The Digital Fruit Fly Brain

几个雄心勃勃、规模庞大、耗资数十亿英镑的研究项目目前正在进行中，这些项目旨在了解人类大脑。在欧洲，人类大脑计划（The Human Brain Project）的重点是通过整合来自众多不同研究项目的数据，通过开发一个多尺度、多层次的人类大脑模型——1000亿个神经元建模和仿真挑战——来加速大脑研究。在美国，“大脑计划”旨在重建整个神经回路中神经活动的完整记录——1000亿个神经元记录挑战。这些显然是巨大但有价值的挑战，我们相信，对更小但足够复杂的大脑的神经计算原理的理解可以从中受益。果蝇脑已成为研究神经计算和将大脑结构与功能联系起来的最流行的模式生物之一。在哺乳动物大脑中表达的许多基因和蛋白质在果蝇的基因组中也是保守的。值得注意的是，果蝇能够做出一系列复杂的非反应性行为，而这些行为是由只有10万个神经元的大脑控制的。苍蝇的大脑和它的行为之间的关系可以通过实验探索，使用强大的基因技术工具包来操纵苍蝇的神经回路。新的实验方法可以精确记录果蝇对刺激的神经元反应，并绘制果蝇神经系统中的神经元和突触，这为果蝇的神经连接图及其对感官刺激的处理提供了大量有价值的数据。这些特征加上越来越多的伦理和经济压力，要求减少在研究中使用哺乳动物，解释了人们对基于果蝇的大脑模型日益增长的兴趣，不仅是为了理解感知、感知和神经计算，而且还为了阐明人类神经退行性疾病，如阿尔茨海默病。尽管在了解果蝇神经回路和优秀的基因组和遗传社区数据库方面投入了大量资金，取得了巨大进展，但了解果蝇大脑的一个主要障碍是缺乏建模社区之间的沟通/协作，以及缺乏共享的模型、建模工具和数据存储库。世界各地的实验室已经产生了大量的实验数据，这些数据尚未被提炼成新的模型，或用于验证和改进现有的模型。由于早期开创性的努力，关于成年黑腹果蝇大脑的详细神经解剖、神经元连接和基因表达的知识和信息已经公开。该项目旨在开发一个开源、模块化的软件平台，帮助研究人员协同工作，利用丰富的知识、数据、模型和工具，建立和模拟一个完整的苍蝇大脑模型。该软件平台利用相对便宜的超级计算服务，使用图形处理器单元（Graphic Processor Units），近年来，英国、美国和世界各地的许多学术机构都采用了图形处理器单元。

Several highly ambitious, large-scale, billion-pound research projects that aim to understand the human brain are currently under way. In Europe, The Human Brain Project is focused on accelerating brain research by integrating data available from a multitude of disparate research projects through the development of a multi-scale, multi-level model of the human brain - the 100 billion neurons modelling and simulation challenge. In US, The Brain Initiative aims to reconstruct the full record of neural activity across complete neural circuits - the 100 billion neurons recording challenge. These are clearly huge but worthy challenges that, we believe, can benefit from an understanding of the principles of neural computation of much smaller but sufficiently complex brains. The fruit fly brain has become one of the most popular model organisms to study neural computation and for relating brain structure to function. Many of the genes and proteins expressed in the mammalian brain are also conserved in the genome of Drosophila. Remarkably, the fruit fly is capable of a host of complex nonreactive behaviors that are governed by a brain containing only ~100000 neurons. The relationship between the fly's brain and its behaviors can be experimentally probed using a powerful toolkit of genetic techniques for manipulation of the fly's neural circuitry. Novel experimental methods for precise recordings of the fly's neuronal responses to stimuli and for mapping neurons and synapses in Drosophila nervous system have provided access to an immense amount of valuable data regarding the fly's neural connectivity map and its processing of sensory stimuli. These features coupled with the growing ethical and economic pressures to reduce the use of mammals in research, explain the growing interest in Drosophila-based brain models, not only to understand sensing, perception and neural computation but also to elucidate human neurodegenerative diseases such as Alzheimer's disease. Despite significant investment and huge progress in understanding Drosophila neural circuits and the availability of excellent genomic and genetic community databases, a major obstacle in understanding the fly brain is the lack of communication/collaboration across the modelling community as well as lack of shared models, modelling tools and data repositories. Vast amounts of experimental data that have yet to be distilled into new models or used to validate and refine existing models, have been generated by labs around the world. Knowledge and information of the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain has been made publicly available thanks to the efforts of earlier pioneering efforts. This aim to develop an open source, modular software platform that will help researchers to work collaboratively and exploit the wealth of knowledge, data, models, and tools available to build and simulate a complete model of the fly brain. The software platform exploits relatively cheap supercomputing services that use Graphic Processor Units, which many academic institutions in the UK, US and worldwide haave adopted in recent years.