In most molecular biology labs, progress still depends on highly manual workflows. From undergraduate students to senior postdoctoral fellows, a rese
archer must carefully transfer microliter volumes of liquids by hand, often hundreds of times per experiment. As one microliter (1 µL) is equivalent to one-millionth of a liter, controlling the transfer of droplets barely visible to the human eye is no easy task. While automation has reshaped pharmaceutical and microbial biotechnology, access to robotic infrastructure has remained limited to public research institutions in the agricultural and life sciences sector.
That gap is especially visible in synthetic biology. “When it comes to engineering biology, the plant community has been lagging behind,” said Dr. Catalin Voiniciuc, associate professor in the UF/IFAS Horticultural Sciences Department. “In plant synthetic biology, we are roughly two decades behind the technical tools available for microbial systems.”
To address this gap, researchers in the Voiniciuc Lab developed BOTany Methods, an open-source toolkit designed to make laboratory automation both affordable and easy to implement.
Detailed in their new publication, BOTany Methods: Accessible Automation for Plant Synthetic Biology, published in Plant Physiology, the BOTany platform lowers both the financial and technical barriers to robotic liquid handling in plant science and teaching laboratories. The robot-assisted workflows will enable the Voiniciuc Lab to accelerate research and development in plant synthetic biology. For instance, to redesign how plant enzymes and the molecules they act on are used for agricultural and biotechnological applications.
Designed with both researchers and educators in mind, the platform allows users to automate essential molecular biology tasks using spreadsheet-based inputs rather than custom code to operate Opentrons OT-2 liquid-handling robots. The result is system that makes automation feasible not just for well-funded biofoundries, but for a variety of molecular labs and plant science programs seeking to modernize their training and research infrastructure.
Behind the Toolkit: Where Design Meets Precision
For first author, Dr. Moni Qiande, who has led the development and implementation of the BOTany Foundry since 2024, the motivation grew out of firsthand experience with the technical bottlenecks common in plant biotechnology. As she and her colleagues began building automation workflows, one challenge became clear.
“Undergraduate students really struggle to use Python to control the robot,” Qiande said. “Most students are trained in biology or computer science, rarely both. We wanted something accessible to anybody, not just people who can code.”
That philosophy is at the core of its design. The platform pairs the modular OT-2 liquid-handling robot with a suite of validated molecular biology protocols tailored to plant research procedures. The system is distinctive in its table-based design. Instead of writing Python scripts to control the robot, users complete structured CSV templates, essentially spreadsheets, to specify reagents, volumes, and transfer steps. The robot reads the table and executes the protocol automatically. This approach dramatically lowers the learning curve.
An additional benefit of automation is the reduction of repetitive manual pipetting, helping minimize the risk of strain and injury.
The platform currently supports a full cloning pipeline, including primer dilution, PCR setup, Golden Gate DNA assembly, E. coli transformation, plasmid preparation, and customizable liquid-transfer workflows. Together, these protocols enable researchers to move from dry primers to purified plasmids largely through automated steps.
For plant synthetic biology in particular, this scalability is critical. By enabling larger, more reproducible experimental sets, BOTany Methods supports data generation at the scale required for predictive modeling and AI-assisted design.
“A biofoundry is a shared infrastructure that employs robots to automate some of the most common procedures in biology, especially genetic engineering,” said Voiniciuc. “The goal is to move away from the artisanal way science has been done for decades toward more reproducible and scalable experimentation.”
Qiande’s ongoing work builds on this, developing pipelines that screen genetic constructs in yeast before transferring promising candidates into plants. In this framework, automation becomes foundational infrastructure, enabling data generation and discovery at a scale impractical through manual procedures alone.
Advancing Equity in Biotechnology Education
Beyond accelerating discovery, the system stands to enhance how molecular biology is taught.
In many undergraduate labs, students still learn molecular biology through hands-on bench techniques that have not changed much in decades. Yet the biotechnology workforce that many students seek to enter increasingly relies on robotic systems and data-driven platforms that remain out of reach for many academic laboratories. Closing that gap through hands-on experience with lab automation is essential for preparing graduates for careers in industry, academic research, and a variety of government roles.
“The pharmaceutical Industry has had automation for decades when it comes to drug screening,” Voiniciuc said. “However, most students and scientists in STEM disciplines have lacked access to robots for molecular biology.”
By integrating BOTany Methods into research as well as coursework, students now design and execute automated workflows themselves. The experience mirrors the tools and systems currently being used in the biotech sector today, helping bridge academic training with industry practice.
Equally important is how the platform is shared. Like the modular Opentrons OT-2 hardware, the team chose to share their entire method open-source on GitHub. The protocols are freely available for anyone to utilize. By making the code, spreadsheet templates, and documentation publicly available, the team lowered both financial and institutional barriers to adoption. Those with limited funding, regional institutions, and emerging programs can replicate the system without licensing fees or proprietary restrictions.
“We intentionally decided to go the open access route,” Voiniciuc said. “We want the methods to be useful to others, adaptable, and future-proof using GitHub’s automated version control.”
Qiande echoed that sentiment, “I don’t really see why we would keep it private,” she said. “It’s the spirit of synthetic biology. Everybody should benefit from a really good design so people can grow faster.”
For a land-grant university, that decision carries particular weight. Expanding equitable access to advanced research infrastructure strengthens workforce development and broadens participation in high-tech biology. In plant science BOTany Methods helps ensure that access to robotics is integrated into everyday teaching and research environments.
About the Voiniciuc Lab
The Voiniciuc Lab (Designer Glycans), at the UF/IFAS Horticultural Sciences Department, focuses on understanding and engineering plant cell wall carbohydrates. Using synthetic biology, genome editing, and computational approaches, the lab investigates how complex glycans are built and regulated, with implications for agriculture, sustainability, and biotechnology.
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