Preparing Fluid Samples under Retention Time Constraints using Flow-based Microfluidic Biochips
Preparing Fluid Samples under Retention Time Constraints using Flow-based Microfluidic Biochips
复制标题
使用基于流的微流控生物芯片在保留时间限制下制备流体样品
DOI：
10.1109/tcad.2023.3237980
复制
发表时间：
2023
影响因子：
2.9
通讯作者：
S. Yamashita and S. Roy
中科院分区：
文献类型：
--
作者：
Kundu;V. L. Sarvasiddi;S. Bhattacharjee;S. Yamashita and S. Roy
样品制备是几乎所有生物方案中必不可少的步骤，可以通过称为混合图的一系列混合步骤有效地实现。在文献中，已经报道了几种技术来确定混合图，其中混合步骤的数量最少，试剂流体的使用最少，浪费最少，或者有时是它们的组合。基于流动的微流体生物芯片（FMB）的保留时间被定义为流体可以存储在微通道内而没有任何流体泄漏的最大持续时间。然而，在使用FMB进行样品制备自动化以获得预定混合图期间，保留时间尚未被视为调度约束。在这篇文章中，我们提出了一种保留时间感知调度方法，称为时间感知列表调度（TALS），它可以与国家的最先进的方法，和一个新的可满足性为基础的混合算法，称为时间感知样本准备（TASP），以获得预定的混合图的目标比率满足保留时间的约束和可用的片上混频器在FMB的数量。仿真结果表明，平均TALS总是优于基线调度方法，同时调度任何混合图，而TASP可以确定最佳的和预定的混合图相比，现有的混合方法结合TALS。
Sample preparation is an essential step in almost all bioprotocols, which can be efficiently achieved via a sequence of mixing steps called mixing graph. In the literature, several techniques have been reported to determine a mixing graph with the minimal number of mixing steps, the minimal usage of reagent fluids, the minimal wastage, or sometimes a combination of them. The retention time of a flow-based microfluidic biochip (FMB) is defined as the maximum duration for which a fluid can be stored within a microchannel without any fluid leakage. However, the retention time has not yet been considered as a scheduling constraint during the automation of the sample preparation using an FMB in order to obtain the scheduled mixing graphs. In this article, we propose a retention time-aware scheduling method called time-aware list scheduling (TALS), which can be used with the state-of-the-art methods, and a new satisfiability-based mixing algorithm called time-aware sample preparation (TASP) to obtain the scheduled mixing graph for a target ratio satisfying the retention time constraint and the number of available on-chip mixers in an FMB. Simulation results suggest that on an average TALS always outperforms a baseline scheduling method while scheduling any mixing graph, whereas TASP can determine the optimal and scheduled mixing graphs compared to the existing mixing methods combined with TALS.