A robot scientist for yeast systems biology

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The application of Artificial Intelligence to scientific research is growing in importance because of the increasing power of computers increased use of laboratory automation. The need for automation is particularly important in the branch of science known as systems biology, where scientists are trying to understand how genes work together to form living cells. Applying Artificial Intelligence to laboratory robotics we have previously developed a Robot Scientist that generates hypotheses about the function of particular genes in bakers yeast, and then designs and carries out experiments to test them. Baker's yeast (Saccharomyces cerevisiae) is used as a model organism for human cells, as it easier to grow and experiment with, and relatively simple (approximately 6,000 genes compared to approximately 30,000 in humans). We set the robot the problem of discovering the function of different genes in yeast. The functions of about 30 per cent of the genes in yeast are still unknown and, with many of these genes thought to be common to the human genome, they could prove to be medically important in the future. The research involved using knockout strains of yeast that have had one gene removed. By observing how the yeast grows, or doesn't grow, on defined chemical substrates, it is possible to start establishing different possible functions for the gene being investigated. It is like trying to understand what the different components in a car do by removing them one by one. The robot scientist generates a set of hypotheses from what it knows about yeast metabolism and then plans an experiment that will eliminate as many hypotheses as possible, as fast and as cheaply as possible. It conducts experiments by dispensing and mixing liquids and then measuring the growth of yeast using an adjacent plate reader that feeds the results back into the system. The robot then evaluates the results against the set of hypotheses, generates new hypotheses, and the process starts again - the same type of cycle human scientists use to understand the world. In this proposal we plan to extend the Robot Scientist in a number of ways: We shall use the Robot Scientist to develop a model of the whole of yeast metabolism. We shall develop new reasoning mechanisms for the robot. We shall use a much bigger robot capable to running many more experiments automatically.