Abstract
Studying biological systems is a difficult but important task. Traditional methods include laboratory experimentation and computer simulations. However, often researchers need to explore important but potentially rare events that are not easily observed or simulated. We use UPPAAL-SMC, a formal verification tool to support a methodology that allows us to model biological systems, specify events and conditions that we want to analyze, and to explore system executions using controlled simulations. We also describe an efficient way to reproduce laboratory experiments in silico. Unlike traditional simulations, we are able to guide the experiment to explore special events and conditions by expressing these conditions in temporal logic formulas. We have applied this methodology to create a more detailed model of Palytoxin-induced Na +/K + pump channels than was previously possible. Moreover, we have reproduced experimental protocols and their associated electrophysiological recordings, which has not been done in previous works. As a consequence, we have been able to propose a new diprotomeric model for the PTX-pump complex and study its behaviour. The use of our methodology has enabled us to reduce the effort and time to perform this research. It can be used to model and analyze other complex biological systems, potentially increasing the productivity of such studies.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
More From: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.