Conceptualization and Analysis of a 3D Virtual Cell

点击翻译按钮获取中文摘要

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.