ShinyCOPASI: a web-based exploratory interface for COPASI models

TL;DR

ShinyCOPASI is a web-based interface that enables users to explore and run simulations on COPASI biochemical models directly through a web browser, enhancing accessibility and ease of use.

Contribution

This work introduces a web application for COPASI models, allowing browser-based interaction and analysis, which was not previously possible with the standalone software.

Findings

Enables web-based exploration of COPASI models

Supports running a subset of COPASI tasks online

Provides both generic and pre-loaded model options

Abstract

COPASI is a popular application for simulation and analysis of biochemical networks and their dynamics. While this software is widely used, it works as a standalone application and until now it was not possible for users to interact with its models through the web. We built ShinyCOPASI, a web-based application that allows COPASI models to be explored through a web browser. ShinyCOPASI was written in R with the CoRC package, which provides a high-level R API for COPASI, and the Shiny package to expose it as a web application. The web view provided by ShinyCOPASI follows a similar interface to the standalone COPASI and allows users to explore the details of a model, as well as running a subset of the tasks available in COPASI from within a browser. A generic version allows users to load model files from their computer, while another one pre-loads a specific model from the server and may be useful to provide web access to published models. The application is available at: http://shiny.copasi.org/; and the source code is at: https://github.com/copasi/shinyCOPASI.