A-S.B.35: A structured evaluation and benchmarking of Boolean modelling tools for systems biology
Biomolecules form complex interaction systems at various levels of biology. The dynamics of these interactions result in cellular phenotypes and responses. One example of a biological interaction system is a signal transduction network. Boolean models characterise the components of these systems with binary state variables and their interactions as governed by rules that determine their influence on each other. This approach does not require kinetic and abundance information about these components. Tools are available to define, analyse, and manage these models, but there is a lack of overview and evaluation of such tools' quality and functionality.
This work aims to facilitate the selection of software tools for Boolean modelling of signal transduction and gene regulatory networks, by developing and applying benchmark and evaluation criteria to the available tools. Twenty-five Boolean modelling tools were identified and assessed for compliance with FAIR4RS. Additionally, usability was assessed using a set of 24 sub-criteria developed for this purpose. Furthermore, the tools' functionalities were analysed and validated, and their ability to simulate and analyse Boolean models of different sizes was benchmarked.
Our comparison revealed that, although the results produced by the 25 tools were consistent, their analytical functionalities and ability to simulate larger models varied considerably. The size constraints for the tools' functionalities ranged from 25 to over 25,000 nodes. Each tool covered only part of the available functionalities and many exhibited room for improvement in terms of FAIR4RS compliance and usability.
Co-authors: Emanuel Lange, Jacob Krüger, Petra Lutter, Robert Heyer
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