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README.md

README.md

viral

you're infected

Usage

Viral is primarily pitched as a tool for performing controlled experiments; after setting up a central server (preferably on a Unix-based system, to make advantage of the visualisation utility), participating subjects should have Android phones with the Viral application running in their possession, and understood the rules of the game. This section is primarily concerned with the necessary details for performing the initial setup and configuration of the server and the Android application. We also provide details of an auxiliary tool that can simulate additional participants performing a random walk and not doing any awareness-related interactions (other than vaccinating themselves if possible and desirable), and present a few results we have obtained in such synthetic experiments.

Installation

Precompiled .apk and .jar files of the Viral server, Android client and "fake" client are readily available in the latest release tag of this repository.

The source may be downloaded as an archive from GitHub, or the repository may be directly cloned by running the following command within a terminal:

$ git clone https://github.com/PetarV-/viral.git

Server compilation and execution

Once the source code has been cloned, it may be compiled by invoking javac on the relevant files. Once in the root folder of the repository, execute the following:

$ cd server/src/main/java
$ javac com/hackbridge/viral/*.java
$ java com.hackbridge.viral.Main <port> <round_duration_ms> <delay_between_rounds_ms> <network_params_file> <run_tikzer?> (<tikzer_port>)

The final command launches the server; the parameters that need to be provided are as follows:

  • <port>: the port the server will listen on for clients;

  • <round_duration_ms>: the duration of a single experiment in milliseconds;

  • <delay_between_rounds_ms>: the delay between experiments in milliseconds;

  • <network_params_file>: a path to a file containing the multiplex network’s parameters (described in more detail in the next paragraph);

  • <run_tikzer?>: a boolean string (true or false) specifying whether or not the visualisation utility should be launched. If true, an additional <tikzer_port> parameter should be provided, specifying the port at which the visualisation utility will be serving the latest visualisation.

Network parameters

The network_params_file contains lines in the format <parameter> <value>. The following parameters are used to configure the properties of the multiplex network:

Parameter Description
initialInfectedProbability The probability a new node is initially diseased (with physical state infected or carrier)
initialAwareProbability The probability a new node has initial awareness state aware, as opposed to unaware
initialSymptomaticProbability The probability that a newly infected node has physical state infected, as opposed to carrier
infectedIfVaccinatedProbability The probability a vaccinated node becomes infected with the disease agent when one of its edges with another infected node is activated
spontaneousRecoveryProbability The probability that a diseased node spontaneously recovers when one of its edges is activated
activateEdgeProbability The probability that an edge is activated
infectorProbability The probability that a new node has the role infector, as opposed to human
developSymptomsProbability The probability that a carrier node becomes infected when one of its edges is activated
lambdaFactor Used in the distance expression. A larger value increases the rate at which an edge’s activation probability decreases with distance
exponentialMultiplier Used in the distance expression, for scaling the edge weights
loggingFrequency The frequency at which the network state is logged to a file (expressed in the number of steps between logs)
edgeSelectionAlgorithm The algorithm used for edge selection (ExactRandom or GibbsSampling)
numStepsForGibbsSampling If the GibbsSampling algorithm is used for edge selection, specifies the number of sampling steps it should make before reporting the edge to be activated.

Android setup

Compiling the Android application from source is heavily dependent on the architecture of the host system as well as the IDE you are using, and therefore we do not recommend setting it up in this fashion. Should you still choose to do this, Android Studio will be required in the least, in order to gain access to all of the required packages for Android development. In all other cases, please proceed by downloading the precompiled Viral.apk file from the latest release tag of this repository.

The Android device chosen to install the application should be more recent than Android level 16. After installing the Viral.apk file, simply press on the Viral icon, and then input the hostname and port of the server set-up as outlined above. After a successful connection has been established, the Viral client will be up and running—no further configuration is needed.

Synthetic experiments

While the primary purpose of Viral is creating data from a controlled and real environment, it also supports the addition of bots (virtual participants), whom the server does not distinguish from users. In the current model, the bots perform random walks and periodically send position updates to the server. Sending the updates is modelled as a Poisson process i.e. the time T between updates is a random variable with an exponential distribution Exp(λ), with the probability density function f(t) = λ exp(-λt). No other behaviour is given to the bots, other than them vaccinating themselves if they have access to the valid vaccine code and have the human role.

Fake client configuration

If you are compiling the fake client from source, execute the following (starting from the root folder of the repository):

$ cd fakeclient
$ javac com/hackbridge/viral/*.java
$ java com.hackbridge.viral.BotGenerator <bot_parameter_file> <server> <port>

The command line arguments that need to be provided are:

  • <bot_parameter_file>: a path to a file that contains the bot parameters (the precise format is described in detail in the next paragraph);

  • <server>: IP address of a Viral server;

  • <port>: the port on which a Viral server is listening for requests.

Bot parameters

A file containing information about bots needs to adhere to the following conventions:

  • The first line of the input contains the format version, which is a positive integer. Currently, 1 is assumed to be the version number.

  • After the version number, any incidence of the pound sign (#) means that the rest of a line is a comment and will not be taken into account by the parser.

  • The next number is n, the number of bots that will be generated. This should be a non-negative integer not greater than 500.

  • The data for the n bots should be placed in n distinct lines. Each bot is described as a 4-tuple of whitespace-separated double precision floating-point numbers:

    • initial longitude;

    • initial latitude;

    • maximum change: represents the maximum change in longitude and latitude between per one second;

    • mean time between updates: expected number of milliseconds between two updates (i.e. mean of the distribution).

License

MIT

References

If you make advantage of Viral or derive it within your research, please cite the following article:

Veličković, P., Ivašković A., Lau, S. and Stanojević, M. (2016) Viral: Real-world competing process simulations on multiplex networks. The 1st Belgrade Bioinformatics Conference (BelBi 2016)