Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models.
Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models.
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COVID-19时期的建模：基于统计和规则的中尺度模型。
DOI：
10.1109/tvcg.2020.3030415
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发表时间：
2021-03
影响因子：
5.2
通讯作者：
Viola I
中科院分区：
文献类型：
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作者：
Nguyen N;Strnad O;Klein T;Luo D;Alharbi R;Wonka P;Maritan M;Mindek P;Autin L;Goodsell DS;Viola I
我们提出了一种快速建模和构建科学准确的介尺度生物模型的新技术。生成的 3D 模型基于一些 2D 显微镜扫描和有关生物实体的最新知识（表示为一组几何关系）。我们新的可视化编程技术基于统计和基于规则的建模方法，这些方法可以快速编写、构建且易于修改。通过一些二维显微镜扫描，我们确定了各种结构方面的统计特性，例如外膜形状、空间特性以及膜上大分子元素的分布特征。该信息用于构建 3D 模型。一旦将所有成像证据纳入模型中，就可以通过交互式定义在空间上表征生物实体其余部分的规则来纳入附加信息，例如大分子之间的相互作用，以及它们相对于其他结构的距离和方向。这些规则通过直观的 3D 交互式可视化定义为可视化编程反馈循环。我们证明了我们的方法在 SARS-CoV-2 病毒体超微结构建模过程的用例中的适用性。我们在此介绍的这种原子模型可以将生物学研究引向新的有希望的方向，以对抗病毒的传播。
We present a new technique for the rapid modeling and construction of scientifically accurate mesoscale biological models. The resulting 3D models are based on a few 2D microscopy scans and the latest knowledge available about the biological entity, represented as a set of geometric relationships. Our new visual-programming technique is based on statistical and rule-based modeling approaches that are rapid to author, fast to construct, and easy to revise. From a few 2D microscopy scans, we determine the statistical properties of various structural aspects, such as the outer membrane shape, the spatial properties, and the distribution characteristics of the macromolecular elements on the membrane. This information is utilized in the construction of the 3D model. Once all the imaging evidence is incorporated into the model, additional information can be incorporated by interactively defining the rules that spatially characterize the rest of the biological entity, such as mutual interactions among macromolecules, and their distances and orientations relative to other structures. These rules are defined through an intuitive 3D interactive visualization as a visual-programming feedback loop. We demonstrate the applicability of our approach on a use case of the modeling procedure of the SARS-CoV-2 virion ultrastructure. This atomistic model, which we present here, can steer biological research to new promising directions in our efforts to fight the spread of the virus.