Regensburg 2025 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 29: Focus Session: Innovations in Research Software Engineering (joint session BP/DY)

BP 29.3: Vortrag

Donnerstag, 20. März 2025, 15:45–16:00, H44

OCTOPOS.jl: A Julia-based tool for synonymous codon optimization — Simon Christ¹, Jan-Hendrik Trösemeier², and •Sophia Rudorf¹ — ¹Institute of Cell Biology and Biophysics, Leibniz University Hannover, Germany — ²independent researcher

OCTOPOS.jl is a research software designed to optimize synonymous mRNA sequences for improved heterologous gene expression in various host organisms. Combining a detailed mechanistic model of in-vivo protein synthesis with machine learning, OCTOPOS.jl predicts protein expression based on codon choice. Originally developed as a Java desktop application, the software has been reimplemented in the Julia programming language to enhance performance, modularity, and scalability. The new implementation serves as the foundation for a graphical user interface and a web application, accessible at https://octopos.cell.uni-hannover.de/. These updates improve accessibility and usability, broadening its appeal to both computational and experimental biologists. OCTOPOS.jl supports organism-specific genetic sequence engineering and detailed analysis of translation dynamics, thus providing a valuable resource for the synthetic biology and biotechnology communities.

Keywords: codon optimization; translation; mRNA; ribosome; research software web application