BIRS Workshop Lecture Videos

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BIRS Workshop Lecture Videos

Interactive simulation of developmental biological models (joint presentation with Andreas Knote) von Mammen, Sebastian


Interactive simulations put the "human in the loop", i.e. they make it possible for the human modeller or analyst to change parameters and immediately see the effects, to explore the model's dynamics in novel directions, to quickly gain an intuition about the most beneficial questions to ask next. Due to the field's importance and the need communicated to us by experts in the field, we are committed to realising according interactive simulations in the domain of developmental biology.

In this joint presentation, we first summarise the challenges developmental biologists laid out for us in terms of data integration, model building, simulation and optimisation. Second, we present our efforts addressing them. In particular, we elaborate on various computational approaches that we have integrated to meet the specified requirements -- from visual programming over importing and editing annotated volumetric data to efficient, GPU-based simulation and effective methods of visualisation and interaction. For honing these aspects, we have devised a virtual cell model that runs at realtime speeds and realises some of the basic morphogenetic interactions, including morphogen-based signalling, adhesion, proliferation, and growth. We present an according prototype that serves as a basis to gain feedback from developmental biologists and experts in developmental models.

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