Dynamic visualization of metabolic pathways
: combining mental maps and static metabolic pathway rendering techniques

  • G.L.F. Direks

Student thesis: Master


In this thesis, we identify the requirements of creating static metabolic pathway layouts and maintaining the mental map when adding additional pathways to an existing visualization in an interactive setting. We describe methods which accomplish a good static layout, as well as methods which maintain the mental map. We combine a static layout algorithm by Karp and Paley with a mental map preserving algorithm by Misue et al. with good results. We also detail how to combine other algorithms to achieve a similar effect. We take special care when trying to find a good balance between maintaining the mental map and creating a clear layout. This results in an algorithm which is good at maintaining the mental map when combining multiple metabolic pathways. The prototype application which implements this algorithm generates these layouts quickly, without any noticeable delay. While the prototype is algorithmically complete, it can use some aesthetic improvements.
Date of Award31 Jan 2014
Original languageEnglish
SupervisorM.A. Westenberg (Supervisor 1) & K. Dinkla (Supervisor 2)

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