Python Framework for Qualitative Modelling of Biological Regulatory Networks

Abstract

The modelling and analysis of biological networks is a key challenge in understanding the functioning of complex cellular systems. Qualitative modelling framework introduced by René Thomas is a well-established method to study the dynamical behavior of biological networks. Significant contributions have been made towards the application of the qualitative modelling framework. However, the availability of the framework as an API and open-source implementation remains a challenge to date. In this work, we have developed an open source python package that can be used by application developers in the area of systems biology and bioinformatics towards analysis of qualitative biological regulatory networks. We demonstrate that our implementation can be used to create qualitative models and perform key computations, such as cycles, deadlock states and generation of dynamic state graphs. We report the processing time for various models from the literature. Moreover, a frontend application is developed as a part of the API is provided to facilitate development of future applications. In future, we aim to improve the scalability of our API for complex networks by employing model reduction and parallel processing techniques.