Towards a biological modelling tool recommending proper subnetworks

Modelling is an essential task in systems biology in order to describe complex biological systems and predict their behaviour. This book focuses on computational models that represent biochemical reaction networks. As larger reaction networks are often assembled from already existing networks of publicly accessible models, tools to easily find and reuse related model parts for the integration in a currently developed model are necessary. Even though tools exist to support a user in searching, merging or combining models, there is still a high degree of manual effort required to perform reusing tasks. Furthermore, the amount and complexity of published models makes it barely feasible to manually search for proper networks. The aim of the research described in this book is to develop methods that suggest the users suitable subnetworks for integration during modelling. The obtained results form a solid basis for the development of a recommender system that provides modellers with recommendations on how to extend their model. Such a recommender system facilitates the efficient reuse of networks and decreases the manual effort to find and integrate relevant structures.