Synthetic Disease

Imagine you are a senior public health researcher in an alternate universe where diseases are not made up of DNA, but are instead made up of Java code. Your task is to extend the Disease Blueprint framework (an abstract Java class) to synthesize a new disease strain for testing purposes. This synthetic disease will be used in lab trials to test junior researchers' skills in programming, analysis, and public health.

Learning Objectives

• Develop a disease that shows off Java concepts.
• Reflect on your design process by maintaining a journal.

Tools

• Cloud9: an online development environment that allows you to develop, compile, an execute Java programs without installing Java locally.
• GitHub: a platform for version control, helping you keep track of files and changes for your projects.
• Google Docs: an online tool for storing and editing files. Use documents to keep track of your journaling and sheets to store and graph data from your simulations.

Getting Started

Accept your invitation to the Cloud9 education platform. This will allow you to create a Cloud9 account without entering any payment information. Open Cloud9 and create a new workspace, selecting our class as the team. Select the "Clone workspace" tab and choose the workspace called defaultjava. This will ensure that you have Java configured on your workspace in Cloud9.

Next, copy the files for this exercise to your Cloud9 workspace by clicking the green "Clone or download" button on your personal repository. Copy the link and then go to your command line (or "terminal") in Cloud9 and run:

git clone https://github.com/illinoistechesi/syntheticdisease-{yourusername}.git

The URL in the clone command is the link you copied from the green button. Now you can try running the project!

Navigate to the directory that contains the Java files and, in your command line, run:

javac *.java

This will compile all files in the directory that have the .java extension. Then run:

java SimulatedHost

This will run the main method of the SimulatedHost class. In your terminal, you'll get an output for the sample disease that might look like this:

Patient infection log for an adult host:
Day,Energy,Bacteria,Description
1,100,0,Day 1: Infection multiplied.
2,150,8,Day 2: Infection multiplied.
3,224,16,Day 3: Infection multiplied.
4,322,24,Day 4: Infection multiplied.
5,444,32,Day 5: Infection multiplied.
6,590,40,Day 6: Infection multiplied.
7,760,48,Day 7: Infection multiplied.
8,954,56,Day 8: Toxin released.
9,618,54,Day 9: Infection exited the host.
10,402,52,Day 10: Toxin released.
11,90,50,Day 11: Infection multiplied.
12,290,58,Day 12: Failed to release toxin.
13,-58,56,Day 13: Infection died out.

Now that you're set up, change the file name of your disease from YourDisease.java to something more interesting. Change the class name in the SimulatedHost.java file as well. Then, make sure it runs as before and save your changes.

Saving Changes

To save your changes in GitHub, run the commands below in your command line. First, add all your changes: (-A means all)

git add -A

Then create a message for this commit: (-m means message)

git commit -m "Start your message with a verb about what you changed"

Save your changes by pushing them to your repository:

git push

You will enter your username and password to the prompts to complete the push.

Graphing

There is a Google sheets template that allows you to easily graph simulation results. Copy the template at this link. To visualize simulation results, follow these steps:

• Clear column O in the Google sheet.
• Copy the simulation output from your Cloud9 terminal.
• Paste the simulation output into column 0.
• Drag the SPLIT function in column A down until it captures all of the simulation output.
• Enjoy the graphs in spreadsheet form!
• Duplicate the sheet when you want to create new logs.

Journaling

Keep your journal of work on this assignment in a Google Doc. It is up to you how to structure this. Before you start this activity, write a response to this question:

How do you think the SimulatedHost works?

Here are some examples of things to keep track of while you journal:

• Links you use to learn about Java or address problems you run into.
• Scientific thinking: anything that explains your process for creating your disease.
• Pseudocode or plans for what you want to implement in your disease. This helps you plan before you code and gives others insight into your thinking process even if you cannot implement the ideas in this exercise.
• Notes about when you use abstractions.
• Notes about when you test your disease.
• Implications of your disease if it were involved in a real public health scenario.

API

API stands for application programming interface, it defines what these programs can do. Below is an explanation of the API for your synthetic disease.

Disease

To create a new disease, write a new class that extends the abstract DiseaseBlueprint class. Some examples are already in the project for you to refer to. Change the class name and returned name property for your disease. For now, ignore the infectivity, toxigencity, and resistance methods and focus only on developing a new move method.

Move Method

This method defines your disease's behavior once it has infected a host. Each day the disease is alive in the simulation, this function will run.

• Params: SimulatedHost host, the host that has been infected
• Return: DiseaseAction, the action to take on a given day.

DiseaseAction Enum

The move method can return any of these options. Search on Google if you want to learn more about enums.

• DiseaseAction.MULTIPLY, represents the disease expanding within the host.
• DiseaseAction.EXIT, represents the disease leaving the host and getting into the environment (e.g., by causing the host to cough or have a runny nose).
• DiseaseAction.RELEASE, represents the disease releasing toxins into the host.

Host Reference

isLatent()

When the latent period ends, the disease is able to exit the host.

• Return: boolean, whether or not the disease has become latent.

isIncubated()

When the incubation period ends, the disease is able to release toxins.

• Return: boolean, whether or not the disease has fully incubated.

getEnergy()

If the disease has no energy left in the host, it will die out.

• Return: int, amount of energy the disease has in the host.

getBacteria()

See if you can figure out the impact that bacteria levels have on the disease's infection of the host.

• Return int, amount of bacteria the disease has in the host.

getDaysSinceInfection()

• Return int, number of days that have passed since the infection began.

There are two more public methods: getDiseaseEvents() and getDiseaseData(). Can you figure out what they do and if they would be useful to you in synthesizing a new disease?