Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction

IF 4.5 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

ACS Synthetic Biology Pub Date : 2026-08-21 Epub Date: 2026-07-07 DOI:10.1021/acssynbio.6c00197

Hector Plahar, Stephen D. Lane, Nina Stawski, Lisa Simirenko, Manjiri Tapaswi, Rita Kuo, Garima Goyal, Nathan J. Hillson, Christopher J. Petzold

{"title":"Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction","authors":"Hector Plahar, Stephen D. Lane, Nina Stawski, Lisa Simirenko, Manjiri Tapaswi, Rita Kuo, Garima Goyal, Nathan J. Hillson, Christopher J. Petzold","doi":"10.1021/acssynbio.6c00197","DOIUrl":null,"url":null,"abstract":"<p>DNA construction, while a prerequisite to many biological\r\nendeavors,\r\nis often a time-consuming distraction from an individual’s\r\nprimary research objectives. We envisioned that with the right software\r\ninfrastructure and cultural mindset, a single person could execute\r\nin parallel the batched DNA construction tasks of an entire research\r\ninstitute, at scales realizing efficiency gains through process and\r\nlaboratory automation. In pursuit of this vision, we developed the\r\nDesign, Implementation, and Verification Automation (DIVA) software\r\nplatform. DIVA’s web interface enables researchers to design\r\nDNA constructs (using visual biological computer-aided design tools\r\nand biological parts repositories), submit designs for construction\r\nto dedicated staff, and track DNA construction as it progresses. DIVA\r\nsupports the dedicated staff through the DNA construction process\r\nand records both successful and unsuccessful attempts toward improving\r\nthe overall process. The platform is publicly available at public-diva.jbei.org and\r\nits open-source code through github.com/JBEI/DIVA.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 8","pages":"3498–3503"},"PeriodicalIF":4.5000,"publicationDate":"2026-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Synthetic Biology","FirstCategoryId":"99","ListUrlMain":"https://pubs.acs.org/doi/10.1021/acssynbio.6c00197","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2026/7/7 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}

引用次数: 0

Abstract

DNA construction, while a prerequisite to many biological endeavors, is often a time-consuming distraction from an individual’s primary research objectives. We envisioned that with the right software infrastructure and cultural mindset, a single person could execute in parallel the batched DNA construction tasks of an entire research institute, at scales realizing efficiency gains through process and laboratory automation. In pursuit of this vision, we developed the Design, Implementation, and Verification Automation (DIVA) software platform. DIVA’s web interface enables researchers to design DNA constructs (using visual biological computer-aided design tools and biological parts repositories), submit designs for construction to dedicated staff, and track DNA construction as it progresses. DIVA supports the dedicated staff through the DNA construction process and records both successful and unsuccessful attempts toward improving the overall process. The platform is publicly available at public-diva.jbei.org and its open-source code through github.com/JBEI/DIVA.

查看原文本刊更多论文

DNA构建的设计、实现和验证自动化（DIVA）软件平台的愿景和发展。

DNA构建虽然是许多生物学努力的先决条件，但往往是耗时的，分散了个人主要研究目标的注意力。我们设想，有了正确的软件基础设施和文化思维，一个人就可以并行地执行整个研究机构的批量DNA构建任务，通过过程和实验室自动化大规模地实现效率提高。为了实现这一愿景，我们开发了设计、实现和验证自动化（DIVA）软件平台。DIVA的网络界面使研究人员能够设计DNA结构（使用视觉生物计算机辅助设计工具和生物部件库），向专门的工作人员提交构建设计，并跟踪DNA构建的进展。DIVA通过DNA构建过程为专业人员提供支持，并记录了改进整个过程的成功和不成功的尝试。该平台可在public-diva.jbei.org上公开获得，其开源代码可通过github.com/JBEI/DIVA获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

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.