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.
