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）：传统上，实验者对扰动生物系统的能力仅限于严格的预编程（“开放循环”）协议。相比之下，“实时控制”使研究人员可以动态探测具有参数扰动的生物系统，这些扰动是瞬时系统测量功能（“闭环”），从而提供了解决不适合传统方法的不同未解决问题的能力。尽管在整个生物学研究中，实时控制应用都丰富，例如，在神经元和心脏细胞中的离子通道功能的动态探测，采用了这种方法滞后。不幸的是，由于许多技术原因，标准的计算机操作系统和软件无法实时控制。此外，商业实时系统的成本高昂，经常针对工业应用量身定制。为了避免这些局限性，我们开发了一个快速且高度的实时生物学实验系统，称为实时实验界面（RTXI）。基于实时Linux，RTXI是开源的，可以免费使用大量的实验硬件，并且可以在Linux或Windows计算机上运行（使用RTXI LiveCD暂时启动到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一部分。除了需要更新和维护这些人和未来最终用户的RTXI外，仍然存在重要的开发途径，这些途径将大大扩展其功能并扩大其对生物学研究社区的效用。因此，对于这种竞争性更新，我们建议：1。通过定期更新其基本代码和核心模块，以保持RTXI保持最前沿。 2。启用新的实验范例。 3。要使用RTXI的模块体系结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不仅是各种生物科学家的宝贵研究工具，而且它的实用性及其实验可以继续扩展。