ShinyCOPASI: a web-based exploratory interface for COPASI models
Abhishekh Gupta, Pedro Mendes

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…
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Taxonomy
TopicsGene Regulatory Network Analysis · Microbial Metabolic Engineering and Bioproduction · Bioinformatics and Genomic Networks
