Prof. Jasmin Fisher
Understanding living systems remains one of the greatest challenges in science, despite an explosion of data in the Biological Sciences. Computational modelling of biological systems is consequently becoming increasingly important in efforts to better understand complex biological behaviours. In my talks I will outline one branch of research aiming to address this important challenge. We distinguish between two types of biological models -mathematical and computational- which differ in their representations of biological phenomena. We call the approach of constructing computational models of biological systems Executable Biology, as it focuses on the design of executable computer algorithms that mimic biological phenomena. In the talks I will survey the main modelling efforts in this direction (e.g., Boolean networks, process calculi, Petri nets, interacting state-machines), emphasize the applicability and benefits of executable models in biological research, mainly through models of cancer-related signalling pathways, and highlight some of the main challenges that executable biology poses for Biology and Computer Science.
Prof. Bud Mishra
In this talk, I will describe a few classical and recent open problems in biology that require careful reasoning (Thought Biology). It is interesting to ask how areas such as systems biology, model checking and quantitative biology may be able to tackle these problems. To address these questions, we will develop a model of causality that is based on the work of various philosophers, starting with John Stuart Mill and David Hume, but more recently by Skyrms, Suppes and Eells. Examples from biology, neuroscience, finance, and web applications will illustrate how we hope to exploit this technology. This is joint work with Samantha Kleinberg.
Prof. Gene Myers
While there have been a few interesting discoveries based on prediction, my own sense is that most of the knowledge accumulated in molecular biology has been based on observation, the more direct, the better. I believe that the main contribution of the genome project(s) has been that we can now do recombinant genetics on a genome-wide scale. The output of such studies are typically images produced by light or EM microscopy. I will describe the growing sub-field of "bio-image informatics" and illustrate projects underway to directly model and measure the cellular anatomy of organs, the meso-scale anatomy of cells, and the developmental trajectory of a genome.