POSE: Phase I: Scoping the transition of Rosetta to a self-sustaining Open Source Ecosystem

该项目由开放源代码生态系统之路（POSE）资助，旨在利用开放源代码开发的力量，为国家和社会重要问题创造新技术解决方案。在过去的二十年里，罗塞塔社区一直引领着蛋白质和RNA建模和设计领域，拥有最先进的生物分子建模和设计软件，高影响力的科学进步，以及一流的生物分子工程培训的员工队伍。随着强大的机器学习方法的出现，生物分子建模领域正在迅速发生变化，最近一些计算设计的蛋白质进入临床试验，标志着该领域历史上的一个转折点。这些干扰促使罗塞塔社区重新设想他们的实践，以便在生物分子建模的下一个时代继续保持领导地位和创新。具体来说，Rosetta现有的付费商业许可模式限制了Rosetta的可访问性和影响力，并降低了行业科学家做出重要贡献的积极性。其次，罗塞塔的巨大成功导致了软件和社区的急剧扩张，但社区的运营结构并没有相应地更新，这限制了劳动力增长、软件开发和观点的多样性，而这些最终会导致更有影响力的科学进步。该项目将通过利用、发展和支持Rosetta社区来提供一流的软件，从而为协调和战略软件开发创造机会。该项目将通过推动下一代领先的生物分子建模和设计软件，使健康、食品和能源部门的科学发现和创新成为可能，从而为国家利益服务。这项研究将为Rosetta软件和社区建立一个开源生态系统（OSE）。具体来说，目标是：(1)创建一个战略计划，通过确定生物分子建模和设计生态系统中具有高影响力的机会来协调努力并推动进展，这些机会体现在罗塞塔OSE中的软件、科学和社区将实现；(2)定义一个能够快速和明智决策的组织结构，授权社区成员和领导者在“做民主”中，这样科学发现，代码开发和社区参与都是平等的激励；(3)确定长期资金和社会参与战略，以扩大活跃的用户和贡献者基础，维持罗塞塔的影响力和领导地位。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This project is funded by Pathways to Enable Open-Source Ecosystems (POSE) which seeks to harness the power of open-source development for the creation of new technology solutions to problems of national and societal importance. The Rosetta community has led the field of protein and RNA modeling and design for the last two decades with state-of-the-art biomolecular modeling and design software, high-impact scientific advances enabled by the software, and a workforce with best-in-class biomolecular engineering training. The biomolecular modeling landscape is rapidly changing with the emergence of powerful machine learning methods, and the recent entry of several computationally designed proteins into clinical trials have marked an inflection point in the history of the field. These disruptions have prompted the Rosetta community to reimagine their practices to enable continued leadership and innovation in the next era of biomolecular modeling. Specifically, Rosetta’s existing paid commercial license model limits Rosetta’s accessibility and impact, and de-incentivizes critical contributions from industry scientists.Second, Rosetta's remarkable success has led to dramatic expansion of both the software and community, yet the operational structure of the community has not been updated accordingly, limiting workforce growth, software development, and the diversity of perspectives thatultimately lead to higher-impact scientific advances. This project will create opportunities for coordinated and strategic software development by leveraging, growing, and supporting the Rosetta community to provide best-in-class software. The project will serve the national interest by driving the next generation of the leading biomolecular modeling and design software that enables scientific discovery and innovation across the health, food, and energy sectors.This research will scope and build an open-source ecosystem (OSE) for the Rosetta software and community. Specifically, the goals are to: (1) Create a Strategic Plan that aligns efforts and drives progress by identifying high-impact opportunities in the biomolecular modelingand design ecosystem that the software, science, and community embodied in a Rosetta OSE will realize; (2) Define an organizational structure capable of rapid and informed decision-making, empowering community members and leaders in a “do-ocracy” such thatscientific discovery, code development, and community engagement are all equally incentivized; and (3) Identify long-term funding and social engagement strategies that yield expanded and active user- and contributor-bases that sustain Rosetta’s impact and leadership. Learn more about Rosetta at http://www.rosettacommons.org.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.