A robot scientist for yeast systems biology

人工智能在科学研究中的应用越来越重要，因为计算机的功能越来越强大，实验室自动化的使用也越来越多。对自动化的需求在被称为系统生物学的科学分支中尤为重要，科学家们正在试图了解基因是如何共同作用形成活细胞的。将人工智能应用于实验室机器人学，我们之前已经开发出一种机器人科学家，它可以生成关于面包师酵母中特定基因功能的假设，然后设计和进行实验来测试它们。面包酵母(酿酒酵母)被用作人类细胞的模式生物，因为它更容易生长和实验，而且相对简单(约6000个基因，而人类约30,000个基因)。我们让机器人解决了发现酵母中不同基因的功能的问题。酵母中约30%的基因的功能尚不清楚，其中许多基因被认为是人类基因组的共同基因，它们可能在未来被证明具有重要的医学意义。这项研究涉及使用剔除了一个基因的酵母基因敲除菌株。通过观察酵母如何在特定的化学底物上生长或不生长，就有可能开始为被研究的基因建立不同的可能功能。这就像试图通过一个接一个地拆卸汽车中的不同部件来理解它们的作用。这位机器人科学家根据它对酵母新陈代谢的了解生成了一系列假设，然后计划进行一项实验，以尽可能多的速度和尽可能低的成本消除尽可能多的假设。它通过分配和混合液体，然后使用相邻的平板读取器测量酵母的生长来进行实验，该读取器将结果反馈到系统中。然后，机器人对照一组假说评估结果，生成新的假说，这个过程再次开始--这与人类科学家用来理解世界的循环类型相同。在这个提案中，我们计划以多种方式扩展机器人科学家：我们将使用机器人科学家来开发整个酵母新陈代谢的模型。我们将为机器人开发新的推理机制。我们将使用一个更大的机器人，能够自动运行更多的实验。

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.