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.

项目摘要/摘要 实验者研究生物系统的能力通常被限制在预先编程的范围内。 基于假设和预定模型来探测系统的开环协议。在……里面 相比之下，实时反馈控制允许动态探测系统的参数扰动 作为瞬时闭环系统测量的函数进行计算，使研究人员能够 解决不适用于开环方法的问题。虽然有许多生物学问题 可以通过这样的反馈控制变得更容易处理-例如，在 神经元或使用听觉和电刺激操纵睡眠网络动态，由真实- 时间脑电反馈--技术上的复杂性往往会阻碍它的采用。 因为计算技术已经有了几十年的进步，这是违反直觉的 使用标准的计算机操作系统(没有昂贵的操作系统)不可能进行实时实验控制 附加组件)。它们根本不是为这种严格计时的任务而设计的。此外，商业 实时系统成本高昂，需要最终用户针对实验室进行定制，因此通常不会 便于更广泛的科学界使用。为了绕过这些限制，我们开发了一种快速和 功能强大的实时生物实验系统--实时实验接口(RTXI)。 RTXI是免费和开源的，与广泛的实验硬件兼容，并且 在标准实验室中通过用户可定制的界面提供可重现的硬实时性能 电脑。重要的是，RTXI为“高级用户”提供了广泛的多功能性和高性能，而 同时提供一个丰富且不断增长的实验控制模板库，只需要很少的 为那些不懂计算的人做些努力。 RTXI已经发展到现在已经成为许多领先的科学计划的宝贵部分 研究小组。除了为这些用户和未来用户更新和维护RTXI之外，还有 重要的开发途径，将极大地扩展RTXI的功能、再现性 对于更广泛的生物研究人员群体来说，这是一种增强和实用。因此，我们建议： 1.通过对其基础代码和核心模块的全面改造，继续推动RTXI的科技创新。 2.实现了几种新的实时实验范式。 3.简化和丰富实验者的用户体验和再现性。 重要的是，这里提出的工作将确保RTXI仍然是各种不同类型的 一批杰出的生物科学家终端用户。此外，我们还将大大扩展RTXI的实用性 通过建立和支持更多的实验和突破性科学课程，他们将 启用。