BOTany Methods: Accessible Automation for Plant Synthetic Biology
Qiande, M., Lin, A., Larson, L., & Voiniciuc, C. (2025). “Accessible Automation for Plant Synthetic Biology.” bioRxiv. 2025.08.21.671538v1.
CV
Abigail Lin
Email: abigaillin35@gmail.com
Phone: (407) 803-1335
Website: https://helloworld7-beep.github.io
LinkedIn: linkedin.com/in/abigail-lin-ufl
Education
University of Florida
Bachelor of Science in Computer Science, Math Minor
August 2022 – May 2026
GPA: 3.82 / 4.00
Relevant Coursework: Linear Algebra for Data Science, Intro to Numerical Analysis, Algorithm Abstraction and Design, Introduction to Probability, Mathematics for Intelligent Systems (Fall 2025)
Research Experience
Purdue University — RCAC Anvil REU
May 2025 – August 2025 | Rosen Center for Advanced Computing
- Designed and implemented a bioinformatics workflow template generator (Bash, Slurm, Python, Urwid) as a simpler, more accessible alternative to Nextflow and Snakemake.
- Used Apptainer and Docker for container creation and deployment to efficiently manage software dependencies.
University of Florida — AI Scholars Program
January 2024 – May 2025 | Voiniciuc Lab & Xie Lab
- Generated 30 CSLA enzyme variants using a Maximum Entropy (MaxEnt) probabilistic AI model on UF’s HiPerGator supercomputer.
- Automated experimental assays to evaluate enzyme variant efficiency in synthesizing β-mannans.
- Benchmarked ProteinGym mutation scores using generative protein language models (ESM2, SaProt).
University of Central Florida — Applied Computational Mathematics NSF REU
May 2024 – July 2024 | Dr. Carlos Borges
- Developed a MATLAB solver for the forward scattering problem of thin-coated objects, comparing impedance and transmission approximations.
- Achieved final error below 10⁻² over 10 weeks as an NSF-funded undergraduate researcher.
University of Florida — Research Assistant
January 2024 – Present | Voiniciuc Lab
- Developed Python programs to automate synthetic biology workflows on Opentrons OT-2 lab robots, reducing pipetting error and improving efficiency.
- Created scripts to automate GenBank file editing in Benchling using Biopython and Pandas.
- Researching generative AI for plant enzyme engineering, applying models to enhance β-mannanase (MAN) enzymes.
Publications
Qiande, M., Lin, A., Larson, L., & Voiniciuc, C. (2025).
BOTany Methods: Accessible Automation for Plant Synthetic Biology.
bioRxiv, 2025-08.
(Under revision as a “Breakthrough Technology” article for Plant Physiology.)
Presentations
Summer Undergraduate Research Symposium
July 2025 | Purdue University
“Empowering Research: Easy-to-Use Bioinformatics Workflow Templates,” Undergraduate Research Symposium, West Lafayette, IN.
UF Spring Undergraduate Research Symposium
April 2025 | University of Florida
“Using the Maximum Entropy Model to Enhance CSLA Enzyme β-Mannan Polysaccharide Synthesis,” Gainesville, FL.
Summer Poster Showcase
July 2024 | University of Central Florida
“Forward Scattering for Thin Coated Domains: Numerical Solution Using Generalized Impedance Boundary Conditions,” Orlando, FL.
Skills
- Programming: Python, MATLAB, Bash, Slurm, Urwid, Biopython, Pandas
- Tools: Git, Docker, Apptainer, Benchling, Opentrons OT-2, High Performance Computing (HPC)
- Areas: Machine Learning, Scientific Computing, Bioinformatics, Synthetic Biology, Workflow Automation
Involvement
Phi Sigma Rho
January 2024 – Present
- Participated in service and outreach events supporting women in STEM.
Women in Computer Science and Engineering (WiCSE)
September 2023 – December 2023
- Mentored a CS underclassman, providing technical and professional guidance.