Conceptualization and Analysis of a 3D Virtual Cell

加州圣地亚哥大学获得了一笔赠款，用于规划活动，从而为S2 I2转化系统生物学研究所（ITSB）进行概念设计，该研究所强调从分子到细胞的生物三维（3D）结构，并解决了可持续性挑战。这个虚拟3D细胞提供了科学框架，以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。我们将借鉴应用程序商店模式，而在日常生活中常用的软件分发范例，并没有被认为是一种分发，维护和发展科学软件的方式。应用商店模型定义了一个软件源，一个对软件进行评论、评级和贡献的地方;一个对软件将如何运行有期望的地方;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，社区将通过一个研讨会和一系列重点研讨会聚集在一起，这些研讨会和研讨会：（I）探索世界领先的从业者在5年内的科学发展方向;（ii）小型研讨会，接受这一愿景，并确定在超分子组装生物学等领域实现这一愿景所需的软件、数据和工具开发，蛋白质-蛋白质相互作用，途径分析和模拟;和（iii）一个研讨会，重点是K12，本科和专业教育和传播，通过视觉线索和组织的内容，将培养下一代的翻译生物学家使用互联网的全部力量。3D虚拟细胞网站将成为一个枢纽，通过它，不同的从业者可以贡献，获得知识和互动。生物学发生在多个尺度上，从分子到细胞到有机体到环境;尺度传统上被单独研究。翻译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，这些工具可以对越来越大，多样化，复杂和广泛分布的数字生物数据进行操作。因此，转化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有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工作方式需要由协调一致的社区努力来补充。开放源码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的重大挑战，而是以零碎的方式解决一些较小的挑战。 因此，可以说，目前的软件开发和维护周期成本太高，时间太长，在太多的筒仓中运行，不太可能是不可持续的，不能满足21世纪世纪生物科学日益增长的挑战。ITSB的更广泛的影响是一个虚拟的生物环境，物理上表现为高级软件和数据基础设施的中心。在内容上，它提供了一个数据源，软件，工具和新兴的3D虚拟细胞的知识。从概念上讲，这是一种汇集实地发展的新模式。因此，任何有互联网连接的人都可以获得一套经过整理和详细描述的数据、工具和知识，这些材料迄今可能只存在于选定的实验室，来自不同背景和机构的广大学者不容易获得。

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.