Physiome Links (PhLynx)

Physiome Links (PhLynx - pronounced "flinks") is a web-based graphical interface for coupling existing CellML modules into a single system model. Common use cases include generating coupled biophysical cell models and patient-specific blood and/or lymph flow networks.

Getting Started

PhLynx is a web application - no installation required. Simply access it through your web browser, and start building models immediately. The latest state of the application can be accessed online at: https://latest-phlynx.netlify.app/

Note

The latest version is not guaranteed to be stable or working at any given time.

Browser Requirements:

• Chrome, Firefox, Safari, or Edge (latest versions recommended)
• JavaScript enabled
• Pop-up blocker disabled for file downloads

Note

Using Chrome will enable users to specify file download location.

About PhLynx

PhLynx is a web application for visually constructing and configuring CellML system models from CellML modules.

Built with Vue 3 and Electron, PhLynx provides a node-based interface (powered by Vue Flow) that allows users to drag, drop, and connect different modular physiological components. It is designed to work with CellML models (using vue3-libcellml.js) and exports flattened CellML (2.0) models for use with web OpenCOR or system configurations (JSON, CSV) for use with the Circulatory Autogen software.

Features

• Visual, Node-Based Editor: Drag and drop components to build complex models.
• CellML Integration: Based on vue3-libcellml.js for working with CellML files.
• Workflow Management: Save and load your visual workflow as a JSON file.
• Model Export: Export your model to formats compatible with Circulatory Autogen.
• Web-based: Runs on macOS, Windows, and Linux in any browser.

For Developers

This guide is for developers who wish to run or build the application from the source code.

Prerequisites

• Node.js (v20 or later recommended)
• A package manager (npm or yarn)

Installation

Clone the repository and install the dependencies:

git clone https://github.com/physiomelinks/phlynx.git
cd phlynx
yarn install

Development

Use the following command to launch the app in your browser with hot-reloading for the Vue frontend.

yarn dev

Deployment

To build the application for production, use the following command:

yarn build

This will create a production-ready build in the dist directory. We can also use the update-docs-changelog script to generate the complete changelog before building the application:

yarn update-docs-changelog
yarn build

To update the changelogs in the changelogs/ directory based on linked pull requests issue information we have to run:

# For a specific range.
yarn gen-changelog -q --from v0.2.0 --to v0.2.1
# For all since the last tag.
yarn gen-changelog -q

This will generate markdown to the terminal and this will need to be saved in the changelogs/ directory under the to version number (v0.2.1.md if following on from the command given above) or latest.md if not generating a specific version.