Developing a Database Supporting Cell Biology Modeling

近年来，人们对计算细胞生物学的兴趣日益浓厚。去年生物物理学会（Biophysical Society）召开了一个关于该主题的研讨会，吸引了600名科学家参加，这是一个很好的指标。在日本，E-CELL项目正试图将单细胞生物的整个基因组整合到一个模型中。相反，该数据库强调模型是理解细胞生物学事件的基石。模型是假设和事实的集合，这些假设和事实汇集在一起，试图理解一种现象。VCELLDB，即虚拟细胞数据库，将成为一个可通过网络访问的生理模型电子存储库。扩展后的数据库建立在一个已经包含细胞内钙动力学、核膜分解、线粒体呼吸和RNA运输的原型基础上，采用易于使用的界面，将包括计算和数据资源，如辞典、与其他数据库的链接和内置的数学功能，以便科学家可以创建一致的模型。它还将有一个社区数据管理功能，允许数据库扩展同行评审机制，这是一种在线出版机制，将导致一个自我维持的公共电子模型存储库。

Interest in computational cell biology has expanded in recent years. A good indicator is the attendance at a workshop on the topic, at the Biophysical Society meeting last year, which drew 600 scientists. In Japan, the E-CELL project is attempting to incorporate the entire genome of a unicellular organism into a model. In contrast, this database emphasizes models as building blocks for understanding cell biological events. Models are a collection of hypotheses and facts that are brought together in an attempt to understand a phenomenon. VCELLDB, the Virtual Cell Database, will be a web-accessible electronic repository of physiological models. Built on a prototype that already includes intracellular calcium dynamics, nuclear envelope breakdown, mitochondrial respiration and RNA trafficking, employing easy-to-use interfaces, the expanded database would include computational and data resources, such as a thesaurus, links to other databases and built-in math functions so that scientists could create consistent models. It will also have a community data curation feature that will permit the database to expand with a peer review mechanism, a sort of online publication mechanism that would lead to a self-sustaining public electronic model repository.