/haiviz

HAIviz: Healthcare Associated Infections Visualization Tool. A web-based application to create an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data.

Primary LanguageJavaScript

HAIviz: Healthcare Associated Infections Visualization Tool

A web-based application to create an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data.

Using HAIviz online.

Visit https://haiviz.fordelab.com/.

Run HAIviz locally, for self hosting or for development.

To run HAIviz locally, for self-hosting, or development, please follow these instructions. Basic command line experience is recommended for the installation process. More detailed, step-by-step instructions are also available in the video tutorials on the HAIviz page Documentation.

  1. Install Node.js

    • Download the Node.js installer (e.g. the LTS version) from https://nodejs.org/en.
    • Installing Node.js will also install the npm package manager. Check if they have been installed correctly by typing the following commands in your terminal: npm -v and node -v. These commands should return the versions of npm and Node.js installed.

  2. Clone or download HAIviz (this) repository.

    • Clone the repository using git by typing: git clone https://github.com/nalarbp/haiviz.git. This will create a new directory named haiviz.
    • Alternatively, you can download the repository by clicking the 'Code' dropdown button and selecting 'Download ZIP'. After downloading, unzip the repository, which will create a new directory named haiviz-main.

  3. To run HAIviz offline or for self-hosting.

    • Install the serve Node.js package by typing: npm install serve -g (or sudo npm install serve -g if admin permission is required)
    • Navigate to HAIviz repository by typing: cd haiviz/ or cd haiviz-main/
    • Use the serve package to serve the build directory by typing: serve -s build/

  4. To run the development mode.

    • The development mode requires Node.js version 16.20.2.
    • Install the n package (for switching between Node.js versions) by typing: npm install n -g (or sudo npm install n -g).
    • Use n to install and switch to the Node.js v16.20.2 by typing: n install 16.20.2 (or sudo n install 16.20.2).
    • Check if the Node.js version has been changed by typing node -v, which should return v16.20.2.
    • Navigate to the HAIviz repository by typing cd haiviz or cd haiviz-main.
    • Install all the required dependency packages by typing npm install -s.
    • Start the development server by typing npm start.
    • Some Warnings may be displayed (e.g: Browserslist: caniuse-lite is outdated. Please run: npx browserslist@latest --update-db), but its safe to ignore and wait until compilation complete.
    • This will open your internet browser with the default local address: http://localhost:3000.
    • This development server and browser will reflect any changes you make to the source code.

Setting up preloaded datasets.

You can setup the preloaded datasets to link your input files directly to HAIviz.

  • Add your input files into the haiviz/build/data/preloaded/ directory
  • Update the configuration file located at haiviz/build/data/preloaded_dataset.json.
  • This feature allows you to create multiple datasets to be included in HAiviz, such as for visualising multiple projects or for continuous update.
  • A basic example on how to programatically update this preloaded datasets is available in haiviz/input_simulation/setup_preloaded_dateaset.R.

Have any questions?

Please feel free to send it to my email: b.permana@uq.edu.au

Cite us

If you use HAIviz please cite HAIviz website: https://haiviz.fordelab.com

License

GPLv3