SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
+49 381 498-7571
Martin Scharm defended his dissertation
Good news, the SBI has baked another PhD!
Today, Martin Scharm has defended his thesis "Improving Reproducibility and Reuse of Modelling Results in the Life Sciences".
Modelling and simulation is a standard tool for research in the life sciences. Moreover, distributed and collaborative modelling has become increasingly prominent. The growing impact of simulation studies is reflected by a rapidly increasing number of computational models in open model repositories. Research results in the life sciences are typically complex and include a variety of heterogeneous data. This development, however, entails a number of computational challenges to facilitate reproducibility and reuse of modelling results. Above all, it is difficult (i) to manage simulation studies, (ii) to ensure model exchangeability, stability and validity, and (iii) to foster communication between project partners.
In his thesis, Martin presents techniques to improve the reproducibility and reuse of modelling results in the life sciences. First, he introduces a method to characterise differences in computational models. At the heart of Martin's method, an algorithm is able to identify differences between models in standard format and an ontology can be used to semantically describe identified changes. Martin shows how his method supports researchers in grasping a model’s evolution and improves collaborative modelling. Second, he developed multiple approaches to obtain shareable and reproducible research results. A novel container format eases the handling of simulation studies. Martin presents various tools to find, explore, create, and share research results. In addition, he describes a fully featured demo study and shows how it can be reproduced.
The solutions presented in his thesis do not just exist in theory. Instead, Martin materialised most of his ideas into code and, thus, a number of reusable free-software tools emerged from his work. Martin shows how his tools have already been successfully integrated in several third-party applications, demonstrating the impact of his ideas and implementations in the systems biology community.
Altogether, Martin's methods and tools foster exchange and reuse of modelling results.