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Background <p>Functional genomics in plant biology relies on the generation, reuse, and long-term management of large numbers of plasmids produced through diverse cloning strategies. As collections expand across users and projects, laboratories face increasing challenges in organization, traceability, and preservation of construction histories. Existing cloning and sequence-design software supports plasmid design but does not address collaborative, laboratory-wide plasmid management.</p> Results <p>We developed PlasmiDB, an open-source, web-based database for managing plasmid collections in multi-user research environments. PlasmiDB provides structured storage of plasmid metadata, explicit tracking of plasmid genealogy, and traceability throughout the plasmid life cycle, including inter-laboratory exchanges. The system implements project-based access control and supports collaborative workflows involving staff, students, and core facilities. Implemented using a standard LAMP architecture and deployable via Docker, PlasmiDB is designed for extensibility without modification of the core database schema. A gene module links genetic targets to associated plasmids, primers, and CRISPR reagents, improving coherence between molecular constructs and experimental objectives. In our laboratory, PlasmiDB currently manages nearly 700 plasmids and facilitates reporting through automated declaration file generation.</p> Conclusions <p>PlasmiDB complements existing cloning tools by providing traceability, collaboration support, and long-term data stewardship for plant molecular biology laboratories. The source code and Docker image are publicly available.</p>

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PlasmiDB: an open-source and customizable database for plasmid lifecycle management in multi-user, multi-project plant molecular biology laboratories

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月1日

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  • Alexandre Soriano,
  • Martine Bes,
  • Anne-Cécile Meunier,
  • Celine Georget,
  • Phonsiri Saengram,
  • Sergi Navarro-Sanz,
  • Aurore Vernet,
  • Murielle Portefaix,
  • Thomas Mauran,
  • Maryline Summo,
  • Gaetan Droc,
  • Christophe Périn

摘要

Background

Functional genomics in plant biology relies on the generation, reuse, and long-term management of large numbers of plasmids produced through diverse cloning strategies. As collections expand across users and projects, laboratories face increasing challenges in organization, traceability, and preservation of construction histories. Existing cloning and sequence-design software supports plasmid design but does not address collaborative, laboratory-wide plasmid management.

Results

We developed PlasmiDB, an open-source, web-based database for managing plasmid collections in multi-user research environments. PlasmiDB provides structured storage of plasmid metadata, explicit tracking of plasmid genealogy, and traceability throughout the plasmid life cycle, including inter-laboratory exchanges. The system implements project-based access control and supports collaborative workflows involving staff, students, and core facilities. Implemented using a standard LAMP architecture and deployable via Docker, PlasmiDB is designed for extensibility without modification of the core database schema. A gene module links genetic targets to associated plasmids, primers, and CRISPR reagents, improving coherence between molecular constructs and experimental objectives. In our laboratory, PlasmiDB currently manages nearly 700 plasmids and facilitates reporting through automated declaration file generation.

Conclusions

PlasmiDB complements existing cloning tools by providing traceability, collaboration support, and long-term data stewardship for plant molecular biology laboratories. The source code and Docker image are publicly available.