Real-time control system for biological experiments

生物实验实时控制系统

• 批准号: 8580461
• 负责人: DAVID J. CHRISTINI
• 金额: $ 69.53万
• 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 2017-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8580461
• 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; Imagery; 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; computerized data processing; experience; flexibility; graphical user interface; improved; in vivo; innovation; microbial alkaline proteinase inhibitor; online tutorial; open source; programs; public health relevance; research study; 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）：实验人员干扰生物系统的能力传统上仅限于严格的预编程（“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，这些参数扰动是瞬时系统测量值的计算函数（“闭环”），从而提供了解决各种未解答的问题的能力，这些问题不适合传统方法。虽然实时控制应用在整个生物研究中非常丰富，包括神经元和心脏细胞中离子通道功能的动态探测，但此类方法的采用滞后。不幸的是，由于多种技术原因，标准计算机操作系统和软件无法实现实时控制。此外，商业实时系统成本高昂，并且通常是为工业应用量身定制的。为了规避这些限制，我们开发了一种快速且高度通用的实时生物实验系统，称为实时实验接口（RTXI）。 RTXI 基于实时 Linux，是开源且免费的，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 临时启动到 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。除了需要为这些以及未来的最终用户更新和维护 RTXI 之外，仍然存在重要的开发途径，可以显着扩展其功能并扩大其对生物研究界的实用性。因此，对于这次竞争性更新，我们建议： 1. 通过定期更新其基础代码和核心模块来保持 RTXI 的领先地位。 2. 启用新的实验范式。 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水平。这里提出的工作将有助于确保 RTXI 不仅仍然是各种生物科学家群体的宝贵研究工具，而且它的实用性及其支持的实验不断扩大。