PlasmiDB: an open-source and customizable database for plasmid lifecycle management in multi-user, multi-project plant molecular biology laboratories
Abstract
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.
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BibTeX
@article{soriano2026plasmidb,
title = {{PlasmiDB: an open-source and customizable database for plasmid lifecycle management in multi-user, multi-project plant molecular biology laboratories}},
author = {Alexandre Soriano and Martine Bes and Anne-Cécile Meunier and Céline Georget and Phonsiri Saengram and Sergi Navarro-Sanz and Aurore Vernet and Murielle Portefaix and Thomas Mauran and Maryline Summo and Gaetan Droc and Christophe Perin},
journal = {Plant Methods},
year = {2026},
month = jul,
doi = {10.1186/s13007-026-01555-0},
url = {https://hal.inrae.fr/hal-05765581v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - PlasmiDB: an open-source and customizable database for plasmid lifecycle management in multi-user, multi-project plant molecular biology laboratories
AU - Alexandre Soriano
AU - Martine Bes
AU - Anne-Cécile Meunier
AU - Céline Georget
AU - Phonsiri Saengram
AU - Sergi Navarro-Sanz
AU - Aurore Vernet
AU - Murielle Portefaix
AU - Thomas Mauran
AU - Maryline Summo
AU - Gaetan Droc
AU - Christophe Perin
PY - 2026
DA - 2026/07/01
JO - Plant Methods
DO - 10.1186/s13007-026-01555-0
UR - https://hal.inrae.fr/hal-05765581v1
AB - 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.
SN - 1746-4811
ER -