CELLM: Bridging Natural Language Processing and Synthetic Genetic Circuit Design with AI

IF 3.9 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

ACS Synthetic Biology Pub Date : 2025-09-04 DOI:10.1021/acssynbio.5c00391

Lucas Abello Castillo*, and , Martín Gutiérrez Pescarmona*,

引用次数: 0

Abstract

The complexity of the genetic circuit design limits accessibility and efficiency in synthetic biology. This study presents an integrated system that combines Cello software with large language models (DeepSeek-R1, Phi-4) and the LangChain framework in Python, which allows the creation, analysis, and optimization of genetic circuits using natural language instructions. CELLM automates the translation of textual descriptions into functional designs using Cello v2.1 as the basis for circuit synthesis and LLM for the interpretation of biological requirements and logical optimization. To the best of our knowledge, this work sets a precedent as the first system that integrates language models with synthetic biology design tools such as Cello, demonstrating that natural language processing can be translated into functional biological designs. This approach removes barriers by allowing researchers without bioengineering expertise to prototype genetic circuits using simple instructions.

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CELLM：连接自然语言处理和人工智能合成遗传电路设计。

遗传电路设计的复杂性限制了合成生物学的可及性和效率。本研究提出了一个集成系统，该系统将大提琴软件与大型语言模型（DeepSeek-R1, Phi-4）和Python中的LangChain框架结合在一起，允许使用自然语言指令创建，分析和优化遗传电路。CELLM将文本描述自动翻译为功能设计，使用Cello v2.1作为电路合成的基础，并使用LLM来解释生物需求和逻辑优化。据我们所知，这项工作作为第一个将语言模型与合成生物学设计工具（如Cello）集成在一起的系统开创了先例，表明自然语言处理可以转化为功能性生物设计。这种方法通过允许没有生物工程专业知识的研究人员使用简单的指令来制作基因电路的原型，从而消除了障碍。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

ACS Synthetic Biology 生物-

CiteScore

8.00

自引率

10.60%

发文量

380

审稿时长

6-12 weeks

期刊介绍： The journal is particularly interested in studies on the design and synthesis of new genetic circuits and gene products; computational methods in the design of systems; and integrative applied approaches to understanding disease and metabolism. Topics may include, but are not limited to: Design and optimization of genetic systems Genetic circuit design and their principles for their organization into programs Computational methods to aid the design of genetic systems Experimental methods to quantify genetic parts, circuits, and metabolic fluxes Genetic parts libraries: their creation, analysis, and ontological representation Protein engineering including computational design Metabolic engineering and cellular manufacturing, including biomass conversion Natural product access, engineering, and production Creative and innovative applications of cellular programming Medical applications, tissue engineering, and the programming of therapeutic cells Minimal cell design and construction Genomics and genome replacement strategies Viral engineering Automated and robotic assembly platforms for synthetic biology DNA synthesis methodologies Metagenomics and synthetic metagenomic analysis Bioinformatics applied to gene discovery, chemoinformatics, and pathway construction Gene optimization Methods for genome-scale measurements of transcription and metabolomics Systems biology and methods to integrate multiple data sources in vitro and cell-free synthetic biology and molecular programming Nucleic acid engineering.