ABI Development: Representation, Visualization, and Modeling of Signaling Pathways in Higher Plants

弗吉尼亚理工学院和州立大学被授予建造基于社区的信标系统的奖项，以提供对生物学家关于信号通路的问题的计算支持。信号转导通路是了解高等植物对干旱、洪水、高温、寒冷、臭氧和盐分等非生物胁迫的早期反应的关键。对于农作物来说，应对这种非生物胁迫的能力可能会极大地影响产量。传统上，信号通路很难合成，也不可能通过计算进行操作。目前的路径工具和数据库仅为将路径作为网络操纵提供了有限的支持。特别是，生物学家不可能采用现有的信号通路并提出假设性的问题，这些问题通过计算得到回答。该项目包括由Beacon工作人员就该系统对公认的权威机构进行培训，从而使植物生物学家能够在Beacon数据库中策划和存档非生物胁迫反应的信号通路。该工具的可用性将通过用户和开发人员之间的持续反馈循环来解决。用户界面是一个编辑环境，它以称为SBGN活动流语言的标准图形符号表示和操作路径，该语言建立在网络可视化工具VANTED和VANTED的扩展SBGN-ED上。本文的研究将扩展SBGN-ED以创建Beacon。其结果将是一个管理工具，允许当局以SBGN活动流程语言输入路径，对其进行编辑、注释，并将其保存到初始Beacon数据库中。数据库表示允许生物学家在路径上施加诸如布尔语义的语义。然后，Beacon模拟引擎能够通过计算实现这些语义，并提供可以查询和可视化的结果。Beacon推理引擎提供了一些工具，使生物学家能够开发有关通路组件的可测试假说。Beacon系统将引起计算科学本科生和实验生物学家的兴趣。弗吉尼亚理工大学成熟的外展计划将用于提供培训和教育外展活动。一个实验部分将在项目的最后几年实施，届时基于Beacon的表型预测将在实验室进行测试。在https://bioinformatics.cs.vt.edu/beacon/，，用户可以访问项目成果。

An award is made to Virginia Polytechnic Institute and State University to build the community-based Beacon system to provide computational support for biologists' questions about signaling pathways. Signal transduction pathways hold the key to understanding the early response of higher plants to abiotic stresses, such as drought, flooding, heat, cold, ozone, and salt. For crop plants, the ability to cope with such abiotic stresses can drastically affect productivity. Traditionally, signaling pathways have been difficult to synthesize and impossible to manipulate computationally. Current pathway tools and databases provide only limited support for manipulating pathways as networks. In particular, it is not possible for a biologist to take an existing signaling pathway and ask hypothetical questions that are answered computationally. The project includes the training of recognized authorities by Beacon staff on the system, thereby empowering plant biologists to curate and archive signaling pathways for abiotic stress responses in the Beacon database. Usability of the tool will be addressed via a continual feedback loop between users and developers. The user interface is an editing environment that represents and manipulates a pathway in a standard graphical notation called SBGN Activity Flow language, built on the network visualization tool VANTED and SBGN-ED, an extension of VANTED. Research herein will extend SBGN-ED to create Beacon. The result will be a curation tool that will allow authorities to enter pathways in SBGN Activity Flow language, edit them, annotate them, and save them to an initial Beacon database. The database representation allows the biologist to impose a semantic, such as Boolean semantics, on a pathway. The Beacon simulation engine is then able to computationally implement those semantics and provide results that can be queried and visualized. The Beacon inference engine provides tools to allow biologist to develop testable hypotheses about pathway components. The Beacon system will interest undergraduate students in computational sciences as well as experimental biologists. Well-established outreach programs at Virginia Tech will be used to provide training and educational outreach activities. An experimental component will be implemented in the final years of the project, where Beacon-based predictions concerning phenotype will be tested in the laboratory. At https://bioinformatics.cs.vt.edu/beacon/, users will have access to project outcomes.