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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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剧本工作流构建器:生物信息学工作流的交互构建.

Daniel J B Clarke1, John Erol Evangelista1, Zhuorui Xie1

  • 1Department of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.

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概括

剧本工作流构建器 (PWB) 允许动态构建和执行生物信息学工作流. 这种用户友好的平台,通过大型语言模型来增强,为各种研究应用提供了假设生成和数据分析.

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科学领域:

  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学
  • 数据科学数据科学数据科学

背景情况:

  • 生物信息学工作流程对于分析复杂的生物数据至关重要.
  • 现有平台可能需要大量的技术专业知识,限制了可访问性.
  • 整合各种数据源和可视化工具是一个挑战.

研究的目的:

  • 引入Playbook Workflow Builder (PWB),这是一个基于Web的平台,用于构建和执行生物信息学工作流.
  • 使用户,包括那些没有广泛的技术专业知识的用户,能够构建和运行复杂的分析.
  • 证明PWB在产生假设和促进数据驱动研究方面的能力.

主要方法:

  • 开发一个基于Web的平台,具有易于使用的界面,用于工作流构建.
  • 集成输入数据集网络,语义注释的API端点和数据可视化工具.
  • 实现一个聊天界面,辅助一个大语言模型 (LLM) 进行工作流设计.
  • 确保与通用工作流语言 (CWL) 的兼容性,以执行和发布工作流.

主要成果:

  • PWB允许通过图形界面或LLM辅助聊天来动态构建生物信息学工作流.
  • 工作流产生全面的报告,包括文本描述,图形,表格和引用.
  • 已证明的使用案例包括使用多个NIH共同基金数据集优先考虑癌症患者的药物标.
  • 生成的工作流可以重复使用,用于使用不同输入数据进行类似分析.

结论:

  • 该PWB使生物信息学工作流程的创建民主化,使复杂的分析可供更广泛的研究社区使用.
  • 该平台通过整合各种生物数据和计算工具来支持假设生成.
  • 由PWB生成的工作流可以发布和重新使用,加速科学发现和协作.