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Optimising time-series experimental design for modelling of circadian rhythms: the value of transient data

机译：优化昼夜节律建模的时序实验设计：瞬态数据的价值

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Abstract: Circadian clocks consist of complex networks that coordinate the daily cycle of most organisms. In light/dark cycles, the clock is synchronized (or entrained) by the environment, which corresponds to a constant rephasing of the oscillations and leads to a steady state regime. Some circadian clocks are endogenous oscillators with rhythms of about 24-hours that persist in constant light or constant darkness. This operating mechanism with and without entrainment provides flexibility and robustness to the clock against perturbations. Most of the clock-oriented experiments are performed under constant photoperiodic regime, overlooking the transitory regime that takes place between light/dark cycles and constant light or darkness. This paper provides a comparative analysis of the informative potential of the transient time-series data with the other regimes for clock modelling. Realistic data were simulated from 2 experimentally validated plant circadian clock models and sliced into several time windows. These windows represent the different regimes that take place before, meanwhile and after the switch to constant light. Then, a network inference tool was used over each window and its capability of retrieving the ground-truth of the network was compared for each window. The results suggest that including the transient data to the network inference technique significally improves its performance.
机译：摘要：生物钟由复杂的网络组成，这些网络协调大多数生物的日常周期。在明/暗周期中，时钟被环境同步（或带动），这对应于振荡的恒定重定相并导致稳定状态。一些生物钟是内源性振荡器，其节奏约为24小时，持续存在于恒定的光照或恒定的黑暗中。这种带有或不带有夹带的操作机制为时钟提供了灵活性和鲁棒性，以防干扰。大多数面向时钟的实验都是在恒定的光周期状态下进行的，而忽略了在明/暗周期与恒定的明暗之间发生的过渡状态。本文对瞬态时间序列数据的信息潜力与其他用于时钟建模的机制进行了比较分析。真实数据是从2个经过实验验证的植物生物钟模型中模拟出来的，并切成多个时间窗口。这些窗口代表在切换到恒定光之前，同时和之后发生的不同状态。然后，在每个窗口上使用一个网络推理工具，并比较每个窗口的检索网络基础的能力。结果表明，将瞬态数据包含到网络推理技术中可显着提高其性能。

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