The Digital Fruit Fly Brain

几个雄心勃勃、规模巨大、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的大脑。在欧洲，人脑项目的重点是通过开发多尺度、多层次的人脑模型来整合大量不同研究项目的数据，从而加速大脑研究--1000亿个神经元建模和模拟的挑战。在美国，大脑倡议旨在重建完整神经回路中神经活动的完整记录-1000亿神经元记录挑战。这些显然是巨大但有价值的挑战，我们相信，理解小得多但足够复杂的大脑的神经计算原理可以受益。果蝇脑已成为研究神经计算和将脑结构与功能联系起来的最受欢迎的模式生物之一。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，这些行为是由只有100000个神经元的大脑控制的。苍蝇的大脑及其行为之间的关系可以用一个强大的遗传技术工具包来实验探索，该工具包用于操纵苍蝇的神经电路。精确记录果蝇对刺激的神经元反应以及绘制果蝇神经系统神经元和突触的新的实验方法，为了解果蝇的神经连接图及其对感觉刺激的处理提供了大量有价值的数据。这些特点，再加上在研究中减少使用哺乳动物的日益增长的伦理和经济压力，解释了人们对基于果蝇的大脑模型越来越感兴趣，不仅是为了理解感觉、感知和神经计算，也是为了阐明阿尔茨海默病等人类神经退行性疾病。尽管在了解果蝇神经回路方面投入了大量资金并取得了巨大进展，并获得了优秀的基因组和遗传社区数据库，但理解苍蝇大脑的一个主要障碍是缺乏整个建模社区的沟通/合作，以及缺乏共享的模型、建模工具和数据储存库。世界各地的实验室已经产生了大量的实验数据，这些数据尚未提炼成新的模型，或用于验证和改进现有的模型。由于早期的开创性努力，关于成年果蝇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。其目的是开发一个开源的模块化软件平台，帮助研究人员协作，并利用丰富的知识、数据、模型和工具来构建和模拟苍蝇大脑的完整模型。该软件平台利用了使用图形处理器的相对廉价的超级计算服务，英国、美国和世界各地的许多学术机构近年来都采用了这种处理器。

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.