials, launch a terminal from within the Notebook Server, type
cd notebooksand clone this repository usinggit clone https://github.com/PHI-Case-Studies/2019-HIV-Prevalence-Botswana.git. - You can then launch the case study notebooks with minimal configuration (may need to
pip install camelot-pyand other required packages using a Jupyter Notebook terminal window).
- Download and install Anaconda here
- Clone this repository. In a Windows Powershell window, or MacOSX or Linux terminal window, type
git clone https://github.com/PHI-Case-Studies/2019-HIV-Prevalence-Botswana.git. You may need to installgitbefore this. - In the same terminal or Powershell window, type
cd 2019-HIV-Prevalence-Botswana, then typeanaconda.shfor MacOSX or Linux, oranaconda.ps1for Windows Powershell. This creates a special kernel (virtual environment) calledcase-python3that contains all the Python packages needed for this case study. - Launch Anaconda-Navigator, then launch Jupyter Notebook
- Navigate to the folder where the cloned repository was downloaded.
- Launch Notebook 0. Then using the Notebook menu, go to "Kernel" then "Switch Kernel" - select
case-python3. Switch to this kernel when you launch the other notebooks from this case study.
After clicking on the "launch binder" link above, wait for a few minutes to have Docker container built.
This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.
The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.
This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.
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