Real-Time eXperiment Interface - Enabling closed-loop biological experiment control

实时实验接口 - 实现闭环生物实验控制

• 批准号: 10088107
• 负责人: DAVID J. CHRISTINI
• 金额: $ 36.34万
• 依托单位: SUNY DOWNSTATE MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-01 至 2025-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10088107
• 关键词: Address; Adoption; Area; Auditory; Back; Benchmarking; Biological; Brain; Closure by clamp; Code; Communities; Computer software; Computers; Custom; Data; Development; Devices; Electrodes; Electroencephalography; Ensure; Feedback; Foundations; Future; Heart; Intuition; Ion Channel; Laboratories; Letters; Libraries; Linux; Measurement; Modality; Modeling; Modification; Monitor; Neurons; Operating System; Optics; Output; Performance; Protocols documentation; Pythons; Real-Time Systems; Reporting; Reproducibility; Research; Research Personnel; Science; Scientist; Sleep; Stimulus; System; Systems Integration; Technology; Time; United States National Institutes of Health; Update; Validation; Work; analog; base; biological systems; complex biological systems; cost; density; digital; experience; experimental study; graphical user interface; innovation; instrument; neuroregulation; open source; programs; software repository; software systems; tool; usability; web site

Project Summary/Abstract The ability of experimentalists to investigate biological systems has often been limited to pre-programmed open-loop protocols whereby systems are probed based on assumptions and predetermined models. In contrast, real-time feedback control allows systems to be dynamically probed with parameter perturbations calculated as functions of instantaneous closed-loop system measurements, enabling researchers to address questions not amenable to open-loop approaches. While there are many biological problems that can be made more tractable by such feedback control – such as dynamic probing of ion-channel function in neurons or manipulation of sleep network dynamics using auditory and electrical stimuli governed by real- time EEG feedback – technical complexities often hinder its adoption. Because there has been a many-decades advance in computing technologies, it is counter-intuitive that real-time experiment control is not possible with standard computer operating systems (without expensive add-on components). They are simply not designed for such strictly timed tasks. Furthermore, commercial real-time systems are costly and require end-user customization for the lab, such that they are typically not portable to the broader scientific community. To circumvent these limitations, we developed a fast and highly versatile real-time biological experimentation system – the Real-Time eXperiment Interface (RTXI). RTXI is free and open source, compatible with an extensive range of experimentation hardware, and delivers reproducible, hard real-time performance via a user-tailorable interface on standard laboratory computers. Importantly, RTXI offers extensive versatility and high-performance to “power users,” while simultaneously providing a rich – and ever growing – library of experiment-control modules that require little effort for those who are not computationally savvy. RTXI has grown to the point where it is now an invaluable part of the scientific programs of many leading research groups. In addition to updating and maintaining RTXI for those, and future, users, there remain important avenues for development that would substantially expand RTXI’s functionality, reproducibility enhancement, and utility for an even broader group of biological researchers. Thus, we propose: 1. To keep RTXI pushing scientific innovation by overhauling its base code and core modules. 2. To enable several new real-time experiment paradigms. 3. To ease and enrich experimentalists’ user experience and reproducibility. Critically, the work proposed here will ensure that RTXI remains a valuable research tool for its varied group of outstanding biological scientist end users. Furthermore, we will expand RTXI’s utility significantly by building and supporting additional classes of experiments and the groundbreaking science they will enable.

项目概要/摘要 实验学家研究生物系统的能力通常仅限于预先编程的 开环协议，根据假设和预定模型来探测系统。 相比之下，实时反馈控制允许通过参数扰动动态探测系统 作为瞬时闭环系统测量的函数进行计算，使研究人员能够 解决开环方法无法解决的问题，尽管有许多生物学问题无法解决。 可以通过这种反馈控制变得更容易处理——例如离子通道功能的动态探测 神经元或使用由真实控制的听觉和电刺激来操纵睡眠网络动态 时间脑电图反馈——技术复杂性往往阻碍其采用。 由于计算技术已经取得了数十年的进步，因此这是违反直觉的 使用标准计算机操作系统不可能实现实时实验控制（没有昂贵的 它们根本不是为这种严格计时的任务而设计的。 实时系统成本高昂，并且需要最终用户为实验室进行定制，因此通常不会 为了规避这些限制，我们开发了一种快速且可移植到更广泛的科学界的方法。 高度通用的实时生物实验系统——实时实验接口（RTXI）。 RTXI 是免费且开源的，与广泛的实验硬件兼容，并且 通过标准实验室上的用户定制界面提供可重复的硬实时性能 重要的是，RTXI 为“高级用户”提供了广泛的多功能性和高性能。 同时提供丰富且不断增长的实验控制模块库，几乎不需要 对于那些不懂计算的人来说是很困难的。 RTXI 已发展到如今已成为许多领先科学项目的重要组成部分 除了为这些用户和未来的用户更新和维护 RTXI 之外，还需要研究小组。 显着扩展 RTXI 功能、可重复性的重要开发途径 因此，我们建议： 1. 通过彻底修改基础代码和核心模块，保持RTXI推动科学创新。 2.启用几种新的实时实验范例。 3. 简化和丰富实验人员的用户体验和可重复性。 至关重要的是，这里提出的工作将确保 RTXI 仍然是其变体的有价值的研究工具 此外，我们将显着扩展 RTXI 的实用性。 通过建立和支持额外的实验类别和突破性科学，他们将 使能够。