EURO 2025 Leeds
Abstract Submission

2412. Modeling and analyzing complex biological systems with Holmes 2.0

Invited abstract in session MB-56: CBBM: Drug Discovery, stream Computational Biology, Bioinformatics and Medicine.

Monday, 10:30-12:00
Room: Liberty 1.11

Authors (first author is the speaker)

1. Marcin Radom
Institute of Computing Science, Poznan University of Technology
2. Bartłomiej Szawulak
Institute of Computing Science, Poznan University of Technology
3. Piotr Formanowicz
Institute of Computing Science, Poznan University of Technology

Abstract

Modeling biological systems presents challenges due to their inherent complexity. A precise and accurate model of such a system can significantly enhance the understanding of how the system works and how one can influence its behavior. Here we introduce Holmes 2.0, a Java-based software tool designed to aid in the creation and analysis of Petri net models of complex biological systems. Holmes allows creation and editing of Petri net models and their subsequent analysis. The intuitive interface ensures that novice and experienced users can easily construct and modify their models. An important feature of Holmes is its support for working with large Petri nets, common for biological models. To manage complexity, the software allows net division into subnets. These subnets can be nested at arbitrary depths, allowing hierarchical structures that preserve the integrity of the model.
Holmes offers a wide array of analytical tools that can provide insights into the structure and behavior of the models. The knockout analysis tool is a significant feature that allows users to explore the impact of excluding certain areas from the net. Minimal Cut Sets module helps in identifying critical elements within the net whose removal could affect system performance, which can be particularly useful in disease modeling, where the objective may be to suppress certain factors such as pathogens or risk factors. The program also provides simulation algorithms which are highly configurable.

Keywords

Status: accepted

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