CI-EN: Collaborative Research: Enhancement of Foldit, a Community Infrastructure Supporting Research on Knowledge Discovery Via Crowdsourcing in Computational Biology

这个项目的重点是通过众包视频游戏Foldit将众包和计算生物化学结合起来。Foldit是一款在线多人游戏，允许玩家竞争和合作，通过计算折叠和设计蛋白质。自2008年推出以来，它已经拥有超过40万名玩家，并展示了通过利用人类解决问题和创造力，人类和计算机可以合作解决计算结构生物学中以前无法解决的问题。Foldit玩家为解决计算结构生物学中的两个“圣杯”问题做出了贡献：蛋白质折叠问题和蛋白质设计问题(也称为反向折叠问题)。新型合成蛋白质的设计是蛋白质工程中最重要的工具之一，它可能会让我们更好地理解构成生命的过程，并使发现在健康、能源、材料和纳米技术中应用的分子成为可能。作为解决生物化学中纯计算方法挑战的一种新方法，科学发现游戏领域最近兴起了通过使用人类问题解决方案和普通公众的创造力来众包解决计算生物化学问题的方法。该项目支持的基础设施将使众包和公民科学方面的新研究成为可能。更广泛的社区将从这个基础设施中受益，作为众包计算生物化学的平台。这个项目旨在增强Foldit游戏的现有基础设施，并允许我们重塑Foldit，以应对计算结构生物学(包括酶和小分子的设计)的下一个重大挑战，同时扩大参与的科学家社区，并继续参与和教育公众。该项目将支持云托管和维护的设备和人员需求，从而提高资源的稳健性和协作性，同时继续进行社区外联。此外，还将为开发用于蛋白质和小分子设计新应用的游戏内工具、科学家的新界面、触摸屏和多点触摸支持以及众包生物化学挑战的新管道提供支持。对游戏客户端的改进将通过Foldit独立版提供--这是游戏的一个非竞争性版本，允许研究人员加载和研究他们自己的结构。教育工作者将能够将这款游戏作为一种教学工具，将生物化学引入课堂，在课堂上，它已经被用于讲课、实验室练习、家庭作业，甚至在教科书和MOOC中使用。Foldit已被iGEM获奖学生团队使用，iGEM是针对合成生物学学生的首屈一指的国际设计比赛。Foldit网站(http://fold.it/))为教育工作者和研究人员提供访问在线多人游戏和资源的途径。

The focus for this project is the combination of crowdsourcing and computational biochemistry through the crowdsourcing video game Foldit. Foldit is an online multiplayer game that allows players to compete and collaborate to computationally fold and design proteins. Since its launch in 2008, it has had over 400,000 players, and demonstrated that by leveraging human problem solving and creativity, humans and computers can work together to solve previously unsolvable problems in computational structural biology. Foldit players have contributed toward solutions for two of the "holy grail" problems in computational structural biology: the protein folding problem and the protein design problem (also known as the inverse folding problem). The design of novel synthetic proteins is one of the most important tools in protein engineering, possibly leading us to a better understanding of the processes that underlie life and allowing the discovery of molecules with applications in health, energy, materials, and nanotechnology. As a new approach to addressing the challenges of purely computational approaches in biochemistry, the field of scientific discovery games has recently arisen to crowdsource solutions to computational biochemistry problems, by using human problem solving and creativity from members of the general public. The infrastructure supported by this project will enable new research in crowdsourcing and citizen science. The broader community will benefit from this infrastructure as a platform for crowdsourcing computational biochemistry.This project aims to enhance the existing infrastructure of the Foldit game, and allow us to recast Foldit to tackle the next big challenges in computational structural biology (including design of enzymes and small molecules), while broadening the community of scientists involved and continuing to engage and educate the public. This project will support equipment and personnel needs for cloud hosting and maintenance, allowing improved robustness and collaborative access to resources, along with continued community outreach. Additionally, support will be provided for developing in-game tools for new applications in protein and small molecule design, new interfaces for scientists, touchscreen and multi-touch support, and a new pipeline for crowdsourced biochemistry challenges. Enhancements made to the game client will be made available via Foldit Standalone -- a non-competitive version of the game that allows researchers to load in and work on their own structures. Educators will be able to use the game as a teaching tool for introducing biochemistry to classrooms, where it is already being used for lectures, lab exercises, homework assignments, and even in textbooks and MOOCs. Foldit has been used by winning student teams in iGEM -- the premiere international design competition for students in synthetic biology. The Foldit website (http://fold.it/) provides access to the online multiplayer game and resources for educators and researchers.