Conceptualization and Analysis of a 3D Virtual Cell

加州大学圣地亚哥分校获得了一笔资助，用于规划一个S2I2转化系统生物学研究所（ITSB）的概念设计活动，该研究所强调从分子到细胞的生物三维（3D）结构，并解决可持续性挑战。这个虚拟3D细胞提供了一个科学框架，以一种实践科学家可以理解的方式收集和传播与分子和细胞生物学各个方面相关的软件。我们将借鉴App store模型，虽然它是日常生活中常用的软件分发范例，但它并没有被认为是一种分发、维护和发展科学软件的方式。应用商店模式定义了软件的来源，一个评论、评价和贡献软件的地方；一个对该软件将如何运行抱有期望的地方；还有一个软件具有标准化接口的地方。ITSB是一个社区驱动的项目，社区将通过研讨会和一系列重点研讨会聚集在一起，这些研讨会将：(I)从世界领先的从业者那里探索5年后的科学发展方向；（ii）采用这一愿景的小型研讨会，并确定在超分子组装生物学、蛋白质-蛋白质相互作用、途径分析和模拟等领域需要哪些软件、数据和工具开发来实现这一愿景；（iii）举办研讨会，重点关注K12、本科和专业教育，并通过视觉线索和内容组织进行传播，以充分利用互联网的力量培养下一代转化生物学家。3D虚拟细胞网站将成为一个中心，通过它，不同的从业者可以贡献，获取知识和互动。生物学发生在多个尺度上，从分子到细胞到生物体再到环境；这些音阶传统上是分开研究的。转化生物学现在正在寻求将这些不同的尺度结合在一起，以达到一个新的理解水平。这种理解需要新的算法开发和分析工具，这些工具可以在日益庞大、多样、复杂和广泛分布的数字生物数据体上运行。因此，翻译生物学面临着与数据可访问性、软件开发、软件重用和可持续性相关的网络基础设施挑战，其规模前所未有。个人软件开发工作的先前操作方式需要得到协调一致的社区努力的补充。开源软件库在这方面是有用的，但它们并不关注网络基础设施来解决生物学上的重大挑战，而是以零零碎碎的方式解决许多较小的挑战。因此，可以说，当前的软件开发和维护周期成本太高，耗时太长，在太多的孤岛中运行，不太可能是不可持续的，也无法满足21世纪生物科学日益增长的挑战。ITSB更广泛的影响是一个虚拟的生物环境，物理上表现为先进软件和数据基础设施的中心。在内容上，它提供了一个数据来源，软件，工具和新兴的三维虚拟细胞的知识。从概念上讲，它是一个汇集该领域发展的新模式。因此，任何有互联网连接的人都可以获得一套经过整理和描述良好的数据、工具和知识，这些材料迄今为止可能只存在于某些实验室中，而来自不同背景和机构的广泛学者群体则不容易获得。

The University of California San Diego is awarded a grant for planning activies leading to a conceptual design for an an S2I2 Institute for Translational Systems Biology (ITSB) that emphasizes biological 3-dimensional (3D) structures from molecule to cell and addresses the sustainability challenge. This virtual 3D cell provides the scientific framework to collect and disseminate software associated with all aspects of molecular and cellular biology in a way that can be understood by practicing scientists. We will draw from the App store model, which, while a software distribution paradigm in common use in daily life, has not been considered as a way to distribute, maintain and evolve scientific software. The app store model defines a source of software, a place to comment, rate and contribute to software; a place with an expectation of how that software will operate; and a place where software has standardized interfaces. The ITSB is a community driven project and the community will be bought together by a symposium and a series of focused workshops that: (I) explore where the science will be in 5 years from the world leading practitioners; (ii) smaller workshops that take that vision and define what software, data and tool development is needed to fulfill that vision in areas such as the biology of supramolecular assemblies, protein-protein interactions, pathway analysis and simulation; and (iii) a workshop that focuses on K12, undergraduate and professional education and dissemination through visual cues and organization of content that will train the next generation of translational biologists using the full power of the Internet. The 3D virtual cell web site will become a hub through which diverse practitioners can contribute, gain knowledge and interact.Biology occurs at multiple scales, from molecules to cells to organisms to environments; scales which have traditionally been studied separately. Translational biology is now seeking to bring these disparate scales together to achieve a new level of understanding. This understanding requires new algorithm development and analysis tools that can operate on an increasingly large, diverse, complex and widely distributed body of digital biological data. Hence, translational biology is faced with cyberinfrastructure challenges related to data accessibility, software development, software reuse, and sustainability on a scale not seen before. The prior modus operandi of individual software development efforts needs to be complemented by a concerted community effort. Open source software repositories are useful in this regard but they do not focus on cyberinfrastructure to solve a biological grand challenge, but rather address a number of smaller challenges in a piecemeal fashion. As a result it could be argued that the current software development and maintenance cycle costs too much, takes too long, operates in too many silos, is unlikely to be unsustainable and cannot meet the ever increasing challenges of 21st century biological sciences. The broader impact of the ITSB is a virtual biological environment physically manifest as a center for advanced software and data infrastructure. In content it provides a source of data, software, tools and knowledge of the emergent 3D virtual cell. In concept it is a new model for aggregating developments in the field. As such anyone with an Internet connection can gain access to a collated and well-described set of data, tools and knowledge, materials that hitherto might only have been present in select laboratories and not easily accessible to a broad community of scholars from diverse backgrounds and institutions.