Real-time control system for biological experiments

生物实验实时控制系统

• 批准号: 8884411
• 负责人: DAVID J. CHRISTINI
• 金额: $ 64.73万
• 依托单位: WEILL MEDICAL COLL OF CORNELL UNIV
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-08-01 至 2016-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8884411
• 关键词: Address; Adopted; Adoption; Age; Animals; Architecture; Biological; Brain; Cardiac; Cells; Code; Communities; Complex; Computer software; Computers; Custom; Data; Data Display; Development; Documentation; Educational workshop; Ensure; Evolution; Foundations; Future; Heart; Ion Channel; Learning; Link; Linux; Measurement; Neurons; Operating System; Optical Methods; Protocols documentation; Real-Time Systems; Research; Research Personnel; Running; Scientist; Stimulus; System; Technology; Time; Update; Work; awake; base; biological research; biological systems; complex biological systems; data visualization; experience; flexibility; graphical user interface; improved; in vivo; innovation; multi-electrode arrays; online tutorial; open source; programs; public health relevance; research study; signal processing; software systems; statistics; tool; web site; wiki

DESCRIPTION (provided by applicant): The ability of experimentalists to perturb biological systems has traditionally been limited to rigid pre- programmed ("open loop") protocols. In contrast, "real-time control" allows the researcher to dynamically probe a biological system with parameter perturbations that are calculated functions of instantaneous system measurements ("closed loop"), thereby providing the ability to address diverse unanswered questions that are not amenable to traditional approaches. While real-time control applications are abundant throughout biological research, including, e.g., dynamic probing of ion-channel function in neurons and cardiac cells, adoption of such approaches lags. Unfortunately, for a number of technical reasons, real-time control is not possible with standard computer operating systems and software. Furthermore, commercial real-time systems are costly and often tailored for industrial applications. To circumvent these limitations, we developed a fast and highly versatile real- time biological experimentation system known as the Real-Time eXperiment Interface (RTXI). Based on Real-Time Linux, RTXI is open source and free, can be used with an extensive range of experimentation hardware, and can be run on Linux or Windows computers (when temporarily booted into Linux using an RTXI LiveCD). Importantly, RTXI has been adopted by many prominent scientific groups and has become an invaluable part of their scientific programs. In addition to the need to update and maintain RTXI for those, and future, end users, there remain important development avenues that would significantly expand its functionality and broaden its utility for the biological research community. Thus, for this competitive renewal, we propose: 1. To keep RTXI on the cutting edge by periodically updating its base code and core modules. 2. To enable new experiment paradigms. 3. To use RTXI's module architecture as the foundation for new protocol classes and application suites. 4. To improve the level of user support and documentation. The work proposed here would help ensure that RTXI not only remains a valuable research tool for a varied group of biological scientists, but that its utility, and the experiments it enables, continue to expand.

描述（由申请人提供）：实验者干扰生物系统的能力传统上限于严格的预编程（“开环”）协议。相比之下，“实时控制”允许研究人员动态地探测具有参数扰动的生物系统，所述参数扰动是瞬时系统测量（“闭环”）的计算函数，从而提供解决不适合传统方法的各种未回答的问题的能力。虽然实时控制应用在整个生物研究中是丰富的，包括，例如，动态探测神经元和心脏细胞中的离子通道功能，这些方法的采用滞后。不幸的是，由于一些技术原因，标准的计算机操作系统和软件不可能实现实时控制。此外，商业实时系统成本高，而且通常是为工业应用定制的。为了规避这些限制，我们开发了一个快速和高度通用的真实的实时生物实验系统称为实时实验接口（RTXI）。RTXI基于实时Linux，是开源和免费的，可以与广泛的实验硬件一起使用，并且可以在Linux或Windows计算机上运行（当使用RTXI LiveCD临时引导到Linux时）。重要的是，RTXI已被许多著名的科学团体采用，并已成为其科学计划的宝贵组成部分。除了需要为这些和未来的最终用户更新和维护RTXI之外，还有重要的发展途径可以显着扩展其功能并扩大其在生物研究界的实用性。因此，对于这种竞争性更新，我们建议：1。通过定期更新其基础代码和核心模块，保持RTXI处于最前沿。2.以实现新的实验范式。3.使用RTXI的模块架构作为新协议类和应用程序套件的基础。4.提高用户支持和文档的水平。这里提出的工作将有助于确保RTXI不仅仍然是一个有价值的研究工具，为不同的生物科学家群体，但它的效用，它使实验，继续扩大。