Toward rigorous comprehension of biological complexity: Modeling, execution, and visualization of thymic T-cell maturation
Toward rigorous comprehension of biological complexity: Modeling, execution, and visualization of thymic T-cell maturation
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DOI：
10.1101/gr.1215303
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发表时间：
2003-11-01
期刊：
影响因子：
7
通讯作者：
Cohen, LR
中科院分区：
文献类型：
--
作者：
Efroni, S;Harel, D;Cohen, LR
生物学家面临的问题之一是数据集太大而无法完全理解。实验者以不断增长的速度生成数据，每个人都来自自己感兴趣的领域。当前的理论最多只能捕获和建模一小部分数据。我们的目标是开发一种通用的建模方法，这将有助于拓宽生物学的理解。胸腺中 T 细胞的成熟是将实验数据积累到大型互不相连的数据集中的一个生动例子。胸腺负责将干细胞成熟为成熟T细胞，其复杂性将研究分为不同领域，例如细胞迁移、细胞分化、组织学、电子显微镜、生物化学、分子生物学等。每个领域都有自己的观点和自己的数据集。在这项研究中，我们展示了对该数据集大部分内容的全面整合的结果。集成以两层可视化方式执行。首先，我们使用状态图的可视化语言，这使得规范精确、清晰且可在计算机上执行。然后，我们建立了一个移动图形界面，动态地动画细胞、它们的受体、不同的梯度以及构成胸腺成熟的相互作用。该界面还提供了一种与模拟交互的方法。
One of the problems biologists face is a data set too large to comprehend in full. Experimenters generate data at ail ever-growing pace, each from their own niche of interest. Current theories are each able, at best, to Capture and model only a small part of the data. We aim to develop a general approach to modeling that will help broaden biological understanding. T-cell maturation in the thymus is a telling example of the accumulation of experimental data into a large disconnected data set. The thymus is responsible for the maturation of stern cells into mature T cells, and its complexity divides research into different fields, for example, cell migration, cell differentiation, histology, electron microscopy, biochemistry, molecular biology, and more. Each field forms its own viewpoint and its own set of data. In this study we present the results of a comprehensive integration of large parts of this data set. The integration is performed in a two-tiered visual manner. First, we use the visual language of Statecharts, which makes specification precise, legible, and executable on computers. We then set up a moving graphical interface that dynamically animates the cells, their receptors, the different gradients, and the interactions that constitute thymic maturation. This interface also provides a means for interacting with the simulation.